1
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Avadhanula V, Agustinho DP, Menon VK, Chemaly RF, Shah DP, Qin X, Surathu A, Doddapaneni H, Muzny DM, Metcalf GA, Cregeen SJ, Gibbs RA, Petrosino JF, Sedlazeck FJ, Piedra PA. Inter and intra-host diversity of RSV in hematopoietic stem cell transplant adults with normal and delayed viral clearance. Virus Evol 2023; 10:vead086. [PMID: 38361816 PMCID: PMC10868550 DOI: 10.1093/ve/vead086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/05/2023] [Accepted: 12/22/2023] [Indexed: 02/17/2024] Open
Abstract
Respiratory syncytial virus (RSV) infection in immunocompromised individuals often leads to prolonged illness, progression to severe lower respiratory tract infection, and even death. How the host immune environment of the hematopoietic stem cell transplant (HCT) adults can affect viral genetic variation during an acute infection is not understood well. In the present study, we performed whole genome sequencing of RSV/A or RSV/B from samples collected longitudinally from HCT adults with normal (<14 days) and delayed (≥14 days) RSV clearance who were enrolled in a ribavirin trial. We determined the inter-host and intra-host genetic variation of RSV and the effect of mutations on putative glycosylation sites. The inter-host variation of RSV is centered in the attachment (G) and fusion (F) glycoprotein genes followed by polymerase (L) and matrix (M) genes. Interestingly, the overall genetic variation was constant between normal and delayed clearance groups for both RSV/A and RSV/B. Intra-host variation primarily occurred in the G gene followed by non-structural protein (NS1) and L genes; however, gain or loss of stop codons and frameshift mutations appeared only in the G gene and only in the delayed viral clearance group. Potential gain or loss of O-linked glycosylation sites in the G gene occurred both in RSV/A and RSV/B isolates. For RSV F gene, loss of N-linked glycosylation site occurred in three RSV/B isolates within an antigenic epitope. Both oral and aerosolized ribavirin did not cause any mutations in the L gene. In summary, prolonged viral shedding and immune deficiency resulted in RSV variation, especially in structural mutations in the G gene, possibly associated with immune evasion. Therefore, sequencing and monitoring of RSV isolates from immunocompromised patients are crucial as they can create escape mutants that can impact the effectiveness of upcoming vaccines and treatments.
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Affiliation(s)
| | | | - Vipin Kumar Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Roy F Chemaly
- Departments of Infectious Diseases, Infection Control & Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Dimpy P Shah
- Department of Population Health Sciences, Mays Cancer Center, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anil Surathu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030,USA
| | - Harshavardhan Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sara Javornik Cregeen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030,USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030,USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Computer Science, Rice University, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030,USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030,USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
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2
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Zhang X, Irajizad E, Hoffman KL, Fahrmann JF, Li F, Seo YD, Browman GJ, Dennison JB, Vykoukal J, Luna PN, Siu W, Wu R, Murage E, Ajami NJ, McQuade JL, Wargo JA, Long JP, Do KA, Lampe JW, Basen-Engquist KM, Okhuysen PC, Kopetz S, Hanash SM, Petrosino JF, Scheet P, Daniel CR. Modulating a prebiotic food source influences inflammation and immune-regulating gut microbes and metabolites: insights from the BE GONE trial. EBioMedicine 2023; 98:104873. [PMID: 38040541 PMCID: PMC10755114 DOI: 10.1016/j.ebiom.2023.104873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/06/2023] [Accepted: 10/31/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Accessible prebiotic foods hold strong potential to jointly target gut health and metabolic health in high-risk patients. The BE GONE trial targeted the gut microbiota of obese surveillance patients with a history of colorectal neoplasia through a straightforward bean intervention. METHODS This low-risk, non-invasive dietary intervention trial was conducted at MD Anderson Cancer Center (Houston, TX, USA). Following a 4-week equilibration, patients were randomized to continue their usual diet without beans (control) or to add a daily cup of study beans to their usual diet (intervention) with immediate crossover at 8-weeks. Stool and fasting blood were collected every 4 weeks to assess the primary outcome of intra and inter-individual changes in the gut microbiome and in circulating markers and metabolites within 8 weeks. This study was registered on ClinicalTrials.gov as NCT02843425, recruitment is complete and long-term follow-up continues. FINDINGS Of the 55 patients randomized by intervention sequence, 87% completed the 16-week trial, demonstrating an increase on-intervention in diversity [n = 48; linear mixed effect and 95% CI for inverse Simpson index: 0.16 (0.02, 0.30); p = 0.02] and shifts in multiple bacteria indicative of prebiotic efficacy, including increased Faecalibacterium, Eubacterium and Bifidobacterium (all p < 0.05). The circulating metabolome showed parallel shifts in nutrient and microbiome-derived metabolites, including increased pipecolic acid and decreased indole (all p < 0.002) that regressed upon returning to the usual diet. No significant changes were observed in circulating lipoproteins within 8 weeks; however, proteomic biomarkers of intestinal and systemic inflammatory response, fibroblast-growth factor-19 increased, and interleukin-10 receptor-α decreased (p = 0.01). INTERPRETATION These findings underscore the prebiotic and potential therapeutic role of beans to enhance the gut microbiome and to regulate host markers associated with metabolic obesity and colorectal cancer, while further emphasizing the need for consistent and sustainable dietary adjustments in high-risk patients. FUNDING This study was funded by the American Cancer Society.
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Affiliation(s)
- Xiaotao Zhang
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Institute for Translational Epidemiology & Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ehsan Irajizad
- Division of Basic Sciences, Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kristi L Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Johannes F Fahrmann
- Red & Charline McCombs Institute for the Early Detection and Treatment of Cancer, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Division of Cancer Prevention and Population Sciences, Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fangyu Li
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yongwoo David Seo
- Division of Surgery, Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gladys J Browman
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer B Dennison
- Red & Charline McCombs Institute for the Early Detection and Treatment of Cancer, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jody Vykoukal
- Red & Charline McCombs Institute for the Early Detection and Treatment of Cancer, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pamela N Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Wesley Siu
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ranran Wu
- Red & Charline McCombs Institute for the Early Detection and Treatment of Cancer, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eunice Murage
- Red & Charline McCombs Institute for the Early Detection and Treatment of Cancer, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nadim J Ajami
- Platform for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer L McQuade
- Division of Cancer Medicine, Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer A Wargo
- Division of Surgery, Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Platform for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James P Long
- Division of Basic Sciences, Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kim-Anh Do
- Division of Basic Sciences, Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Johanna W Lampe
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Karen M Basen-Engquist
- Division of Cancer Prevention and Population Sciences, Department of Heath Disparities Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pablo C Okhuysen
- Department of Infectious Diseases, Infection Control, and Employee Health, Division of Internal Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Samir M Hanash
- Red & Charline McCombs Institute for the Early Detection and Treatment of Cancer, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Division of Cancer Prevention and Population Sciences, Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Paul Scheet
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carrie R Daniel
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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3
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Lin J, Moradi E, Salenius K, Lehtipuro S, Häkkinen T, Laiho JE, Oikarinen S, Randelin S, Parikh HM, Krischer JP, Toppari J, Lernmark Å, Petrosino JF, Ajami NJ, She JX, Hagopian WA, Rewers MJ, Lloyd RE, Rautajoki KJ, Hyöty H, Nykter M. Distinct transcriptomic profiles in children prior to the appearance of type 1 diabetes-linked islet autoantibodies and following enterovirus infection. Nat Commun 2023; 14:7630. [PMID: 37993433 PMCID: PMC10665402 DOI: 10.1038/s41467-023-42763-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 10/17/2023] [Indexed: 11/24/2023] Open
Abstract
Although the genetic basis and pathogenesis of type 1 diabetes have been studied extensively, how host responses to environmental factors might contribute to autoantibody development remains largely unknown. Here, we use longitudinal blood transcriptome sequencing data to characterize host responses in children within 12 months prior to the appearance of type 1 diabetes-linked islet autoantibodies, as well as matched control children. We report that children who present with insulin-specific autoantibodies first have distinct transcriptional profiles from those who develop GADA autoantibodies first. In particular, gene dosage-driven expression of GSTM1 is associated with GADA autoantibody positivity. Moreover, compared with controls, we observe increased monocyte and decreased B cell proportions 9-12 months prior to autoantibody positivity, especially in children who developed antibodies against insulin first. Lastly, we show that control children present transcriptional signatures consistent with robust immune responses to enterovirus infection, whereas children who later developed islet autoimmunity do not. These findings highlight distinct immune-related transcriptomic differences between case and control children prior to case progression to islet autoimmunity and uncover deficient antiviral response in children who later develop islet autoimmunity.
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Grants
- U01 DK063821 NIDDK NIH HHS
- UC4 DK063863 NIDDK NIH HHS
- UL1 TR002535 NCATS NIH HHS
- HHSN267200700014C NIDDK NIH HHS
- U01 DK128847 NIDDK NIH HHS
- U01 DK063790 NIDDK NIH HHS
- UL1 TR000064 NCATS NIH HHS
- U01 DK063836 NIDDK NIH HHS
- U01 DK063829 NIDDK NIH HHS
- U01 DK063865 NIDDK NIH HHS
- UC4 DK095300 NIDDK NIH HHS
- UC4 DK063861 NIDDK NIH HHS
- UC4 DK063829 NIDDK NIH HHS
- UC4 DK063821 NIDDK NIH HHS
- UC4 DK117483 NIDDK NIH HHS
- UC4 DK063836 NIDDK NIH HHS
- UC4 DK112243 NIDDK NIH HHS
- U01 DK124166 NIDDK NIH HHS
- U01 DK063861 NIDDK NIH HHS
- UC4 DK063865 NIDDK NIH HHS
- U01 DK063863 NIDDK NIH HHS
- UC4 DK106955 NIDDK NIH HHS
- UC4 DK100238 NIDDK NIH HHS
- Academy of Finland (Suomen Akatemia)
- Sigrid Juséliuksen Säätiö (Sigrid Jusélius Foundation)
- U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- The TEDDY Study is funded by U01 DK63829, U01 DK63861, U01 DK63821, U01 DK63865, U01 DK63863, U01 DK63836, U01 DK63790, UC4 DK63829, UC4 DK63861, UC4 DK63821, UC4 DK63865, UC4 DK63863, UC4 DK63836, UC4 DK95300, UC4 DK100238, UC4 DK106955, UC4 DK112243, UC4 DK117483, U01 DK124166, U01 DK128847, and Contract No. HHSN267200700014C from the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institute of Allergy and Infectious Diseases (NIAID), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institute of Environmental Health Sciences (NIEHS), Centers for Disease Control and Prevention (CDC), and JDRF. This work is supported in part by the NIH/NCATS Clinical and Translational Science Awards to the University of Florida (UL1 TR000064) and the University of Colorado (UL1 TR002535).
- Päivikki and Sakari Sohlberg's Foundation
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Affiliation(s)
- Jake Lin
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Biostatistics, Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland
- Finnish Institute of Molecular Medicine, FIMM, University of Helsinki, 00290, Helsinki, Finland
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Elaheh Moradi
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70150, Finland
| | - Karoliina Salenius
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Suvi Lehtipuro
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Tomi Häkkinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Jutta E Laiho
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sami Oikarinen
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sofia Randelin
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Hemang M Parikh
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Jorma Toppari
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, and Centre for Population Health Research, University of Turku, Turku, Finland
- Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University CRC, Skåne University Hospital, Malmö, Sweden
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Platform for Innovative Microbiome & Translational Research (PRIME-TR), Moon Shots™ Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jin-Xiong She
- Jinfiniti Precision Medicine, Inc., Augusta, GA, USA
| | - William A Hagopian
- Pacific Northwest Research Institute, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Marian J Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO, USA
| | - Richard E Lloyd
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kirsi J Rautajoki
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland.
| | - Heikki Hyöty
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
- Fimlab Laboratories, Tampere, Finland.
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland.
- Foundation for the Finnish Cancer Institute, Helsinki, Finland.
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4
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Colbert LE, El Alam MB, Wang R, Karpinets T, Lo D, Lynn EJ, Harris TA, Elnaggar JH, Yoshida-Court K, Tomasic K, Bronk JK, Sammouri J, Yanamandra AV, Olvera AV, Carlin LG, Sims T, Delgado Medrano AY, Napravnik TC, O'Hara M, Lin D, Abana CO, Li HX, Eifel PJ, Jhingran A, Joyner M, Lin L, Ramondetta LM, Futreal AM, Schmeler KM, Mathew G, Dorta-Estremera S, Zhang J, Wu X, Ajami NJ, Wong M, Taniguchi C, Petrosino JF, Sastry KJ, Okhuysen PC, Martinez SA, Tan L, Mahmud I, Lorenzi PL, Wargo JA, Klopp AH. Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring. Cancer Cell 2023; 41:1945-1962.e11. [PMID: 37863066 PMCID: PMC10841640 DOI: 10.1016/j.ccell.2023.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 07/01/2023] [Accepted: 09/25/2023] [Indexed: 10/22/2023]
Abstract
Tumor microbiota can produce active metabolites that affect cancer and immune cell signaling, metabolism, and proliferation. Here, we explore tumor and gut microbiome features that affect chemoradiation response in patients with cervical cancer using a combined approach of deep microbiome sequencing, targeted bacterial culture, and in vitro assays. We identify that an obligate L-lactate-producing lactic acid bacterium found in tumors, Lactobacillus iners, is associated with decreased survival in patients, induces chemotherapy and radiation resistance in cervical cancer cells, and leads to metabolic rewiring, or alterations in multiple metabolic pathways, in tumors. Genomically similar L-lactate-producing lactic acid bacteria commensal to other body sites are also significantly associated with survival in colorectal, lung, head and neck, and skin cancers. Our findings demonstrate that lactic acid bacteria in the tumor microenvironment can alter tumor metabolism and lactate signaling pathways, causing therapeutic resistance. Lactic acid bacteria could be promising therapeutic targets across cancer types.
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Affiliation(s)
- Lauren E Colbert
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Molly B El Alam
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rui Wang
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tatiana Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David Lo
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erica J Lynn
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Timothy A Harris
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jacob H Elnaggar
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; LSU School of Medicine, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Kyoko Yoshida-Court
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Katarina Tomasic
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Julianna K Bronk
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Julie Sammouri
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ananta V Yanamandra
- Department of Translational and Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Adilene V Olvera
- Departments of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lily G Carlin
- Departments of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Travis Sims
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrea Y Delgado Medrano
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tatiana Cisneros Napravnik
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Madison O'Hara
- Department of Thoracic Head and Neck Medical Oncology at The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Daniel Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chike O Abana
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hannah X Li
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patricia J Eifel
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anuja Jhingran
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Melissa Joyner
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lilie Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lois M Ramondetta
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrew M Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kathleen M Schmeler
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Geena Mathew
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaogang Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nadim J Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Platform for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew Wong
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Platform for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cullen Taniguchi
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, The Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA
| | - K Jagannadha Sastry
- Department of Thoracic Head and Neck Medical Oncology at The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pablo C Okhuysen
- Departments of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sara A Martinez
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lin Tan
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Iqbal Mahmud
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Philip L Lorenzi
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer A Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; LSU School of Medicine, Louisiana State University, Baton Rouge, LA 70803, USA; Platform for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ann H Klopp
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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5
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Lönnrot M, Lynch KF, Rewers M, Lernmark Å, Vehik K, Akolkar B, Hagopian W, Krischer J, McIndoe RA, Toppari J, Ziegler AG, Petrosino JF, Lloyd R, Hyöty H. Gastrointestinal Infections Modulate the Risk for Insulin Autoantibodies as the First-Appearing Autoantibody in the TEDDY Study. Diabetes Care 2023; 46:1908-1915. [PMID: 37607456 PMCID: PMC10620548 DOI: 10.2337/dc23-0518] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/31/2023] [Indexed: 08/24/2023]
Abstract
OBJECTIVE To investigate gastrointestinal infection episodes (GIEs) in relation to the appearance of islet autoantibodies in The Environmental Determinants of Diabetes in the Young (TEDDY) cohort. RESEARCH DESIGN AND METHODS GIEs on risk of autoantibodies against either insulin (IAA) or GAD (GADA) as the first-appearing autoantibody were assessed in a 10-year follow-up of 7,867 children. Stool virome was characterized in a nested case-control study. RESULTS GIE reports (odds ratio [OR] 2.17 [95% CI 1.39-3.39]) as well as Norwalk viruses found in stool (OR 5.69 [1.36-23.7]) at <1 year of age were associated with an increased IAA risk at 2-4 years of age. GIEs reported at age 1 to <2 years correlated with a lower risk of IAA up to 10 years of age (OR 0.48 [0.35-0.68]). GIE reports at any other age were associated with an increase in IAA risk (OR 2.04 for IAA when GIE was observed 12-23 months prior [1.41-2.96]). Impacts on GADA risk were limited to GIEs <6 months prior to autoantibody development in children <4 years of age (OR 2.16 [1.54-3.02]). CONCLUSIONS Bidirectional associations were observed. GIEs were associated with increased IAA risk when reported before 1 year of age or 12-23 months prior to IAA. Norwalk virus was identified as one possible candidate factor. GIEs reported during the 2nd year of life were associated with a decreased IAA risk.
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Affiliation(s)
- Maria Lönnrot
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, and Department of Dermatology, Tampere University Hospital, Wellbeing Services County of Pirkanmaa, Tampere, Finland
| | - Kristian F. Lynch
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University Clinical Research Center, Skåne University Hospital, Malmo, Sweden
| | - Kendra Vehik
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD
| | | | - Jeffrey Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Rickhard A. McIndoe
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA
| | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, and Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland
| | - Anette-G. Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, Neuherberg, Germany
- Klinikum rechts der Isar, Technische Universität München, Neuherberg, Germany
- Forschergruppe Diabetes e.V., Neuherberg, Germany
| | - Joseph F. Petrosino
- Baylor Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX
| | - Richard Lloyd
- Baylor Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX
| | - Heikki Hyöty
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, and Fimlab Laboratories, Wellbeing Services County of Pirkanmaa, Tampere, Finland
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6
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Tisza M, Javornik Cregeen S, Avadhanula V, Zhang P, Ayvaz T, Feliz K, Hoffman KL, Clark JR, Terwilliger A, Ross MC, Cormier J, Moreno H, Wang L, Payne K, Henke D, Troisi C, Wu F, Rios J, Deegan J, Hansen B, Balliew J, Gitter A, Zhang K, Li R, Bauer CX, Mena KD, Piedra PA, Petrosino JF, Boerwinkle E, Maresso AW. Wastewater sequencing reveals community and variant dynamics of the collective human virome. Nat Commun 2023; 14:6878. [PMID: 37898601 PMCID: PMC10613200 DOI: 10.1038/s41467-023-42064-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 09/25/2023] [Indexed: 10/30/2023] Open
Abstract
Wastewater is a discarded human by-product, but its analysis may help us understand the health of populations. Epidemiologists first analyzed wastewater to track outbreaks of poliovirus decades ago, but so-called wastewater-based epidemiology was reinvigorated to monitor SARS-CoV-2 levels while bypassing the difficulties and pit falls of individual testing. Current approaches overlook the activity of most human viruses and preclude a deeper understanding of human virome community dynamics. Here, we conduct a comprehensive sequencing-based analysis of 363 longitudinal wastewater samples from ten distinct sites in two major cities. Critical to detection is the use of a viral probe capture set targeting thousands of viral species or variants. Over 450 distinct pathogenic viruses from 28 viral families are observed, most of which have never been detected in such samples. Sequencing reads of established pathogens and emerging viruses correlate to clinical data sets of SARS-CoV-2, influenza virus, and monkeypox viruses, outlining the public health utility of this approach. Viral communities are tightly organized by space and time. Finally, the most abundant human viruses yield sequence variant information consistent with regional spread and evolution. We reveal the viral landscape of human wastewater and its potential to improve our understanding of outbreaks, transmission, and its effects on overall population health.
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Affiliation(s)
- Michael Tisza
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sara Javornik Cregeen
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ping Zhang
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Tulin Ayvaz
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Karen Feliz
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kristi L Hoffman
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Justin R Clark
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- TAILOR Labs, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Austen Terwilliger
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- TAILOR Labs, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Matthew C Ross
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Juwan Cormier
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hannah Moreno
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Li Wang
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Katelyn Payne
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Catherine Troisi
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Fuqing Wu
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, Houston, 77030, USA
| | - Janelle Rios
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
| | - Jennifer Deegan
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
| | - Blake Hansen
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, Houston, 77030, USA
| | | | - Anna Gitter
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, Houston, 77030, USA
| | - Kehe Zhang
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Department of Biostatistics and Data Science, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
- Center for Spatial-temporal Modeling for Applications in Population Sciences, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
| | - Runze Li
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Department of Biostatistics and Data Science, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
- Center for Spatial-temporal Modeling for Applications in Population Sciences, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
| | - Cici X Bauer
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
- Department of Biostatistics and Data Science, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
- Center for Spatial-temporal Modeling for Applications in Population Sciences, UTHealth Houston School of Public Health, Houston, TX, 77030, USA
| | - Kristina D Mena
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, Houston, 77030, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Joseph F Petrosino
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Eric Boerwinkle
- School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Texas Epidemiologic Public Health Institute (TEPHI), Houston, TX, USA.
- Department of Epidemiology, Human Genetics and Environmental Sciences, UTHealth Houston School of Public Health, Houston, 77030, USA.
| | - Anthony W Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.
- TAILOR Labs, Baylor College of Medicine, Houston, TX, 77030, USA.
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Tisza M, Lloyd R, Hoffman K, Smith D, Rewers M, Cregeen SJ, Petrosino JF. Phage-bacteria dynamics during the first years of life revealed by trans-kingdom marker gene analysis. bioRxiv 2023:2023.09.28.559994. [PMID: 37808738 PMCID: PMC10557657 DOI: 10.1101/2023.09.28.559994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Humans are colonized with commensal bacteria soon after birth, and, while this colonization is affected by lifestyle and other factors, bacterial colonization proceeds through well-studied phases. However, less is known about phage communities in early human development due to small study sizes, inability to leverage large databases, and lack of appropriate bioinformatics tools. In this study, whole genome shotgun sequencing data from the TEDDY study, composed of 12,262 longitudinal samples from 887 children in 4 countries, is reanalyzed to assess phage and bacterial dynamics simultaneously. Reads from these samples were mapped to marker genes from both bacteria and a new database of tens of thousands of phage taxa from human microbiomes. We uncover that each child is colonized by hundreds of different phages during the early years, and phages are more transitory than bacteria. Participants' samples continually harbor new phage species over time whereas the diversification of bacterial species begins to saturate. Phage data improves the ability for machine learning models to discriminate samples by country. Finally, while phage populations were individual-specific, striking patterns arose from the larger dataset, showing clear trends of ecological succession amongst phages, which correlated well with putative host bacteria. Improved understanding of phage-bacterial relationships may reveal new means by which to shape and modulate the microbiome and its constituents to improve health and reduce disease, particularly in vulnerable populations where antibiotic use and/or other more drastic measures may not be advised.
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Affiliation(s)
- Michael Tisza
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Richard Lloyd
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kristi Hoffman
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Daniel Smith
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO, USA
| | - Sara Javornik Cregeen
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Joseph F Petrosino
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
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8
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Carter H, Clark J, Carlin LG, Vaughan E, Rajan A, Olvera A, Yu X, Zeng XL, Kambal A, Holder M, Qin X, Gibbs RA, Petrosino JF, Muzny DM, Doddapaneni H, Menon VK, Hoffman KL, Meng Q, Ross MC, Javornik Cregeen SJ, Metcalf G, Jenq R, Blutt S, Estes MK, Maresso A, Okhuysen PC. Functional Genomics of Gastrointestinal Escherichia coli Isolated from Patients with Cancer and Diarrhea. bioRxiv 2023:2023.05.31.543115. [PMID: 37398483 PMCID: PMC10312547 DOI: 10.1101/2023.05.31.543115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
We describe the epidemiology and clinical characteristics of 29 patients with cancer and diarrhea in whom Enteroaggregative Escherichia coli (EAEC) was initially identified by GI BioFire panel multiplex. E. coli strains were successfully isolated from fecal cultures in 14 of 29 patients. Six of the 14 strains were identified as EAEC and 8 belonged to other diverse E. coli groups of unknown pathogenesis. We investigated these strains by their adherence to human intestinal organoids, cytotoxic responses, antibiotic resistance profile, full sequencing of their genomes, and annotation of their functional virulome. Interestingly, we discovered novel and enhanced adherence and aggregative patterns for several diarrheagenic pathotypes that were not previously seen when co-cultured with immortalized cell lines. EAEC isolates displayed exceptional adherence and aggregation to human colonoids compared not only to diverse GI E. coli , but also compared to prototype strains of other diarrheagenic E. coli . Some of the diverse E. coli strains that could not be classified as a conventional pathotype also showed an enhanced aggregative and cytotoxic response. Notably, we found a high carriage rate of antibiotic resistance genes in both EAEC strains and diverse GI E. coli isolates and observed a positive correlation between adherence to colonoids and the number of metal acquisition genes carried in both EAEC and the diverse E. coli strains. This work indicates that E. coli from cancer patients constitute strains of remarkable pathotypic and genomic divergence, including strains of unknown disease etiology with unique virulomes. Future studies will allow for the opportunity to re-define E. coli pathotypes with greater diagnostic accuracy and into more clinically relevant groupings.
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Di Gesù CM, Matz LM, Bolding IJ, Fultz R, Hoffman KL, Gammazza AM, Petrosino JF, Buffington SA. Maternal gut microbiota mediate intergenerational effects of high-fat diet on descendant social behavior. Cell Rep 2023; 42:112498. [PMID: 37133995 PMCID: PMC10399135 DOI: 10.1016/j.celrep.2023.112498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
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10
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Torrez WVV, Grimaldo MT, Clowers MJ, Yuan B, del Aguila Soto S, Bouchelkia I, Barragan JEM, Karandikar UC, Petrosino JF, McAllister F, Kadara H, Hoffman KL, Moghaddam SJ. Abstract 649: Comparative effects of combustible cigarette versus electronic cigarette exposures on K-ras mutant lung cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Combustible cigarette smoking (CCS) is causally related to ~90% of all lung cancers and induces various tumor-initiating effects, some of which (e.g., inflammation) are not reversible even after smoking cessation. More recently, use of non-combustible smoking vectors, such as electronic cigarette vapors (ECV), have rapidly increased, especially among youth. Despite this emerging public health concern, the long-term impact of ECV exposure is poorly understood. Our lab sought to assess the safety of ECV and determine their influence on immune dysfunction and lung cancer progression by comparing the effects of CCS and ECV in an airway epithelial specific K-ras mutant mouse model of lung adenocarcinoma (CC-LR). Three cohorts of 6-week-old CC-LR mice were exposed to either room air, CCS, or ECV 5 days per week for 8 weeks. For CCS exposure, mice were exposed to CCS from 3R4F research cigarettes at a rate of 3 puffs/min for 2 hours each day using the SCIREQ integrated Cigarette Smoking Robot. For ECV exposure, mice were exposed to 72 mg/ml of liquid nicotine in 50% propylene glycol/vegetable glycerin solution at a rate of 3 puffs/min for 2 hours using the SCIREQ Electronic Nicotine Delivery System. While CCS led to a significant increase in tumor burden (25%), ECV showed no significant changes compared to room air-exposed control. Bronchoalveolar lavage fluid had significantly increased total lung immune cell infiltrates in both CCS (30%) and ECV (25%), particularly in macrophage and lymphocyte populations. Immunophenotyping of CCS and ECV exposed lungs displayed pronounced pro-tumor immunosuppressive phenotypes, characterized by significantly decreased CD4+ IFNγ+ and CD8+ GZMB+ cytotoxic T cells along with a significantly elevated CD4+ FOXP3+ regulatory T cells. Furthermore, the cytotoxic cytokine IFNγ was significantly reduced in lungs of CCS- (7-fold) and ECV-exposed (2-fold) mice compared to room air-exposed controls. We also found increased levels of the immunosuppressive cytokine IL-10 in lungs of CCS- and ECV-exposed mice. Previous studies have shown IL-10 to play an important role in microbiome-associated immune modulation, hence we performed a preliminary gut and lung microbiome study to assess microbiome dissimilarity in these cohorts. Taxonomic profiling via 16S rRNA gene sequencing of matched stool and lung samples showed differences in the relative abundance of several lung Proteobacteria spp. while gut Firmicutes, particularly Turicibacter and Ileibacterium, were increased by CCS and ECV. In conclusion, while both CCS and ECV increased immune suppression, ECV did not significantly promote tumorigenesis during this timeframe of intervention. Future studies probing differences in microbiome-modulated CCS and ECV immune dysfunction can help pave way for identification of new targets that foster new interception and early treatment strategies for K-ras mutant lung cancer.
Citation Format: Walter V. Velasco Torrez, Maria T. Grimaldo, Michael J. Clowers, Bo Yuan, Segundo del Aguila Soto, Iman Bouchelkia, Javier Eduardo Moreno Barragan, Umesh C. Karandikar, Joseph F. Petrosino, Florencia McAllister, Humam Kadara, Kristi Louise Hoffman, Seyed Javad Moghaddam. Comparative effects of combustible cigarette versus electronic cigarette exposures on K-ras mutant lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 649.
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Affiliation(s)
| | - Maria T. Grimaldo
- 2The University of Texas MD Anderson Cancer Center, UT Health Houston Graduate School of Biomedical Sciences, Houston, TX
| | - Michael J. Clowers
- 2The University of Texas MD Anderson Cancer Center, UT Health Houston Graduate School of Biomedical Sciences, Houston, TX
| | - Bo Yuan
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Iman Bouchelkia
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | - Humam Kadara
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
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Dai A, Hoffman K, Xu AA, Gurwara S, White DL, Kanwal F, Jang A, El-Serag HB, Petrosino JF, Jiao L. The Association between Caffeine Intake and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Preliminary Investigation. Nutrients 2023; 15:nu15071747. [PMID: 37049587 PMCID: PMC10096519 DOI: 10.3390/nu15071747] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 03/29/2023] [Accepted: 03/29/2023] [Indexed: 04/14/2023] Open
Abstract
We examined the association between caffeine and coffee intake and the community composition and structure of colonic microbiota. A total of 34 polyp-free adults donated 97 colonic biopsies. Microbial DNA was sequenced for the 16S rRNA gene V4 region. The amplicon sequence variant was assigned using DADA2 and SILVA. Food consumption was ascertained using a food frequency questionnaire. We compared the relative abundance of taxonomies by low (<82.9 mg) vs. high (≥82.9 mg) caffeine intake and by never or <2 cups vs. 2 cups vs. ≥3 cups coffee intake. False discovery rate-adjusted p values (q values) <0.05 indicated statistical significance. Multivariable negative binomial regression models were used to estimate the incidence rate ratio and its 95% confidence interval of having a non-zero count of certain bacteria by intake level. Higher caffeine and coffee intake was related to higher alpha diversity (Shannon index p < 0.001), higher relative abundance of Faecalibacterium and Alistipes, and lower relative abundance of Erysipelatoclostridium (q values < 0.05). After adjustment of vitamin B2 in multivariate analysis, the significant inverse association between Erysipelatoclostridium count and caffeine intake remained statistically significant. Our preliminary study could not evaluate other prebiotics in coffee.
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Affiliation(s)
- Annie Dai
- Department of Dermatology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kristi Hoffman
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anthony A Xu
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shawn Gurwara
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna L White
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX 77021, USA
| | - Fasiha Kanwal
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX 77021, USA
- Section of Gastroenterology, Michael E. DeBakey VA Medical Center, Houston, TX 77030, USA
| | - Albert Jang
- Deming Department of Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Hashem B El-Serag
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX 77021, USA
- Section of Gastroenterology, Michael E. DeBakey VA Medical Center, Houston, TX 77030, USA
| | - Joseph F Petrosino
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX 77030, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Li Jiao
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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12
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Piedra FA, Henke D, Rajan A, Muzny DM, Doddapaneni H, Menon VK, Hoffman KL, Ross MC, Javornik Cregeen SJ, Metcalf G, Gibbs RA, Petrosino JF, Avadhanula V, Piedra PA. Modeling nonsegmented negative-strand RNA virus (NNSV) transcription with ejective polymerase collisions and biased diffusion. Front Mol Biosci 2023; 9:1095193. [PMID: 36699700 PMCID: PMC9868645 DOI: 10.3389/fmolb.2022.1095193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Infections by non-segmented negative-strand RNA viruses (NNSV) are widely thought to entail gradient gene expression from the well-established existence of a single promoter at the 3' end of the viral genome and the assumption of constant transcriptional attenuation between genes. But multiple recent studies show viral mRNA levels in infections by respiratory syncytial virus (RSV), a major human pathogen and member of NNSV, that are inconsistent with a simple gradient. Here we integrate known and newly predicted phenomena into a biophysically reasonable model of NNSV transcription. Our model succeeds in capturing published observations of respiratory syncytial virus and vesicular stomatitis virus (VSV) mRNA levels. We therefore propose a novel understanding of NNSV transcription based on the possibility of ejective polymerase-polymerase collisions and, in the case of RSV, biased polymerase diffusion.
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Affiliation(s)
- Felipe-Andrés Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States,*Correspondence: Felipe-Andrés Piedra,
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Donna M. Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Harsha Doddapaneni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Vipin K. Menon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Kristi L. Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Matthew C. Ross
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Sara J. Javornik Cregeen
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Ginger Metcalf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, Unites States
| | - Joseph F. Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, Unites States,Department of Pediatrics, Baylor College of Medicine, Houston, TX, Unites States
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13
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Cui J, Ramesh G, Wu M, Jensen ET, Crago O, Bertoni AG, Gao C, Hoffman KL, Sheridan PA, Wong KE, Wood AC, Chen YDI, Rotter JI, Petrosino JF, Rich SS, Goodarzi MO. Butyrate-Producing Bacteria and Insulin Homeostasis: The Microbiome and Insulin Longitudinal Evaluation Study (MILES). Diabetes 2022; 71:2438-2446. [PMID: 35972231 PMCID: PMC9630078 DOI: 10.2337/db22-0168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022]
Abstract
Gut microbiome studies have documented depletion of butyrate-producing taxa in type 2 diabetes. We analyzed associations between butyrate-producing taxa and detailed measures of insulin homeostasis, whose dysfunction underlies diabetes in 224 non-Hispanic Whites and 129 African Americans, all of whom completed an oral glucose tolerance test. Stool microbiome was assessed by whole-metagenome shotgun sequencing with taxonomic profiling. We examined associations among 36 butyrate-producing taxa (n = 7 genera and 29 species) and insulin sensitivity, insulin secretion, disposition index, insulin clearance, and prevalence of dysglycemia (prediabetes plus diabetes, 46% of cohort), adjusting for age, sex, BMI, and race. The genus Coprococcus was associated with higher insulin sensitivity (β = 0.14; P = 0.002) and disposition index (β = 0.12; P = 0.012) and a lower rate of dysglycemia (odds ratio [OR] 0.91; 95% CI 0.85-0.97; P = 0.0025). In contrast, Flavonifractor was associated with lower insulin sensitivity (β = -0.13; P = 0.004) and disposition index (β = -0.11; P = 0.04) and higher prevalence of dysglycemia (OR 1.22; 95% CI 1.08-1.38; P = 0.0013). Species-level analyses found 10 bacteria associated with beneficial directions of effects and two bacteria with adverse associations on insulin homeostasis and dysglycemia. Although most butyrate producers analyzed appear to be metabolically beneficial, this is not the case for all such bacteria, suggesting that microbiome-directed therapeutic measures to prevent or treat diabetes should be targeted to specific butyrate-producing taxa rather than all butyrate producers.
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Affiliation(s)
- Jinrui Cui
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Gautam Ramesh
- School of Medicine, University of California San Diego, La Jolla, CA
| | - Martin Wu
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Elizabeth T. Jensen
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC
| | - Osa Crago
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC
| | - Alain G. Bertoni
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, NC
| | - Chunxu Gao
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX
| | | | | | - Alexis C. Wood
- U.S. Department of Agriculture, Agricultural Research Service, Children's Nutrition Research Center, Baylor College of Medicine, Houston, TX
| | - Yii-Der I. Chen
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation and Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
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14
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Di Gesù CM, Matz LM, Bolding IJ, Fultz R, Hoffman KL, Marino Gammazza A, Petrosino JF, Buffington SA. Maternal gut microbiota mediate intergenerational effects of high-fat diet on descendant social behavior. Cell Rep 2022; 41:111461. [PMID: 36223744 PMCID: PMC9597666 DOI: 10.1016/j.celrep.2022.111461] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/03/2022] [Accepted: 09/15/2022] [Indexed: 12/11/2022] Open
Abstract
Dysbiosis of the maternal gut microbiome during pregnancy is associated with adverse neurodevelopmental outcomes. We previously showed that maternal high-fat diet (MHFD) in mice induces gut dysbiosis, social dysfunction, and underlying synaptic plasticity deficits in male offspring (F1). Here, we reason that, if HFD-mediated changes in maternal gut microbiota drive offspring social deficits, then MHFD-induced dysbiosis in F1 female MHFD offspring would likewise impair F2 social behavior. Metataxonomic sequencing reveals reduced microbial richness among female F1 MHFD offspring. Despite recovery of microbial richness among MHFD-descendant F2 mice, they display social dysfunction. Post-weaning Limosilactobacillus reuteri treatment increases the abundance of short-chain fatty acid-producing taxa and rescues MHFD-descendant F2 social deficits. L. reuteri exerts a sexually dimorphic impact on gut microbiota configuration, increasing discriminant taxa between female cohorts. Collectively, these results show multigenerational impacts of HFD-induced dysbiosis in the maternal lineage and highlight the potential of maternal microbiome-targeted interventions for neurodevelopmental disorders.
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Affiliation(s)
- Claudia M. Di Gesù
- Department of Neurobiology, The University of Texas Medical Branch, Galveston, TX 77555, USA,Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy,Current address: Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston,These authors contributed equally
| | - Lisa M. Matz
- Department of Neurobiology, The University of Texas Medical Branch, Galveston, TX 77555, USA,These authors contributed equally
| | - Ian J. Bolding
- Department of Neurobiology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert Fultz
- Department of Neurobiology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antonella Marino Gammazza
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (BIND), University of Palermo, 90127 Palermo, Italy
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shelly A. Buffington
- Department of Neurobiology, The University of Texas Medical Branch, Galveston, TX 77555, USA,Sealy Center for Microbiome Research, The University of Texas Medical Branch, Galveston, TX 77555, USA,Lead contact,Correspondence:
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15
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Karpinets TV, Wu X, Solley T, El Alam MB, Sims TT, Yoshida-Court K, Lynn E, Ahmed-Kaddar M, Biegert G, Yue J, Song X, Sun H, Petrosino JF, Mezzari MP, Okhuysen P, Eifel PJ, Jhingran A, Lin LL, Schmeler KM, Ramondetta L, Ajami N, Jenq RR, Futreal A, Zhang J, Klopp AH, Colbert LE. Metagenomes of rectal swabs in larger, advanced stage cervical cancers have enhanced mucus degrading functionalities and distinct taxonomic structure. BMC Cancer 2022; 22:945. [PMID: 36050658 PMCID: PMC9438314 DOI: 10.1186/s12885-022-09997-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 08/11/2022] [Indexed: 11/10/2022] Open
Abstract
Background Gut microbiome community composition differs between cervical cancer (CC) patients and healthy controls, and increased gut diversity is associated with improved outcomes after treatment. We proposed that functions of specific microbial species adjoining the mucus layer may directly impact the biology of CC. Method Metagenomes of rectal swabs in 41 CC patients were examined by whole-genome shotgun sequencing to link taxonomic structures, molecular functions, and metabolic pathway to patient’s clinical characteristics. Results Significant association of molecular functions encoded by the metagenomes was found with initial tumor size and stage. Profiling of the molecular function abundances and their distributions identified 2 microbial communities co-existing in each metagenome but having distinct metabolism and taxonomic structures. Community A (Clostridia and Proteobacteria predominant) was characterized by high activity of pathways involved in stress response, mucus glycan degradation and utilization of degradation byproducts. This community was prevalent in patients with larger, advanced stage tumors. Conversely, community B (Bacteroidia predominant) was characterized by fast growth, active oxidative phosphorylation, and production of vitamins. This community was prevalent in patients with smaller, early-stage tumors. Conclusions In this study, enrichment of mucus degrading microbial communities in rectal metagenomes of CC patients was associated with larger, more advanced stage tumors. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09997-0.
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Affiliation(s)
- Tatiana V Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaogang Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Travis Solley
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Molly B El Alam
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Travis T Sims
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kyoko Yoshida-Court
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erica Lynn
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mustapha Ahmed-Kaddar
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Greyson Biegert
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jingyan Yue
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xingzhi Song
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Huandong Sun
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Melissa P Mezzari
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Pablo Okhuysen
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Patricia J Eifel
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anuja Jhingran
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lilie L Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathleen M Schmeler
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lois Ramondetta
- Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nadim Ajami
- Program for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert R Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Program for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jianhua Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Ann H Klopp
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Lauren E Colbert
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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16
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Auchtung TA, Stewart CJ, Smith DP, Triplett EW, Agardh D, Hagopian WA, Ziegler AG, Rewers MJ, She JX, Toppari J, Lernmark Å, Akolkar B, Krischer JP, Vehik K, Auchtung JM, Ajami NJ, Petrosino JF. Temporal changes in gastrointestinal fungi and the risk of autoimmunity during early childhood: the TEDDY study. Nat Commun 2022; 13:3151. [PMID: 35672407 PMCID: PMC9174155 DOI: 10.1038/s41467-022-30686-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 05/09/2022] [Indexed: 12/11/2022] Open
Abstract
Fungal infections are a major health problem that often begin in the gastrointestinal tract. Gut microbe interactions in early childhood are critical for proper immune responses, yet there is little known about the development of the fungal population from infancy into childhood. Here, as part of the TEDDY (The Environmental Determinants of Diabetes in the Young) study, we examine stool samples of 888 children from 3 to 48 months and find considerable differences between fungi and bacteria. The metagenomic relative abundance of fungi was extremely low but increased while weaning from milk and formula. Overall fungal diversity remained constant over time, in contrast with the increase in bacterial diversity. Fungal profiles had high temporal variation, but there was less variation from month-to-month in an individual than among different children of the same age. Fungal composition varied with geography, diet, and the use of probiotics. Multiple Candida spp. were at higher relative abundance in children than adults, while Malassezia and certain food-associated fungi were lower in children. There were only subtle fungal differences associated with the subset of children that developed islet autoimmunity or type 1 diabetes. Having proper fungal exposures may be crucial for children to establish appropriate responses to fungi and limit the risk of infection: the data here suggests those gastrointestinal exposures are limited and variable.
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Grants
- U01 DK063821 NIDDK NIH HHS
- UC4 DK063863 NIDDK NIH HHS
- UC4 DK112243 NIDDK NIH HHS
- UC4 DK117483 NIDDK NIH HHS
- U01 DK124166 NIDDK NIH HHS
- U01 DK063863 NIDDK NIH HHS
- UL1 TR000064 NCATS NIH HHS
- UC4 DK106955 NIDDK NIH HHS
- UC4 DK100238 NIDDK NIH HHS
- UL1 TR002535 NCATS NIH HHS
- HHSN267200700014C NLM NIH HHS
- P30 ES030285 NIEHS NIH HHS
- U01 DK128847 NIDDK NIH HHS
- This research was performed on behalf of the TEDDY Study Group, which is funded by U01 DK63829, U01 DK63861, U01 DK63821, U01 DK63865, U01 DK63863, U01 DK63836, U01 DK63790, UC4 DK63829, UC4 DK63861, UC4 DK63821, UC4 DK63865, UC4 DK63863, UC4 DK63836, UC4 DK95300, UC4 DK100238, UC4 DK106955, UC4 DK112243, UC4 DK117483, U01 DK124166, U01 DK128847, and Contract No. HHSN267200700014C from the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institute of Allergy and Infectious Diseases (NIAID), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institute of Environmental Health Sciences (NIEHS), Centers for Disease Control and Prevention (CDC), and JDRF. This work is supported in part by the NIH/NCATS Clinical and Translational Science Awards to the University of Florida (UL1 TR000064) and the University of Colorado (UL1 TR002535).
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Affiliation(s)
- Thomas A Auchtung
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Christopher J Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel P Smith
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Eric W Triplett
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Daniel Agardh
- Department of Clinical Sciences, Lund University Clinical Research Center, Skåne University Hospital, Malmö, Sweden
| | | | - Anette G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, Munich, Germany
- Forschergruppe Diabetes, Technische Universität München, Klinikum Rechts der Isar, Munich, Germany
- Forschergruppe Diabetes e.V. at Helmholtz Zentrum München, Munich, Germany
| | - Marian J Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO, USA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta University, Augusta, GA, USA
- Jinfiniti Precision Medicine, Inc, Augusta, GA, USA
| | - Jorma Toppari
- Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology, University of Turku, Turku, Finland
- Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skane University Hospital, Malmö, Sweden
| | - Beena Akolkar
- National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, MD, USA
| | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Kendra Vehik
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Jennifer M Auchtung
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Program for Innovative Microbiome and Translational Research, Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
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17
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Shi H, Nelson JW, Phillips S, Petrosino JF, Bryan RM, Durgan DJ. Alterations of the gut microbial community structure and function with aging in the spontaneously hypertensive stroke prone rat. Sci Rep 2022; 12:8534. [PMID: 35595870 PMCID: PMC9122926 DOI: 10.1038/s41598-022-12578-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/11/2022] [Indexed: 01/04/2023] Open
Abstract
Gut dysbiosis, a pathological imbalance of bacteria, has been shown to contribute to the development of hypertension (HT), systemic- and neuro-inflammation, and blood-brain barrier (BBB) disruption in spontaneously hypertensive stroke prone rats (SHRSP). However, to date individual species that contribute to HT in the SHRSP model have not been identified. One potential reason, is that nearly all studies of the SHRSP gut microbiota have analyzed samples from rats with established HT. The goal of this study was to examine the SHRSP gut microbiota before, during, and after the onset of hypertension, and in normotensive WKY control rats over the same age range. We hypothesized that we could identify key microbes involved in the development of HT by comparing WKY and SHRSP microbiota during the pre-hypertensive state and longitudinally. Systolic blood pressure (SBP) was measured by tail-cuff plethysmography and fecal microbiota analyzed by16S rRNA gene sequencing. SHRSP showed significant elevations in SBP, as compared to WKY, beginning at 8 weeks of age (p < 0.05 at each time point). Bacterial community structure was significantly different between WKY and SHRSP as early as 4 weeks of age, and remained different throughout the study (p = 0.001-0.01). At the phylum level we observed significantly reduced Firmicutes and Deferribacterota, and elevated Bacteroidota, Verrucomicrobiota, and Proteobacteria, in pre-hypertensive SHRSP, as compared to WKY. At the genus level we identified 18 bacteria whose relative abundance was significantly different in SHRSP versus WKY at the pre-hypertensive ages of 4 or 6 weeks. In an attempt to further refine bacterial candidates that might contribute to the SHRSP phenotype, we compared the functional capacity of WKY versus SHRSP microbial communities. We identified significant differences in amino acid metabolism. Using untargeted metabolomics we found significant reductions in metabolites of the tryptophan-kynurenine pathway and increased indole metabolites in SHRSP versus WKY plasma. Overall, we provide further evidence that gut dysbiosis contributes to hypertension in the SHRSP model, and suggest for the first time the potential involvement of tryptophan metabolizing microbes.
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Affiliation(s)
- Huanan Shi
- Department of Anesthesiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James W Nelson
- Department of Anesthesiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrated Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sharon Phillips
- Department of Anesthesiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Joseph F Petrosino
- Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- The Alkek Center for Metagenomics and Microbiota Research, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Robert M Bryan
- Department of Anesthesiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David J Durgan
- Department of Anesthesiology, Baylor College of Medicine, Houston, TX, 77030, USA.
- Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA.
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18
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Lin D, Alam MBE, Jaoude JA, Kouzy R, Phan JL, Elnaggar JH, Resendiz B, Medrano AYD, Lynn EJ, Nguyen ND, Noticewala SS, Mathew GG, Holliday EB, Minsky BD, Das P, Morris VK, Eng C, Mezzari MP, Petrosino JF, Ajami NJ, Klopp AH, Taniguchi CM, Colbert LE. Microbiome Dynamics During Chemoradiotherapy for Anal Cancer. Int J Radiat Oncol Biol Phys 2022; 113:974-984. [DOI: 10.1016/j.ijrobp.2022.04.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 10/18/2022]
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19
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Jiao L, Kourkoumpetis T, Hutchinson D, Ajami NJ, Hoffman K, White DL, Graham DY, Hair C, Shah R, Kanwal F, Jarbrink-Sehgal M, Husain N, Hernaez R, Hou J, Cole R, Velez M, Ketwaroo G, Kramer J, El-Serag HB, Petrosino JF. Spatial Characteristics of Colonic Mucosa-Associated Gut Microbiota in Humans. Microb Ecol 2022; 83:811-821. [PMID: 34223947 DOI: 10.1007/s00248-021-01789-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/07/2021] [Indexed: 06/13/2023]
Abstract
Limited data exist on the spatial distribution of the colonic bacteria in humans. We collected the colonic biopsies from five segments of 27 polyp-free adults and collected feces from 13 of them. We sequenced the V4 region of the bacterial 16S rRNA gene using the MiSeq platform. The sequencing data were assigned to the amplicon sequence variant (ASV) using SILVA. Biodiversity and the relative abundance of the ASV were compared across the colonic segments and between the rectal and fecal samples. Bacterial functional capacity was assessed using Tax4fun. Each individual had a unique bacterial community composition (Weighted Bray-Curtis P value = 0.001). There were no significant differences in richness, evenness, community composition, and the taxonomic structure across the colon segments in all the samples. Firmicutes (47%), Bacteroidetes (39%), and Proteobacteria (6%) were the major phyla in all segments, followed by Verrucomicrobia, Fusobacteria, Desulfobacterota, and Actinobacteria. There were 15 genera with relative abundance > 1%, including Bacteroides, Faecalibacterium, Escherichia/Shigella, Sutterella, Akkermansia, Parabacteroides, Prevotella, Lachnoclostridium, Alistipes, Fusobacterium, Erysipelatoclostridium, and four Lachnospiraceae family members. Intra-individually, the community compositional dissimilarity was the greatest between the cecum and the rectum. There were significant differences in biodiversity and the taxonomic structure between the rectal and fecal bacteria. The bacterial community composition and structure were homogeneous across the large intestine in adults. The inter-individual variability of the bacteria was greater than inter-segment variability. The rectal and fecal bacteria differed in the community composition and structure.
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Affiliation(s)
- Li Jiao
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
- Center for Innovations in Quality, Effectiveness and Safety (IQuESt), Michael E. DeBakey VA Medical Center, Houston, TX, 77030, USA.
- Texas Medical Center Digestive Disease Center, Houston, TX, 77030, USA.
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
- Center for Translational Research On Inflammatory Diseases (CTRID), Michael E. DeBakey VA Medical Center, Houston, TX, 77030, USA.
| | - Themistoklis Kourkoumpetis
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Diane Hutchinson
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nadim J Ajami
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kristi Hoffman
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Donna L White
- Center for Innovations in Quality, Effectiveness and Safety (IQuESt), Michael E. DeBakey VA Medical Center, Houston, TX, 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX, 77030, USA
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Translational Research On Inflammatory Diseases (CTRID), Michael E. DeBakey VA Medical Center, Houston, TX, 77030, USA
| | - David Y Graham
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX, 77030, USA
| | - Clark Hair
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX, 77030, USA
| | - Rajesh Shah
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX, 77030, USA
| | - Fasiha Kanwal
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX, 77030, USA
| | - Maria Jarbrink-Sehgal
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX, 77030, USA
| | - Nisreen Husain
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX, 77030, USA
| | - Ruben Hernaez
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Innovations in Quality, Effectiveness and Safety (IQuESt), Michael E. DeBakey VA Medical Center, Houston, TX, 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX, 77030, USA
| | - Jason Hou
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Innovations in Quality, Effectiveness and Safety (IQuESt), Michael E. DeBakey VA Medical Center, Houston, TX, 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX, 77030, USA
| | - Rhonda Cole
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maria Velez
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Gyanprakash Ketwaroo
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX, 77030, USA
| | - Jennifer Kramer
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Innovations in Quality, Effectiveness and Safety (IQuESt), Michael E. DeBakey VA Medical Center, Houston, TX, 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX, 77030, USA
| | - Hashem B El-Serag
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
- Center for Innovations in Quality, Effectiveness and Safety (IQuESt), Michael E. DeBakey VA Medical Center, Houston, TX, 77030, USA
- Texas Medical Center Digestive Disease Center, Houston, TX, 77030, USA
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Joseph F Petrosino
- Texas Medical Center Digestive Disease Center, Houston, TX, 77030, USA
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
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20
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Menon VK, Okhuysen PC, Chappell CL, Mahmoud M, Mahmoud M, Meng Q, Doddapaneni H, Vee V, Han Y, Salvi S, Bhamidipati S, Kottapalli K, Weissenberger G, Shen H, Ross MC, Hoffman KL, Cregeen SJ, Muzny DM, Metcalf GA, Gibbs RA, Petrosino JF, Sedlazeck FJ. Fully resolved assembly of Cryptosporidium parvum. Gigascience 2022; 11:6528769. [PMID: 35166336 PMCID: PMC8848321 DOI: 10.1093/gigascience/giac010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/07/2021] [Accepted: 01/20/2022] [Indexed: 11/17/2022] Open
Abstract
Background Cryptosporidium parvum is an apicomplexan parasite commonly found across many host species with a global infection prevalence in human populations of 7.6%. Understanding its diversity and genomic makeup can help in fighting established infections and prohibiting further transmission. The basis of every genomic study is a high-quality reference genome that has continuity and completeness, thus enabling comprehensive comparative studies. Findings Here, we provide a highly accurate and complete reference genome of Cryptosporidium parvum. The assembly is based on Oxford Nanopore reads and was improved using Illumina reads for error correction. We also outline how to evaluate and choose from different assembly methods based on 2 main approaches that can be applied to other Cryptosporidium species. The assembly encompasses 8 chromosomes and includes 13 telomeres that were resolved. Overall, the assembly shows a high completion rate with 98.4% single-copy BUSCO genes. Conclusions This high-quality reference genome of a zoonotic IIaA17G2R1 C. parvum subtype isolate provides the basis for subsequent comparative genomic studies across the Cryptosporidium clade. This will enable improved understanding of diversity, functional, and association studies.
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Affiliation(s)
- Vipin K Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pablo C Okhuysen
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cynthia L Chappell
- Center for Infectious Diseases, The University of Texas School of Public Health, Houston, TX 77030, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vanesa Vee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yi Han
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sejal Salvi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sravya Bhamidipati
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - George Weissenberger
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hua Shen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew C Ross
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kristi L Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ginger A Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
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21
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Ferrat LA, Vehik K, Sharp SA, Lernmark Å, Rewers MJ, She JX, Ziegler AG, Toppari J, Akolkar B, Krischer JP, Weedon MN, Oram RA, Hagopian WA, Barbour A, Bautista K, Baxter J, Felipe-Morales D, Driscoll K, Frohnert BI, Stahl M, Gesualdo P, Hoffman M, Karban R, Liu E, Norris J, Peacock S, Shorrosh H, Steck A, Stern M, Villegas E, Waugh K, Simell OG, Adamsson A, Ahonen S, Åkerlund M, Hakola L, Hekkala A, Holappa H, Hyöty H, Ikonen A, Ilonen J, Jäminki S, Jokipuu S, Karlsson L, Kero J, Kähönen M, Knip M, Koivikko ML, Koskinen M, Koreasalo M, Kurppa K, Kytölä J, Latva-aho T, Lindfors K, Lönnrot M, Mäntymäki E, Mattila M, Miettinen M, Multasuo K, Mykkänen T, Niininen T, Niinistö S, Nyblom M, Oikarinen S, Ollikainen P, Othmani Z, Pohjola S, Rajala P, Rautanen J, Riikonen A, Riski E, Pekkola M, Romo M, Ruohonen S, Simell S, Sjöberg M, Stenius A, Tossavainen P, Vähä-Mäkilä M, Vainionpää S, Varjonen E, Veijola R, Viinikangas I, Virtanen SM, Schatz D, Hopkins D, Steed L, Bryant J, Silvis K, Haller M, Gardiner M, McIndoe R, Sharma A, Anderson SW, Jacobsen L, Marks J, Towe PD, Bonifacio E, Gezginci C, Heublein A, Hohoff E, Hummel S, Knopff A, Koch C, Koletzko S, Ramminger C, Roth R, Schmidt J, Scholz M, Stock J, Warncke K, Wendel L, Winkler C, Agardh D, Aronsson CA, Ask M, Bennet R, Cilio C, Dahlberg S, Engqvist H, Ericson-Hallström E, Fors AB, Fransson L, Gard T, Hansen M, Jisser H, Johansen F, Jonsdottir B, Elding Larsson H, Lindström M, Lundgren M, Maziarz M, Månsson-Martinez M, Melin J, Mestan Z, Nilsson C, Ottosson K, Rahmati K, Ramelius A, Salami F, Sjöberg A, Sjöberg B, Törn C, Wimar Å, Killian M, Crouch CC, Skidmore J, Chavoshi M, Meyer A, Meyer J, Mulenga D, Powell N, Radtke J, Romancik M, Roy S, Schmitt D, Zink S, Becker D, Franciscus M, Smith MDE, Daftary A, Klein MB, Yates C, Austin-Gonzalez S, Avendano M, Baethke S, Burkhardt B, Butterworth M, Clasen J, Cuthbertson D, Eberhard C, Fiske S, Garmeson J, Gowda V, Heyman K, Hsiao B, Karges C, Laras FP, Li Q, Liu S, Liu X, Lynch K, Maguire C, Malloy J, McCarthy C, Parikh H, Remedios C, Shaffer C, Smith L, Smith S, Sulman N, Tamura R, Tewey D, Toth M, Uusitalo U, Vijayakandipan P, Wood K, Yang J, Yu L, Miao D, Bingley P, Williams A, Chandler K, Kelland I, Khoud YB, Zahid H, Randell M, Chavoshi M, Radtke J, Zink S, Ke S, Mulholland N, Rich SS, Chen WM, Onengut-Gumuscu S, Farber E, Pickin RR, Davis J, Davis J, Gallo D, Bonnie J, Campolieto P, Petrosino JF, Ajami NJ, Lloyd RE, Ross MC, O’Brien JL, Hutchinson DS, Smith DP, Wong MC, Tian X, Ayvaz T, Tamegnon A, Truong N, Moreno H, Riley L, Moreno E, Bauch T, Kusic L, Metcalf G, Muzny D, Doddapaneni H, Gibbs R, Bourcier K, Briese T, Johnson SB, Triplett E, Ziegler AG, Tamura R, Norris J, Virtanen SM, Frohnert BI, Gesualdo P, Koreasalo M, Miettinen M, Niinistö S, Riikonen A, Silvis K, Hohoff E, Hummel S, Winkler C, Aronsson CA, Skidmore J, Smith MDE, Butterworth M, Li Q, Liu X, Tamura R, Uusitalo U, Yang J, Rich SS, Norris J, Steck A, Ilonen J, Ziegler AG, Törn C, Li Q, Liu X, Parikh H, Erlich H, Chen WM, Onengut-Gumuscu S, Schatz D, Ziegler AG, Cilio C, Bonifacio E, Knip M, Schatz D, Burkhardt B, Lynch K, Yu L, Bingley P, Bourcier K, Hyöty H, Triplett E, Lloyd R, Gesualdo P, Waugh K, Lönnrot M, Agardh D, Cilio C, Larsson HE, Killian M, Burkhardt B, Lynch K, Briese T, Waugh K, Schatz D, Killian M, Johnson SB, Roth R, Baxter J, Driscoll K, Schatz D, Stock J, Fiske S, Liu X, Lynch K, Smith L, Baxter J, Lernmark Å, Baxter J, Killian M, Bautista K, Gesualdo P, Hoffman M, Karban R, Norris J, Waugh K, Adamsson A, Kähönen M, Niininen T, Stenius A, Varjonen E, Hopkins D, Steed L, Bryant J, Gardiner M, Marks J, Ramminger C, Stock J, Winkler C, Aronsson CA, Jonsdottir B, Melin J, Killian M, Crouch CC, Mulenga D, McCarthy C, Smith L, Smith S, Tamura R, Johnson SB, Agardh D, Liu E, Koletzko S, Kurppa K, Stahl M, Hoffman M, Kurppa K, Lindfors K, Simell S, Steed L, Aronsson CA, Killian M, Tamura R, Haller M, Larsson HE, Frohnert BI, Gesualdo P, Hoffman M, Steck A, Kähönen M, Veijola R, Steed L, Jacobsen L, Marks J, Stock J, Warncke K, Lundgren M, Wimar Å, Crouch CC, Liu X, Tamura R. Author Correction: A combined risk score enhances prediction of type 1 diabetes among susceptible children. Nat Med 2022; 28:599. [DOI: 10.1038/s41591-021-01631-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Vitko D, McQuaid JW, Gheinani AH, Hasegawa K, DiMartino S, Davis KH, Chung CY, Petrosino JF, Adam RM, Mansbach JM, Lee RS. Urinary Tract Infections in Children with Vesicoureteral Reflux Are Accompanied by Alterations in Urinary Microbiota and Metabolome Profiles. Eur Urol 2022; 81:151-154. [PMID: 34538688 DOI: 10.1016/j.eururo.2021.08.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 08/20/2021] [Indexed: 12/21/2022]
Abstract
Children with vesicoureteral reflux (VUR) are at an increased risk of recurrent urinary tract infections (UTIs) and renal scarring. Gut microbiota are associated with disease phenotypes, but there has been no study that associates urinary microbiota (uMB) and metabolic profiles with VUR pathology. To identify dominant uMB genera and metabolites associated with UTIs in VUR, urine samples collected under sterile conditions underwent 16S ribosomal RNA sequencing (n = 49) and metabolomic analysis by mass spectrometry (n = 96). Alterations in uMB and metabolomic profiles in VUR patients suggest remodeling of urinary bacterial communities after UTIs: Dorea- and Escherichia-dominant uMB profiles were more frequently identified in participants with VUR. Prevotella- and Lactobacillus-dominant uMB profiles were more prevalent in controls (p < 0.001). Microbial composition varied based on recurrent febrile UTI status (p = 0.001). A total of 243 urinary metabolites involved in energy, amino acid, nucleotide, and lipid metabolism were altered in VUR patients with UTIs (p < 0.05). Importantly, VUR specimens revealed changes in the bacteria-associated metabolic pathways such as glutamate degradation, methyl-citrate cycle, and bile acid metabolism. PATIENT SUMMARY: Differences in urinary commensal bacteria and metabolites exist between children with and without vesicoureteral reflux (VUR). These changes may be utilized to identify patients at risk of VUR-associated kidney damage.
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Affiliation(s)
- Dijana Vitko
- Department of Urology, Boston Children's Hospital, Boston, MA, USA; Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Joseph W McQuaid
- Department of Urology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ali Hashemi Gheinani
- Department of Urology, Boston Children's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kylie H Davis
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
| | - Candace Y Chung
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Rosalyn M Adam
- Department of Urology, Boston Children's Hospital, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Surgery, Harvard Medical School, Boston, MA, USA
| | | | - Richard S Lee
- Department of Urology, Boston Children's Hospital, Boston, MA, USA; Department of Surgery, Harvard Medical School, Boston, MA, USA.
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23
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Spencer CN, McQuade JL, Gopalakrishnan V, McCulloch JA, Vetizou M, Cogdill AP, Khan AW, Zhang X, White MG, Peterson CB, Wong MC, Morad G, Rodgers T, Badger JH, Helmink BA, Andrews MC, Rodrigues RR, Morgun A, Kim YS, Roszik J, Hoffman KL, Zheng J, Zhou Y, Medik YB, Kahn LM, Johnson S, Hudgens CW, Wani K, Gaudreau PO, Harris AL, Jamal MA, Baruch EN, Perez-Guijarro E, Day CP, Merlino G, Pazdrak B, Lochmann BS, Szczepaniak-Sloane RA, Arora R, Anderson J, Zobniw CM, Posada E, Sirmans E, Simon J, Haydu LE, Burton EM, Wang L, Dang M, Clise-Dwyer K, Schneider S, Chapman T, Anang NAAS, Duncan S, Toker J, Malke JC, Glitza IC, Amaria RN, Tawbi HA, Diab A, Wong MK, Patel SP, Woodman SE, Davies MA, Ross MI, Gershenwald JE, Lee JE, Hwu P, Jensen V, Samuels Y, Straussman R, Ajami NJ, Nelson KC, Nezi L, Petrosino JF, Futreal PA, Lazar AJ, Hu J, Jenq RR, Tetzlaff MT, Yan Y, Garrett WS, Huttenhower C, Sharma P, Watowich SS, Allison JP, Cohen L, Trinchieri G, Daniel CR, Wargo JA. Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response. Science 2021; 374:1632-1640. [PMID: 34941392 PMCID: PMC8970537 DOI: 10.1126/science.aaz7015] [Citation(s) in RCA: 318] [Impact Index Per Article: 106.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Gut bacteria modulate the response to immune checkpoint blockade (ICB) treatment in cancer, but the effect of diet and supplements on this interaction is not well studied. We assessed fecal microbiota profiles, dietary habits, and commercially available probiotic supplement use in melanoma patients and performed parallel preclinical studies. Higher dietary fiber was associated with significantly improved progression-free survival in 128 patients on ICB, with the most pronounced benefit observed in patients with sufficient dietary fiber intake and no probiotic use. Findings were recapitulated in preclinical models, which demonstrated impaired treatment response to anti–programmed cell death 1 (anti–PD-1)–based therapy in mice receiving a low-fiber diet or probiotics, with a lower frequency of interferon-γ–positive cytotoxic T cells in the tumor microenvironment. Together, these data have clinical implications for patients receiving ICB for cancer.
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Affiliation(s)
- Christine N. Spencer
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer L. McQuade
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - John A. McCulloch
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Marie Vetizou
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Alexandria P. Cogdill
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - A. Wadud Khan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaotao Zhang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael G. White
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christine B. Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew C. Wong
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Golnaz Morad
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Theresa Rodgers
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jonathan H. Badger
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Beth A. Helmink
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Miles C. Andrews
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Richard R. Rodrigues
- Frederick National Laboratory for Cancer Research, and Microbiome and Genetics Core, Laboratory of Integrative Cancer Immunology, CCR, NCI, NIH, Bethesda, MD 20852, USA
| | - Andrey Morgun
- Department of Pharmaceutical Science, Oregon State University, Corvallis, OR 97331, USA
| | - Young S. Kim
- Nutritional Science Research Group, Division of Cancer Prevention, NCI, NIH, Rockville, MD 20850, USA
| | - Jason Roszik
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kristi L. Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jiali Zheng
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yifan Zhou
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yusra B. Medik
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Laura M. Kahn
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- MD Anderson University of Texas Health Graduate School, Houston, TX 77030, USA
| | - Sarah Johnson
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Courtney W. Hudgens
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Khalida Wani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Pierre-Olivier Gaudreau
- Canadian Cancer Trials Group and Department of Oncology, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Angela L. Harris
- Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mohamed A. Jamal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erez N. Baruch
- Department of Internal Medicine, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Eva Perez-Guijarro
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Glenn Merlino
- Laboratory of Cancer Biology and Genetics, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Barbara Pazdrak
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Brooke S. Lochmann
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Reetakshi Arora
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jaime Anderson
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chrystia M. Zobniw
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eliza Posada
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elizabeth Sirmans
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Julie Simon
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lauren E. Haydu
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elizabeth M. Burton
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Minghao Dang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Karen Clise-Dwyer
- Advanced Cytometry and Sorting Facility at South Campus, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Hematopoietic Biology and Malignancy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sarah Schneider
- Advanced Cytometry and Sorting Facility at South Campus, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Thomas Chapman
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nana-Ama A. S. Anang
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sheila Duncan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Joseph Toker
- Department of Neurosurgery, Harvard University, Cambridge, MA 02138, USA
- Department of Oncology, University of Cambridge, Cambridge CB2 1TN, UK
| | - Jared C. Malke
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Isabella C. Glitza
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rodabe N. Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hussein A. Tawbi
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Adi Diab
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael K. Wong
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sapna P. Patel
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott E. Woodman
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael A. Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Merrick I. Ross
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey E. Gershenwald
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey E. Lee
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Patrick Hwu
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vanessa Jensen
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ravid Straussman
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Nadim J. Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kelly C. Nelson
- Department of Dermatology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Luigi Nezi
- Dipartimento di Oncologia Sperimentale, Instituto Europeo di Oncologia, Milan, P.I. 08691440153, Italy
| | - Joseph F. Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - P. Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alexander J. Lazar
- MD Anderson University of Texas Health Graduate School, Houston, TX 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jianhua Hu
- Department of Biostatistics, Columbia University, New York, NY 10032, USA
| | - Robert R. Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Stem Cell Transplant, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael T. Tetzlaff
- Departments of Pathology and Dermatology, Dermatopathology and Oral Pathology Unit, University of California San Francisco, San Francisco, CA 94115, USA
| | - Yan Yan
- Department of Biostatistics and the Harvard T.H. Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Wendy S. Garrett
- Department of Molecular Metabolism, T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Curtis Huttenhower
- Department of Biostatistics and the Harvard T.H. Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Padmanee Sharma
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Parker Institute for Cancer Immunotherapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stephanie S. Watowich
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - James P. Allison
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Parker Institute for Cancer Immunotherapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lorenzo Cohen
- Department of Palliative, Rehabilitation, and Integrative Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Giorgio Trinchieri
- Laboratory of Integrative Cancer Immunology, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Carrie R. Daniel
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer A. Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Masi AC, Fofanova TY, Lamb CA, Auchtung JM, Britton RA, Estes MK, Ramani S, Cockell SJ, Coxhead J, Embleton ND, Berrington JE, Petrosino JF, Stewart CJ. Distinct gene expression profiles between human preterm-derived and adult-derived intestinal organoids exposed to Enterococcus faecalis: a pilot study. Gut 2021; 71:gutjnl-2021-326552. [PMID: 34921063 PMCID: PMC9231289 DOI: 10.1136/gutjnl-2021-326552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/06/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Andrea C Masi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Tatiana Y Fofanova
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Christopher A Lamb
- Translational & Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Jennifer M Auchtung
- Nebraska Food for Health Center and Department of Food Science and Technology, University of Nebraska, Lincoln, Nebraska, USA
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Mary K Estes
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Simon J Cockell
- Bioinformatics Support Unit, Newcastle University, Newcastle Upon Tyne, UK
| | - Jonathan Coxhead
- Bioscience Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Nicholas D Embleton
- Newcastle Neonatal Service, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Janet E Berrington
- Newcastle Neonatal Service, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
| | - Joseph F Petrosino
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, The Baylor College of Medicine, Houston, Texas, USA
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
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25
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Masi AC, Embleton ND, Lamb CA, Young G, Granger CL, Najera J, Smith DP, Hoffman KL, Petrosino JF, Bode L, Berrington JE, Stewart CJ. Human milk oligosaccharide DSLNT and gut microbiome in preterm infants predicts necrotising enterocolitis. Gut 2021; 70:2273-2282. [PMID: 33328245 PMCID: PMC9231288 DOI: 10.1136/gutjnl-2020-322771] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Necrotising enterocolitis (NEC) is a devastating intestinal disease primarily affecting preterm infants. The underlying mechanisms are poorly understood: mother's own breast milk (MOM) is protective, possibly relating to human milk oligosaccharide (HMO) and infant gut microbiome interplay. We investigated the interaction between HMO profiles and infant gut microbiome development and its association with NEC. DESIGN We performed HMO profiling of MOM in a large cohort of infants with NEC (n=33) with matched controls (n=37). In a subset of 48 infants (14 with NEC), we also performed longitudinal metagenomic sequencing of infant stool (n=644). RESULTS Concentration of a single HMO, disialyllacto-N-tetraose (DSLNT), was significantly lower in MOM received by infants with NEC compared with controls. A MOM threshold level of 241 nmol/mL had a sensitivity and specificity of 0.9 for NEC. Metagenomic sequencing before NEC onset showed significantly lower relative abundance of Bifidobacterium longum and higher relative abundance of Enterobacter cloacae in infants with NEC. Longitudinal development of the microbiome was also impacted by low MOM DSLNT associated with reduced transition into preterm gut community types dominated by Bifidobacterium spp and typically observed in older infants. Random forest analysis combining HMO and metagenome data before disease accurately classified 87.5% of infants as healthy or having NEC. CONCLUSION These results demonstrate the importance of HMOs and gut microbiome in preterm infant health and disease. The findings offer potential targets for biomarker development, disease risk stratification and novel avenues for supplements that may prevent life-threatening disease.
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Affiliation(s)
- Andrea C Masi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Nicholas D Embleton
- Newcastle Neonatal Service, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK,Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Christopher A Lamb
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK,Gastroenterology, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Gregory Young
- School of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Claire L Granger
- Newcastle Neonatal Service, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
| | - Julia Najera
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California San Diego, La Jolla, California, USA
| | - Daniel P Smith
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Kristi L Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California San Diego, La Jolla, California, USA
| | - Janet E Berrington
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK .,Newcastle Neonatal Service, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
| | - Christopher J Stewart
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
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26
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Criss ZK, Bhasin N, Di Rienzi SC, Rajan A, Deans-Fielder K, Swaminathan G, Kamyabi N, Zeng XL, Doddapaneni H, Menon VK, Chakravarti D, Estrella C, Yu X, Patil K, Petrosino JF, Fleet JC, Verzi MP, Christakos S, Helmrath MA, Arimura S, DePinho RA, Britton RA, Maresso AW, Grande-Allen KJ, Blutt SE, Crawford SE, Estes MK, Ramani S, Shroyer NF. Drivers of transcriptional variance in human intestinal epithelial organoids. Physiol Genomics 2021; 53:486-508. [PMID: 34612061 DOI: 10.1152/physiolgenomics.00061.2021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Human intestinal epithelial organoids (enteroids and colonoids) are tissue cultures used for understanding the physiology of the human intestinal epithelium. Here, we explored the effect on the transcriptome of common variations in culture methods, including extracellular matrix substrate, format, tissue segment, differentiation status, and patient heterogeneity. RNA-sequencing datasets from 276 experiments performed on 37 human enteroid and colonoid lines from 29 patients were aggregated from several groups in the Texas Medical Center. DESeq2 and gene set enrichment analysis (GSEA) were used to identify differentially expressed genes and enriched pathways. PERMANOVA, Pearson's correlation, and dendrogram analysis of the data originally indicated three tiers of influence of culture methods on transcriptomic variation: substrate (collagen vs. Matrigel) and format (3-D, transwell, and monolayer) had the largest effect; segment of origin (duodenum, jejunum, ileum, colon) and differentiation status had a moderate effect; and patient heterogeneity and specific experimental manipulations (e.g., pathogen infection) had the smallest effect. GSEA identified hundreds of pathways that varied between culture methods, such as IL1 cytokine signaling enriched in transwell versus monolayer cultures and E2F target genes enriched in collagen versus Matrigel cultures. The transcriptional influence of the format was furthermore validated in a synchronized experiment performed with various format-substrate combinations. Surprisingly, large differences in organoid transcriptome were driven by variations in culture methods such as format, whereas experimental manipulations such as infection had modest effects. These results show that common variations in culture conditions can have large effects on intestinal organoids and should be accounted for when designing experiments and comparing results between laboratories. Our data constitute the largest RNA-seq dataset interrogating human intestinal epithelial organoids.
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Affiliation(s)
- Zachary K Criss
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Nobel Bhasin
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Sara C Di Rienzi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Kali Deans-Fielder
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | | | | | - Xi-Lei Zeng
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Vipin K Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Deepavali Chakravarti
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Clarissa Estrella
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Xiaomin Yu
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Ketki Patil
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - James C Fleet
- Department of Nutrition Sciences, The University of Texas, Austin, Texas
| | - Michael P Verzi
- Department of Genetics, Rutgers University, Piscataway, New Jersey
| | - Sylvia Christakos
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, New Jersey
| | - Michael A Helmrath
- Department of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Sumimasa Arimura
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Ronald A DePinho
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert A Britton
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Anthony W Maresso
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | | | - Sarah E Blutt
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Sue E Crawford
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Noah F Shroyer
- Section of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, Texas
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27
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Xu AA, Hoffman K, Gurwara S, White DL, Kanwal F, El-Serag HB, Petrosino JF, Jiao L. Oral Health and the Altered Colonic Mucosa-Associated Gut Microbiota. Dig Dis Sci 2021; 66:2981-2991. [PMID: 32974807 PMCID: PMC7987909 DOI: 10.1007/s10620-020-06612-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/10/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Systemic diseases have been associated with oral health and gut microbiota. We examined the association between oral health and the community composition and structure of the adherent colonic gut microbiota. METHODS We obtained 197 snap-frozen colonic biopsies from 62 colonoscopy-confirmed polyp-free individuals. Microbial DNA was sequenced for the 16S rRNA V4 region using the Illumina MiSeq, and the sequences were assigned to the operational taxonomic unit based on SILVA. We used a questionnaire to ascertain tooth loss, gum disease, and lifestyle factors. We compared biodiversity and relative abundance of bacterial taxa based on the amount of tooth loss and the presence of gum disease. The multivariable negative binomial regression model for panel data was used to estimate the association between the bacterial count and oral health. False discovery rate-adjusted P value (q value) < .05 indicated statistical significance. RESULTS More tooth loss and gum disease were associated with lower bacterial alpha diversity. The relative abundance of Faecalibacterium was lower (q values < .05) with more tooth loss. The association was significant after adjusting for age, ethnicity, obesity, smoking, alcohol use, hypertension, diabetes, and the colon segment. The relative abundance of Bacteroides was higher in those with gum disease. CONCLUSIONS Oral health was associated with alteration in the community composition and structure of the adherent gut bacteria in the colon. The reduced anti-inflammatory Faecalibacterium in participants with more tooth loss may indicate systemic inflammation. Future studies are warranted to confirm our findings and investigate the systemic role of Faecalibacterium.
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Affiliation(s)
- Anthony A Xu
- Department of Medicine, Baylor College of Medicine, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
| | - Kristi Hoffman
- Department of Molecular Virology and Microbiology, The Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
| | - Shawn Gurwara
- Department of Medicine, Baylor College of Medicine, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
| | - Donna L White
- Department of Medicine, Baylor College of Medicine, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
- Texas Medical Center Digestive Disease Center, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey VA Medical Center, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
| | - Fasiha Kanwal
- Department of Medicine, Baylor College of Medicine, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
- Section of Gastroenterology, Michael E. DeBakey VA Medical Center, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
- Texas Medical Center Digestive Disease Center, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
| | - Hashem B El-Serag
- Department of Medicine, Baylor College of Medicine, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
- Section of Gastroenterology, Michael E. DeBakey VA Medical Center, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
- Texas Medical Center Digestive Disease Center, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, The Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
- Texas Medical Center Digestive Disease Center, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA
| | - Li Jiao
- Department of Medicine, Baylor College of Medicine, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA.
- Section of Gastroenterology, Michael E. DeBakey VA Medical Center, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA.
- Texas Medical Center Digestive Disease Center, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA.
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA.
- Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey VA Medical Center, 2002 Holcombe Blvd, MS152, Houston, 77030, TX, USA.
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28
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Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. PLoS One 2021; 16:e0244468. [PMID: 34432798 PMCID: PMC8386831 DOI: 10.1371/journal.pone.0244468] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 08/09/2021] [Indexed: 02/06/2023] Open
Abstract
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity among samples. Mixed allelic frequencies along the 20kb ORF1ab gene in one sample, suggested the presence of a defective viral RNA species subpopulation maintained in mixture with functional RNA in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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Affiliation(s)
- Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vipin Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Erin Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Felipe-Andres Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
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Assfalg R, Knoop J, Hoffman KL, Pfirrmann M, Zapardiel-Gonzalo JM, Hofelich A, Eugster A, Weigelt M, Matzke C, Reinhardt J, Fuchs Y, Bunk M, Weiss A, Hippich M, Halfter K, Hauck SM, Hasford J, Petrosino JF, Achenbach P, Bonifacio E, Ziegler AG. Oral insulin immunotherapy in children at risk for type 1 diabetes in a randomised controlled trial. Diabetologia 2021; 64:1079-1092. [PMID: 33515070 PMCID: PMC8012335 DOI: 10.1007/s00125-020-05376-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/12/2020] [Indexed: 12/13/2022]
Abstract
AIMS/HYPOTHESIS Oral administration of antigen can induce immunological tolerance. Insulin is a key autoantigen in childhood type 1 diabetes. Here, oral insulin was given as antigen-specific immunotherapy before the onset of autoimmunity in children from age 6 months to assess its safety and immune response actions on immunity and the gut microbiome. METHODS A phase I/II randomised controlled trial was performed in a single clinical study centre in Germany. Participants were 44 islet autoantibody-negative children aged 6 months to 2.99 years who had a first-degree relative with type 1 diabetes and a susceptible HLA DR4-DQ8-containing genotype. Children were randomised 1:1 to daily oral insulin (7.5 mg with dose escalation to 67.5 mg) or placebo for 12 months using a web-based computer system. The primary outcome was immune efficacy pre-specified as induction of antibody or T cell responses to insulin and measured in a central treatment-blinded laboratory. RESULTS Randomisation was performed in 44 children. One child in the placebo group was withdrawn after the first study visit and data from 22 insulin-treated and 21 placebo-treated children were analysed. Oral insulin was well tolerated with no changes in metabolic variables. Immune responses to insulin were observed in children who received both insulin (54.5%) and placebo (66.7%), and the trial did not demonstrate an effect on its primary outcome (p = 0.54). In exploratory analyses, there was preliminary evidence that the immune response and gut microbiome were modified by the INS genotype Among children with the type 1 diabetes-susceptible INS genotype (n = 22), antibody responses to insulin were more frequent in insulin-treated (72.7%) as compared with placebo-treated children (18.2%; p = 0.03). T cell responses to insulin were modified by treatment-independent inflammatory episodes. CONCLUSIONS/INTERPRETATION The study demonstrated that oral insulin immunotherapy in young genetically at-risk children was safe, but was not associated with an immune response as predefined in the trial primary outcome. Exploratory analyses suggested that antibody responses to oral insulin may occur in children with a susceptible INS genotype, and that inflammatory episodes may promote the activation of insulin-responsive T cells. TRIAL REGISTRATION Clinicaltrials.gov NCT02547519 FUNDING: The main funding source was the German Center for Diabetes Research (DZD e.V.).
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Affiliation(s)
- Robin Assfalg
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany
- German Center for Diabetes Research (DZD), Munich, Germany
| | - Jan Knoop
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Kristi L Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Markus Pfirrmann
- Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Jose Maria Zapardiel-Gonzalo
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Anna Hofelich
- Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany
| | - Anne Eugster
- Technische Universität Dresden, Center for Regenerative Therapies Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
| | - Marc Weigelt
- Technische Universität Dresden, Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Claudia Matzke
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Julia Reinhardt
- Technische Universität Dresden, Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Yannick Fuchs
- Technische Universität Dresden, Center for Regenerative Therapies Dresden, Dresden, Germany
| | - Melanie Bunk
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Andreas Weiss
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Markus Hippich
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Kathrin Halfter
- Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
| | - Jörg Hasford
- Institute for Medical Information Processing, Biometry, and Epidemiology, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Peter Achenbach
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany
- Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany
- German Center for Diabetes Research (DZD), Munich, Germany
| | - Ezio Bonifacio
- German Center for Diabetes Research (DZD), Munich, Germany
- Technische Universität Dresden, Center for Regenerative Therapies Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital Carl Gustav Carus and Faculty of Medicine, TU Dresden, Dresden, Germany
- Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, Munich-Neuherberg, Germany
| | - Anette-Gabriele Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany.
- Forschergruppe Diabetes, Technical University Munich, at Klinikum rechts der Isar, Munich, Germany.
- German Center for Diabetes Research (DZD), Munich, Germany.
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30
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Abstract
[Figure: see text].
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Affiliation(s)
- Huanan Shi
- Department of Anesthesiology, Baylor College of Medicine,
Houston TX, USA
- Department of Molecular Physiology and Biophysics, Baylor
College of Medicine, Houston TX, USA
| | - Bojun Zhang
- Department of Anesthesiology, Baylor College of Medicine,
Houston TX, USA
| | - Taylor Abo-Hamzy
- School of Health Professions, Baylor College of Medicine,
Houston TX, USA
| | - James W. Nelson
- Department of Anesthesiology, Baylor College of Medicine,
Houston TX, USA
- Integrated Molecular and Biomedical Sciences Graduate
Program, Baylor College of Medicine, Houston TX, USA
| | | | - Joseph F. Petrosino
- Department of Molecular Virology and Microbiology, The
Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine,
Houston TX, USA
| | - Robert M. Bryan
- Department of Anesthesiology, Baylor College of Medicine,
Houston TX, USA
- Department of Molecular Physiology and Biophysics, Baylor
College of Medicine, Houston TX, USA
| | - David J. Durgan
- Department of Anesthesiology, Baylor College of Medicine,
Houston TX, USA
- Department of Molecular Physiology and Biophysics, Baylor
College of Medicine, Houston TX, USA
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31
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Sims TT, El Alam MB, Karpinets TV, Dorta-Estremera S, Hegde VL, Nookala S, Yoshida-Court K, Wu X, Biegert GWG, Delgado Medrano AY, Solley T, Ahmed-Kaddar M, Chapman BV, Sastry KJ, Mezzari MP, Petrosino JF, Lin LL, Ramondetta L, Jhingran A, Schmeler KM, Ajami NJ, Wargo J, Colbert LE, Klopp AH. Gut microbiome diversity is an independent predictor of survival in cervical cancer patients receiving chemoradiation. Commun Biol 2021; 4:237. [PMID: 33619320 PMCID: PMC7900251 DOI: 10.1038/s42003-021-01741-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 01/13/2021] [Indexed: 02/07/2023] Open
Abstract
Diversity of the gut microbiome is associated with higher response rates for cancer patients receiving immunotherapy but has not been investigated in patients receiving radiation therapy. Additionally, current studies investigating the gut microbiome and outcomes in cancer patients may not have adjusted for established risk factors. Here, we sought to determine if diversity and composition of the gut microbiome was independently associated with survival in cervical cancer patients receiving chemoradiation. Our study demonstrates that the diversity of gut microbiota is associated with a favorable response to chemoradiation. Additionally, compositional variation among patients correlated with short term and long-term survival. Short term survivor fecal samples were significantly enriched in Porphyromonas, Porphyromonadaceae, and Dialister, whereas long term survivor samples were significantly enriched in Escherichia Shigella, Enterobacteriaceae, and Enterobacteriales. Moreover, analysis of immune cells from cervical tumor brush samples by flow cytometry revealed that patients with a high microbiome diversity had increased tumor infiltration of CD4+ lymphocytes as well as activated subsets of CD4 cells expressing ki67+ and CD69+ over the course of radiation therapy. Modulation of the gut microbiota before chemoradiation might provide an alternative way to enhance treatment efficacy and improve treatment outcomes in cervical cancer patients.
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Affiliation(s)
- Travis T Sims
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Molly B El Alam
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tatiana V Karpinets
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stephanie Dorta-Estremera
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center and the UTHealth Graduate School of Biomedical Sciences at Houston, Houston, TX, USA
| | - Venkatesh L Hegde
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center and the UTHealth Graduate School of Biomedical Sciences at Houston, Houston, TX, USA
| | - Sita Nookala
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center and the UTHealth Graduate School of Biomedical Sciences at Houston, Houston, TX, USA
| | - Kyoko Yoshida-Court
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaogang Wu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Greyson W G Biegert
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrea Y Delgado Medrano
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Travis Solley
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mustapha Ahmed-Kaddar
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bhavana V Chapman
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - K Jagannadha Sastry
- Department of Thoracic Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center and the UTHealth Graduate School of Biomedical Sciences at Houston, Houston, TX, USA
| | - Melissa P Mezzari
- Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - Lilie L Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lois Ramondetta
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anuja Jhingran
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathleen M Schmeler
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nadim J Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lauren E Colbert
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Ann H Klopp
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Nelson JW, Phillips SC, Ganesh BP, Petrosino JF, Durgan DJ, Bryan RM. The gut microbiome contributes to blood-brain barrier disruption in spontaneously hypertensive stroke prone rats. FASEB J 2021; 35:e21201. [PMID: 33496989 PMCID: PMC8238036 DOI: 10.1096/fj.202001117r] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 10/09/2020] [Accepted: 11/03/2020] [Indexed: 11/11/2022]
Abstract
In recent years, it has become apparent that the gut microbiome can influence the functioning and pathological states of organs and systems throughout the body. In this study, we tested the hypothesis that the gut microbiome has a major role in the disruption of the blood-brain barrier (BBB) in the spontaneously hypertensive stroke prone rats (SHRSP), an animal model for hypertensive cerebral small vessel disease (CSVD). Loss of BBB is thought to be an early and initiating component to the full expression of CSVD in animal models and humans. To test this hypothesis, newly born SHRSP pups were placed with foster dams of the SHRSP strain or dams of the WKY strain, the control strain that does not demonstrate BBB dysfunction or develop hypertensive CSVD. Similarly, WKY pups were placed with foster dams of the same or opposite strain. The rationale for cross fostering is that the gut microbiomes are shaped by environmental bacteria of the foster dam and the nesting surroundings. Analysis of the bacterial genera in feces, using 16S rRNA analysis, demonstrated that the gut microbiome in the rat pups was influenced by the foster dam. SHRSP offspring fostered on WKY dams had systolic blood pressures (SBPs) that were significantly decreased by 26 mmHg (P < .001) from 16-20 weeks, compared to SHRSP offspring fostered on SHRSP dams. Similarly WKY offspring fostered on SHRSP dams had significantly increased SBP compared to WKY offspring fostered on WKY dams, although the magnitude of SBP change was not as robust. At ~20 weeks of age, rats fostered on SHRSP dams showed enhanced inflammation in distal ileum regardless of the strain of the offspring. Disruption of BBB integrity, an early marker of CSVD onset, was improved in SHRSPs that were fostered on WKY dams when compared to the SHRSP rats fostered on SHRSP dams. Although SHRSP is a genetic model for CSVD, environmental factors such as the gut microbiota of the foster dam have a major influence in the loss of BBB integrity.
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Affiliation(s)
- James W. Nelson
- Department of Anesthesiology, Baylor College of Medicine, Houston, TX, USA
- Integrated Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX, USA
| | - Sharon C. Phillips
- Department of Anesthesiology, Baylor College of Medicine, Houston, TX, USA
| | - Bhanu P. Ganesh
- Department of Neurology, University of Texas Health Sciences Center, Houston, TX, USA
| | - Joseph F. Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- The Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, USA
| | - David J. Durgan
- Department of Anesthesiology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | - Robert M. Bryan
- Department of Anesthesiology, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
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33
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Chumpitazi BP, Hoffman KL, Smith DP, McMeans AR, Musaad S, Versalovic J, Petrosino JF, Shulman RJ. Fructan-sensitive children with irritable bowel syndrome have distinct gut microbiome signatures. Aliment Pharmacol Ther 2021; 53:499-509. [PMID: 33314183 PMCID: PMC8281336 DOI: 10.1111/apt.16204] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/09/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Dietary fructans may worsen gastrointestinal symptoms in children with irritable bowel syndrome (IBS). AIM To determine whether gut microbiome composition and function are associated with childhood IBS fructan-induced symptoms. METHODS Faecal samples were collected from 38 children aged 7-17 years with paediatric Rome III IBS, who previously completied a double-blind, randomised, placebo-controlled crossover (fructan vs maltodextrin) trial. Fructan sensitivity was defined as an increase of ≥30% in abdominal pain frequency during the fructan diet. Gut microbial composition was determined via 16Sv4 rDNA sequencing. LEfSe evaluated taxonomic composition differences. Tax4Fun2 predicted microbial fructan metabolic pathways. RESULTS At baseline, 17 fructan-sensitive (vs 21 fructan-tolerant) subjects had lower alpha diversity (q < 0.05) and were enriched in the genus Holdermania. In contrast, fructan-tolerant subjects were enriched in 14 genera from the class Clostridia. During the fructan diet, fructan-sensitive (vs tolerant) subjects were enriched in both Agathobacter (P = 0.02) and Cyanobacteria (P = 0.0001). In contrast, fructan-tolerant subjects were enriched in three genera from the Clostridia class. Comparing the fructan vs maltodextrin diet, fructan-sensitive subjects had a significantly increased relative abundance of Bifidobacterium (P = 0.02) while fructan-tolerant subjects had increased Anaerostipes (P = 0.03) during the fructan diet. Only fructan-sensitive subjects had a trend towards increased predicted β-fructofuranosidase during the fructan vs maltodextrin diet. CONCLUSIONS Fructan-sensitive children with IBS have distinct gut microbiome signatures. These microbiome signatures differ both at baseline and in response to a fructan challenge.
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Affiliation(s)
- Bruno P. Chumpitazi
- Department of Pediatrics, Baylor College of Medicine, Houston, TX,Children’s Nutrition Research Center, United States Department of Agriculture, Houston, TX
| | - Kristi L. Hoffman
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX,Alkek Center for Metagenomic and Microbiome Research, Houston, TX
| | - Daniel P. Smith
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX,Alkek Center for Metagenomic and Microbiome Research, Houston, TX
| | - Ann R. McMeans
- Department of Pediatrics, Baylor College of Medicine, Houston, TX,Children’s Nutrition Research Center, United States Department of Agriculture, Houston, TX
| | - Salma Musaad
- Children’s Nutrition Research Center, United States Department of Agriculture, Houston, TX
| | - James Versalovic
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX,Texas Children’s Microbiome Center, Houston, TX
| | - Joseph F. Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX,Alkek Center for Metagenomic and Microbiome Research, Houston, TX
| | - Robert J. Shulman
- Department of Pediatrics, Baylor College of Medicine, Houston, TX,Children’s Nutrition Research Center, United States Department of Agriculture, Houston, TX
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Matz LM, Petrosino JF. A study of innate immune kinetics reveals a role for a chloride transporter in a virulent Francisella tularensis type B strain. Microbiologyopen 2021; 10:e1170. [PMID: 33970545 PMCID: PMC8483402 DOI: 10.1002/mbo3.1170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 11/26/2022] Open
Abstract
Tularemia is a zoonotic disease of global proportions. Francisella tularensis subspecies tularensis (type A) and holarctica (type B) cause disease in healthy humans, with type A infections resulting in higher mortality. Repeated passage of a type B strain in the mid-20th century generated the Live Vaccine Strain (LVS). LVS remains unlicensed, does not protect against high inhalational doses of type A, and its exact mechanisms of attenuation are poorly understood. Recent data suggest that live attenuated vaccines derived from type B may cross-protect against type A. However, there is a dearth of knowledge regarding virulent type B pathogenesis and its capacity to stimulate the host's innate immune response. We therefore sought to increase our understanding of virulent type B in vitro characteristics using strain OR96-0246 as a model. Adding to our knowledge of innate immune kinetics in macrophages following infection with virulent type B, we observed robust replication of strain OR96-0246 in murine and human macrophages, reduced expression of pro-inflammatory cytokine genes from "wild type" type B-infected macrophages compared to LVS, and delayed macrophage cell death suggesting that virulent type B may suppress macrophage activation. One disruption in LVS is in the gene encoding the chloride transporter ClcA. We investigated the role of ClcA in macrophage infection and observed a replication delay in a clcA mutant. Here, we propose its role in acid tolerance. A greater understanding of LVS attenuation may reveal new mechanisms of pathogenesis and inform strategies toward the development of an improved vaccine against tularemia.
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Affiliation(s)
- Lisa M. Matz
- The Alkek Center for Metagenomics and Microbiome ResearchBaylor College of MedicineHoustonTXUSA
- The Department of Molecular Virology and MicrobiologyBaylor College of MedicineHoustonTXUSA
- Baylor College of MedicineHoustonTXUSA
| | - Joseph F. Petrosino
- The Alkek Center for Metagenomics and Microbiome ResearchBaylor College of MedicineHoustonTXUSA
- The Department of Molecular Virology and MicrobiologyBaylor College of MedicineHoustonTXUSA
- Baylor College of MedicineHoustonTXUSA
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35
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Oluyomi AO, Panthagani K, Sotelo J, Gu X, Armstrong G, Luo DN, Hoffman KL, Rohlman D, Tidwell L, Hamilton WJ, Symanski E, Anderson K, Petrosino JF, Walker CL, Bondy M. Houston hurricane Harvey health (Houston-3H) study: assessment of allergic symptoms and stress after hurricane Harvey flooding. Environ Health 2021; 20:9. [PMID: 33468146 PMCID: PMC7816385 DOI: 10.1186/s12940-021-00694-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 01/12/2021] [Indexed: 05/19/2023]
Abstract
BACKGROUND In August 2017, Hurricane Harvey caused unprecedented flooding across the greater Houston area. Given the potential for widespread flood-related exposures, including mold and sewage, and the emotional and mental toll caused by the flooding, we sought to evaluate the short- and long-term impact of flood-related exposures on the health of Houstonians. Our objectives were to assess the association of flood-related exposures with allergic symptoms and stress among Houston-area residents at two time points: within approximately 30 days (T1) and 12 months (T2) after Hurricane Harvey's landfall. METHODS The Houston Hurricane Harvey Health (Houston-3H) Study enrolled a total of 347 unique participants from four sites across Harris County at two times: within approximately 1-month of Harvey (T1, n = 206) and approximately 12-months after Harvey (T2, n = 266), including 125 individuals who participated at both time points. Using a self-administered questionnaire, participants reported details on demographics, flood-related exposures, and health outcomes, including allergic symptoms and stress. RESULTS The majority of participants reported hurricane-related flooding in their homes at T1 (79.1%) and T2 (87.2%) and experienced at least one allergic symptom after the hurricane (79.4% at T1 and 68.4% at T2). In general, flood-exposed individuals were at increased risk of upper respiratory tract allergic symptoms, reported at both the T1 and T2 time points, with exposures to dirty water and mold associated with increased risk of multiple allergic symptoms. The mean stress score of study participants at T1 was 8.0 ± 2.1 and at T2, 5.1 ± 3.2, on a 0-10 scale. Participants who experienced specific flood-related exposures reported higher stress scores when compared with their counterparts, especially 1 year after Harvey. Also, a supplementary paired-samples analysis showed that reports of wheezing, shortness of breath, and skin rash did not change between T1 and T2, though other conditions were less commonly reported at T2. CONCLUSION These initial Houston-3H findings demonstrate that flooding experiences that occurred as a consequence of Hurricane Harvey had lasting impacts on the health of Houstonians up to 1 year after the hurricane.
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Affiliation(s)
- Abiodun O. Oluyomi
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, One Baylor Plaza, Jewish Building, Room 607D, (MS BCM307), Houston, TX USA
- Department of Family and Community Medicine, Environmental Health Service, Baylor College of Medicine, Houston, TX USA
| | - Kristen Panthagani
- Genetics and Genomics, Baylor College of Medicine, Houston, TX USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX USA
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX USA
| | - Jesus Sotelo
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, One Baylor Plaza, Jewish Building, Room 607D, (MS BCM307), Houston, TX USA
| | - Xiangjun Gu
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, One Baylor Plaza, Jewish Building, Room 607D, (MS BCM307), Houston, TX USA
| | - Georgina Armstrong
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, One Baylor Plaza, Jewish Building, Room 607D, (MS BCM307), Houston, TX USA
| | - Dan Na Luo
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX USA
| | - Kristi L. Hoffman
- Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX USA
| | - Diana Rohlman
- Environmental and Occupational Health, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR USA
| | - Lane Tidwell
- Food Safety and Environmental Stewardship Program, Oregon State University, Corvallis, OR USA
| | - Winifred J. Hamilton
- Department of Family and Community Medicine, Environmental Health Service, Baylor College of Medicine, Houston, TX USA
| | - Elaine Symanski
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, One Baylor Plaza, Jewish Building, Room 607D, (MS BCM307), Houston, TX USA
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX USA
| | - Kimberly Anderson
- Food Safety and Environmental Stewardship Program, Oregon State University, Corvallis, OR USA
| | - Joseph F. Petrosino
- Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX USA
| | - Cheryl Lyn Walker
- Genetics and Genomics, Baylor College of Medicine, Houston, TX USA
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX USA
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX USA
| | - Melissa Bondy
- Department of Epidemiology and Population Health, Stanford Cancer Institute, Stanford University, Stanford, CA USA
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LaPelusa M, Donoviel D, Branzini SE, Carlson PE, Culler S, Cheema AK, Kaddurah-Daouk R, Kelly D, de Cremoux I, Knight R, Krajmalnik-Brown R, Mayo SL, Mazmanian SK, Mayer EA, Petrosino JF, Garrison K. Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020. Microbiome 2021; 9:2. [PMID: 33397500 PMCID: PMC7781430 DOI: 10.1186/s40168-020-00951-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
The inaugural "Microbiome for Mars" virtual workshop took place on July 13, 2020. This event assembled leaders in microbiome research and development to discuss their work and how it may relate to long-duration human space travel. The conference focused on surveying current microbiome research, future endeavors, and how this growing field could broadly impact human health and space exploration. This report summarizes each speaker's presentation in the order presented at the workshop.
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Affiliation(s)
- Michael LaPelusa
- Department of Medicine, Vanderbilt University Medical Center, One Hundred Oaks - North 719 Thompson Lane Suite 20400, Nashville, TN, 37204, USA.
| | - Dorit Donoviel
- Department of Pharmacology and Chemical Biology, Center for Space Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Sergio E Branzini
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA, 94158, USA
| | - Paul E Carlson
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Stephanie Culler
- Persephone Biosciences Inc, JLABS, 3210 Merryfield Row, San Diego, CA, 92121, USA
| | - Amrita K Cheema
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC, 20007, USA
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Department of Medicine and the Duke Institute for Brain Sciences, Duke University, Durham, NC, 27708, USA
| | - Denise Kelly
- Seventure Partners, 5-7 rue de Monttessuy, 75340 Cedex 07, Paris, France
| | | | - Rob Knight
- Departments of Pediatrics, Bioengineering, and Computer Science & Engineering, University of California San Diego, 9500 Gilman Drive, MC 0763, La Jolla, CA, 92093-0763, USA
| | - Rosa Krajmalnik-Brown
- Biodesign Center for Health Through Microbiomes, Arizona State University, Tempe, AZ, USA
- School of Sustainable Engineering and the Built Environment, Arizona State University, Tempe, AZ, USA
| | - Stephen L Mayo
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Bl, Pasadena, CA, 91125, USA
| | - Sarkis K Mazmanian
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Bl, Pasadena, CA, 91125, USA
| | - Emeran A Mayer
- G. Oppenheimer Family Center for Neurobiology of Stress and Resilience, Ingestive Behavior and Obesity Program, University of California Los Angeles, Los Angeles, CA, USA
- Vatche and Tamar Manoukian Division of Digestive Diseases, University of California Los Angeles, Los Angeles, CA, USA
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Joseph F Petrosino
- Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Keith Garrison
- Department of Medicine, The University of Texas at Houston Health Sciences Center, 6431 Fannin St, Houston, TX, 77030, USA.
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Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide Capture Sequencing of the SARS-CoV-2 Genome and Subgenomic Fragments from COVID-19 Individuals. bioRxiv 2020:2020.12.11.421057. [PMID: 33330863 PMCID: PMC7743067 DOI: 10.1101/2020.12.11.421057] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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Affiliation(s)
- Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vipin Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Erin Nicholson
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America, USA
| | - David Henke
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
| | - Felipe-Andres Piedra
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Houston, Texas, United States of America, USA
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
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38
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Zhang X, Hoffman KL, Wei P, Elhor Gbito KY, Joseph R, Li F, Scheet P, Chang S, Petrosino JF, Daniel CR. Baseline Oral Microbiome and All-cancer Incidence in a Cohort of Nonsmoking Mexican American Women. Cancer Prev Res (Phila) 2020; 14:383-392. [PMID: 33277317 DOI: 10.1158/1940-6207.capr-20-0405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/12/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022]
Abstract
Given the increasing evidence that the oral microbiome is involved in obesity, diabetes, and cancer risk, we investigated baseline oral microbiota profiles in relation to all-cancer incidence among nonsmoking women enrolled in a Texas cohort of first- and second-generation immigrants of Mexican origin. We characterized the 16Sv4 rDNA microbiome in oral mouthwash samples collected at baseline from a representative subset of 305 nonsmoking women, ages 20-75 years. We evaluated within- (alpha) and between-sample (beta) diversity by incident cancer status and applied linear discriminant analysis (LDA) effect size analysis to assess differentially abundant taxa. Diversity and candidate taxa in relation to all-cancer incidence were evaluated in multivariable-adjusted Cox regression models. Over 8.8 median years of follow-up, 31 incident cancer cases were identified and verified. Advanced age, greater acculturation, and cardiometabolic risk factors were associated with all-cancer incidence. Higher alpha diversity (age-adjusted P difference < 0.01) and distinct biological communities (P difference = 0.002) were observed by incident cancer status. Each unit increase in the Shannon diversity index yielded >8-fold increase in all-cancer and obesity-related cancer risk [multivariable-adjusted HR (95% confidence interval), 8.11 (3.14-20.94) and 10.72 (3.30-34.84), respectively] with similar findings for the inverse Simpson index. Streptococcus was enriched among women who did not develop cancer, while Fusobacterium, Prevotella, Mogibacterium, Campylobacter, Lachnoanaerobaculum, Dialister, and Atopobium were higher among women who developed cancer (LDA score ≥ 3; q-value < 0.01). This initial study of oral microbiota and overall cancer risk in nonsmoking Mexican American women suggests the readily accessible oral microbiota as a promising biomarker. PREVENTION RELEVANCE: Mexican American women suffer a disproportionate burden of chronic health conditions that increase cancer risk. Few investigations of the microbiome, a key determinant of host health, have been conducted among this group. Oral microbiota profiles may provide early and accessible cancer biomarker data on invasive bacteria or community disruptions.
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Affiliation(s)
- Xiaotao Zhang
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas.,Dan L Duncan Comprehensive Cancer Center, Epidemiology & Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Kristi L Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Peng Wei
- Division of Cancer Prevention and Population Sciences, Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kplola Y Elhor Gbito
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Reji Joseph
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Fangyu Li
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Paul Scheet
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shine Chang
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Carrie R Daniel
- Division of Cancer Prevention and Population Sciences, Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Karpinets TV, Solley TN, Mikkelson MD, Dorta-Estremera S, Nookala SS, Medrano AYD, Petrosino JF, Mezzari MP, Zhang J, Futreal PA, Sastry KJ, Colbert LE, Klopp A. Effect of Antibiotics on Gut and Vaginal Microbiomes Associated with Cervical Cancer Development in Mice. Cancer Prev Res (Phila) 2020; 13:997-1006. [PMID: 32917644 PMCID: PMC10583130 DOI: 10.1158/1940-6207.capr-20-0103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/06/2020] [Accepted: 08/25/2020] [Indexed: 11/16/2022]
Abstract
Antibiotics affect microbial diversity in the gut, leading to dysbiosis and impaired immunity. However, the impact of antibiotics on microbial communities at other sites, such as vagina is less understood. It is also not clear whether changes induced by antibiotics in both microbiomes affect the development of cervical cancer. In this study, we utilized the murine model to evaluate these questions. We show that oral application of broad-spectrum antibiotics in mice changed not only diversity, but composition and sharing of gut and vaginal microbiomes in mice and influenced cervical cancer development in an orthotopic tumor model. Antibiotics decreased richness and diversity indexes in the gut but increased them in the vagina. Some beneficial taxa, such as Bacteroides, Ruminococcaceae, and Lachnospiraceae increased their abundance in the vagina while other pathogenic species, such as Proteobacteria, were decreased. As a result of the changes, mice with greater richness and diversity of the vaginal microbiome after antibiotics exposure were less likely developed tumors. No association between richness and diversity of the gut microbiome and tumor development was identified.
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Affiliation(s)
| | - Travis N Solley
- Department of Radiation Oncology, MD Anderson Cancer Center, Houston, Texas
| | - Megan D Mikkelson
- Department of Radiation Oncology, MD Anderson Cancer Center, Houston, Texas
| | | | - Sita S Nookala
- Department of Thoracic Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, Texas
| | | | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas
| | - Melissa P Mezzari
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas
| | - Jinghua Zhang
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, Texas
| | - P Andrew Futreal
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, Texas
| | - K Jagannadha Sastry
- Department of Thoracic Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, Texas
| | - Lauren E Colbert
- Department of Radiation Oncology, MD Anderson Cancer Center, Houston, Texas.
| | - Ann Klopp
- Department of Radiation Oncology, MD Anderson Cancer Center, Houston, Texas.
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40
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Santiago-Rodriguez TM, Garoutte A, Adams E, Nasser W, Ross MC, La Reau A, Henseler Z, Ward T, Knights D, Petrosino JF, Hollister EB. Metagenomic Information Recovery from Human Stool Samples Is Influenced by Sequencing Depth and Profiling Method. Genes (Basel) 2020; 11:E1380. [PMID: 33233349 PMCID: PMC7700633 DOI: 10.3390/genes11111380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/20/2022] Open
Abstract
Sequencing of the 16S rRNA gene (16S) has long been a go-to method for microbiome characterization due to its accessibility and lower cost compared to shotgun metagenomic sequencing (SMS). However, 16S sequencing rarely provides species-level resolution and cannot provide direct assessment of other taxa (e.g., viruses and fungi) or functional gene content. Shallow shotgun metagenomic sequencing (SSMS) has emerged as an approach to bridge the gap between 16S sequencing and deep metagenomic sequencing. SSMS is cost-competitive with 16S sequencing, while also providing species-level resolution and functional gene content insights. In the present study, we evaluated the effects of sequencing depth on marker gene-mapping- and alignment-based annotation of bacteria in healthy human stool samples. The number of identified taxa decreased with lower sequencing depths, particularly with the marker gene-mapping-based approach. Other annotations, including viruses and pathways, also showed a depth-dependent effect on feature recovery. These results refine the understanding of the suitability and shortcomings of SSMS, as well as annotation tools for metagenomic analyses in human stool samples. Results may also translate to other sample types and may open the opportunity to explore the effect of sequencing depth and annotation method.
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Affiliation(s)
| | - Aaron Garoutte
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Emmase Adams
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Waleed Nasser
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
| | - Matthew C. Ross
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alex La Reau
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Zachariah Henseler
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Tonya Ward
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
| | - Dan Knights
- Diversigen Inc., Saint Paul, MN 55112, USA; (A.L.R.); (Z.H.); (T.W.); (D.K.)
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Biotechnology Institute, College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - Joseph F. Petrosino
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX 77030, USA;
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Emily B. Hollister
- Diversigen Inc., Houston, TX 77021, USA; (A.G.); (E.A.); (W.N.); (J.F.P.); (E.B.H.)
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41
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Zheng J, Hoffman KL, Chen JS, Shivappa N, Sood A, Browman GJ, Dirba DD, Hanash S, Wei P, Hebert JR, Petrosino JF, Schembre SM, Daniel CR. Dietary inflammatory potential in relation to the gut microbiome: results from a cross-sectional study. Br J Nutr 2020; 124:931-942. [PMID: 32475373 PMCID: PMC7554089 DOI: 10.1017/s0007114520001853] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Diet has direct and indirect effects on health through inflammation and the gut microbiome. We investigated total dietary inflammatory potential via the literature-derived index (Dietary Inflammatory Index (DII®)) with gut microbiota diversity, composition and function. In cancer-free patient volunteers initially approached at colonoscopy and healthy volunteers recruited from the medical centre community, we assessed 16S ribosomal DNA in all subjects who provided dietary assessments and stool samples (n 101) and the gut metagenome in a subset of patients with residual fasting blood samples (n 34). Associations of energy-adjusted DII scores with microbial diversity and composition were examined using linear regression, permutational multivariate ANOVA and linear discriminant analysis. Spearman correlation was used to evaluate associations of species and pathways with DII and circulating inflammatory markers. Across DII levels, α- and β-diversity did not significantly differ; however, Ruminococcus torques, Eubacterium nodatum, Acidaminococcus intestini and Clostridium leptum were more abundant in the most pro-inflammatory diet group, while Akkermansia muciniphila was enriched in the most anti-inflammatory diet group. With adjustment for age and BMI, R. torques, E. nodatum and A. intestini remained significantly associated with a more pro-inflammatory diet. In the metagenomic and fasting blood subset, A. intestini was correlated with circulating plasminogen activator inhibitor-1, a pro-inflammatory marker (rho = 0·40), but no associations remained significant upon correction for multiple testing. An index reflecting overall inflammatory potential of the diet was associated with specific microbes, but not overall diversity of the gut microbiome in our study. Findings from this preliminary study warrant further research in larger samples and prospective cohorts.
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Affiliation(s)
- Jiali Zheng
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
| | - Kristi L Hoffman
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX77030, USA
| | - Jiun-Sheng Chen
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
- Quantitative Sciences Program, The University of Texas Graduate School of Biomedical Sciences at Houston and MD Anderson Cancer Center, Houston, TX77030, USA
| | - Nitin Shivappa
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC29208, USA
| | - Akhil Sood
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
- Internal Medicine, University of Texas Medical Branch, Galveston, TX77555, USA
| | - Gladys J Browman
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
| | - Danika D Dirba
- Department of Behavioral Science, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
| | - Samir Hanash
- Department of Clinical Cancer Prevention, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
| | - Peng Wei
- Quantitative Sciences Program, The University of Texas Graduate School of Biomedical Sciences at Houston and MD Anderson Cancer Center, Houston, TX77030, USA
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
| | - James R Hebert
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC29208, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX77030, USA
| | - Susan M Schembre
- Department of Behavioral Science, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
- Department of Family and Community Medicine, University of Arizona, Tucson, AZ85721, USA
| | - Carrie R Daniel
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
- Quantitative Sciences Program, The University of Texas Graduate School of Biomedical Sciences at Houston and MD Anderson Cancer Center, Houston, TX77030, USA
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42
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Jensen ET, Bertoni AG, Crago OL, Hoffman KL, Wood AC, Arzumanyan Z, Lam LSK, Roll K, Sandow K, Wu M, Rich SS, Rotter JI, Chen YDI, Petrosino JF, Goodarzi MO. Rationale, design and baseline characteristics of the Microbiome and Insulin Longitudinal Evaluation Study (MILES). Diabetes Obes Metab 2020; 22:1976-1984. [PMID: 32687239 PMCID: PMC8444996 DOI: 10.1111/dom.14145] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/06/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023]
Abstract
AIM To investigate the role of the gut microbiome in regulating key insulin homeostasis traits (insulin sensitivity, insulin secretion and insulin clearance) whose dysfunction leads to type 2 diabetes (T2D). MATERIALS AND METHODS The Microbiome and Insulin Longitudinal Evaluation Study (MILES) focuses on African American and non-Hispanic white participants aged 40-80 years without diabetes. Three study visits are planned (at baseline, 15 and 30 months). Baseline measurements include assessment of the stool microbiome and administration of an oral glucose tolerance test, which will yield indexes of insulin sensitivity, insulin secretion and insulin clearance. The gut microbiome profile (composition and function) will be determined using whole metagenome shotgun sequencing along with analyses of plasma short chain fatty acids. Additional data collected include dietary history, sociodemographic factors, health habits, anthropometry, medical history, medications and family history. Most assessments are repeated 15 and 30 months following baseline. RESULTS After screening 875 individuals, 129 African American and 224 non-Hispanic white participants were enrolled. At baseline, African American participants have higher blood pressure, weight, body mass index, waist and hip circumferences but similar waist-hip ratio compared with the non-Hispanic white participants. On average, African American participants are less insulin-sensitive and have higher acute insulin secretion and lower insulin clearance. CONCLUSIONS The longitudinal design and robust characterization of potential mediators will allow for the assessment of glucose and insulin homeostasis and gut microbiota as they change over time, improving our ability to discern causal relationships between the microbiome and the insulin homeostasis traits whose deterioration determines T2D, setting the stage for future microbiome-directed therapies to prevent and treat T2D.
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Affiliation(s)
- Elizabeth T. Jensen
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Alain G. Bertoni
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Osa L. Crago
- Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Kristi L. Hoffman
- Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas
| | - Alexis C. Wood
- USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, Texas
| | - Zorayr Arzumanyan
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation and Harbor-UCLA Medical Center, Torrance, California
| | - Lok-Sze Kelvin Lam
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation and Harbor-UCLA Medical Center, Torrance, California
| | - Kathryn Roll
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation and Harbor-UCLA Medical Center, Torrance, California
| | - Kevin Sandow
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation and Harbor-UCLA Medical Center, Torrance, California
| | - Martin Wu
- Department of Biology, University of Virginia, Charlottesville, Virginia
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Jerome I. Rotter
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation and Harbor-UCLA Medical Center, Torrance, California
| | - Yii-Der I. Chen
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation and Harbor-UCLA Medical Center, Torrance, California
| | - Joseph F. Petrosino
- Department of Molecular Virology and Microbiology, Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
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Toivonen L, Karppinen S, Schuez-Havupalo L, Waris M, He Q, Hoffman KL, Petrosino JF, Dumas O, Camargo CA, Hasegawa K, Peltola V. Longitudinal Changes in Early Nasal Microbiota and the Risk of Childhood Asthma. Pediatrics 2020; 146:peds.2020-0421. [PMID: 32934151 DOI: 10.1542/peds.2020-0421] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/10/2020] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVES Although the airway microbiota is a highly dynamic ecology, the role of longitudinal changes in airway microbiota during early childhood in asthma development is unclear. We aimed to investigate the association of longitudinal changes in early nasal microbiota with the risk of developing asthma. METHODS In this prospective, population-based birth cohort study, we followed children from birth to age 7 years. The nasal microbiota was tested by using 16S ribosomal RNA gene sequencing at ages 2, 13, and 24 months. We applied an unsupervised machine learning approach to identify longitudinal nasal microbiota profiles during age 2 to 13 months (the primary exposure) and during age 2 to 24 months (the secondary exposure) and examined the association of these profiles with the risk of physician-diagnosed asthma at age 7 years. RESULTS Of the analytic cohort of 704 children, 57 (8%) later developed asthma. We identified 4 distinct longitudinal nasal microbiota profiles during age 2 to 13 months. In the multivariable analysis, compared with the persistent Moraxella dominance profile during age 2 to 13 months, the persistent Moraxella sparsity profile was associated with a significantly higher risk of asthma (adjusted odds ratio, 2.74; 95% confidence interval, 1.20-6.27). Similar associations were observed between the longitudinal changes in nasal microbiota during age 2 to 24 months and risk of asthma. CONCLUSIONS Children with an altered longitudinal pattern in the nasal microbiota during early childhood had a high risk of developing asthma. Our data guide the development of primary prevention strategies (eg, early identification of children at high risk and modification of microbiota) for childhood asthma. These observations present a new avenue for risk modification for asthma (eg, microbiota modification).
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Affiliation(s)
- Laura Toivonen
- Department of Emergency Medicine, Massachusetts General Hospital and Harvard Medical School, Harvard University, Boston, Massachusetts; .,Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Sinikka Karppinen
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Linnea Schuez-Havupalo
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | | | - Qiushui He
- Department of Microbiology, Virology and Immunology and Institute of Biomedicine, University of Turku, Turku, Finland.,Department of Medical Microbiology, Capital Medical University, Beijing, China
| | - Kristi L Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Orianne Dumas
- INSERM U1168, VIMA: Aging and Chronic Diseases, Epidemiological and Public Health Approaches, Villejuif, France; and.,UMR-S 1168, Université de Versailles Saint-Quentin-en-Yvelines, Montigny-le-Bretonneux, France
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital and Harvard Medical School, Harvard University, Boston, Massachusetts
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital and Harvard Medical School, Harvard University, Boston, Massachusetts
| | - Ville Peltola
- Department of Paediatrics and Adolescent Medicine, Turku University Hospital and University of Turku, Turku, Finland
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Gurwara S, Dai A, Ajami NJ, Graham DY, White DL, Chen L, Jang A, Chen E, El-Serag HB, Petrosino JF, Jiao L. Alcohol use alters the colonic mucosa-associated gut microbiota in humans. Nutr Res 2020; 83:119-128. [PMID: 33096423 DOI: 10.1016/j.nutres.2020.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 08/26/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022]
Abstract
Alcohol misuse is a risk factor for many adverse health outcomes. Alcohol misuse has been associated with an imbalance of gut microbiota in preclinical models and alcoholic diseases. We hypothesized that daily alcohol use would change the community composition and structure of the human colonic gut microbiota. Thirty-four polyp-free individuals donated 97 snap-frozen colonic biopsies. Microbial DNA was sequenced for the 16S ribosomal RNA gene hypervariable region 4. The SILVA database was used for operational taxonomic unit classification. Alcohol use was assessed using a food frequency questionnaire. We compared the biodiversity and relative abundance of the taxa among never drinkers (ND, n = 9), former drinkers (FD, n = 10), current light drinkers (LD, <2 drinks daily, n = 9), and current heavy drinkers (HD, ≥2 drinks daily, n = 6). False discovery rate-adjusted P values (q values) < .05 indicated statistical significance. HD had the lowest α diversity (Shannon index q value < 0.001), and HD's microbial composition differed the most from the other groups (P value = .002). LD had the highest relative abundance of Akkermansia (q values < 0.001). HD had the lowest relative abundance of Subdoligranulum, Roseburia, and Lachnospiraceaeunc91005 but the highest relative abundance of Lachnospiraceaeunc8895 (all q values < 0.05). The multivariable negative binomial regression model supported these observations. ND and FD had a similar microbial profile. Heavy alcohol use was associated with impaired gut microbiota that may partially mediate its effect on health outcomes.
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Affiliation(s)
- Shawn Gurwara
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
| | - Annie Dai
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
| | - Nadim J Ajami
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
| | - David Y Graham
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA; Section of Gastroenterology, Michael E. DeBakey VA Medical Center, Houston, TX, USA.
| | - Donna L White
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA; Texas Medical Center Digestive Disease Center, Houston, TX, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Center for Innovations in Quality, Effectiveness and Safety, Houston, TX, USA; Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey VA Medical Center, Houston, TX, USA.
| | - Liang Chen
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA; Center for Innovations in Quality, Effectiveness and Safety, Houston, TX, USA.
| | - Albert Jang
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
| | - Ellie Chen
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
| | - Hashem B El-Serag
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA; Section of Gastroenterology, Michael E. DeBakey VA Medical Center, Houston, TX, USA; Texas Medical Center Digestive Disease Center, Houston, TX, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Center for Innovations in Quality, Effectiveness and Safety, Houston, TX, USA.
| | - Joseph F Petrosino
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA; Texas Medical Center Digestive Disease Center, Houston, TX, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| | - Li Jiao
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA; Section of Gastroenterology, Michael E. DeBakey VA Medical Center, Houston, TX, USA; Texas Medical Center Digestive Disease Center, Houston, TX, USA; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Center for Innovations in Quality, Effectiveness and Safety, Houston, TX, USA; Center for Translational Research on Inflammatory Diseases (CTRID), Michael E. DeBakey VA Medical Center, Houston, TX, USA.
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Engevik MA, Banks LD, Engevik KA, Chang-Graham AL, Perry JL, Hutchinson DS, Ajami NJ, Petrosino JF, Hyser JM. Rotavirus infection induces glycan availability to promote ileum-specific changes in the microbiome aiding rotavirus virulence. Gut Microbes 2020; 11:1324-1347. [PMID: 32404017 PMCID: PMC7524290 DOI: 10.1080/19490976.2020.1754714] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Multiple studies have identified changes within the gut microbiome in response to diarrheal-inducing bacterial pathogens. However, examination of the microbiome in response to viral pathogens remains understudied. Compounding this, many studies use fecal samples to assess microbiome composition; which may not accurately mirror changes within the small intestine, the primary site for most enteric virus infections. As a result, the functional significance of small intestinal microbiome shifts during infection is not well defined. To address these gaps, rotavirus-infected neonatal mice were examined for changes in bacterial community dynamics, host gene expression, and tissue recovery during infection. Profiling bacterial communities using 16S rRNA sequencing suggested significant and distinct changes in ileal communities in response to rotavirus infection, with no significant changes for other gastrointestinal (GI) compartments. At 1-d post-infection, we observed a loss in Lactobacillus species from the ileum, but an increase in Bacteroides and Akkermansia, both of which exhibit mucin-digesting capabilities. Concomitant with the bacterial community shifts, we observed a loss of mucin-filled goblet cells in the small intestine at d 1, with recovery occurring by d 3. Rotavirus infection of mucin-producing cell lines and human intestinal enteroids (HIEs) stimulated release of stored mucin granules, similar to in vivo findings. In vitro, incubation of mucins with Bacteroides or Akkermansia members resulted in significant glycan degradation, which altered the binding capacity of rotavirus in silico and in vitro. Taken together, these data suggest that the response to and recovery from rotavirus-diarrhea is unique between sub-compartments of the GI tract and may be influenced by mucin-degrading microbes.
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Affiliation(s)
- Melinda A. Engevik
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA,Department of Pathology, Texas Children’s Hospital, Houston, TX, USA
| | - Lori D. Banks
- Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, TX, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kristen A. Engevik
- Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, TX, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Alexandra L. Chang-Graham
- Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, TX, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Jacob L. Perry
- Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, TX, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Diane S. Hutchinson
- Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, TX, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Nadim J. Ajami
- Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, TX, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Joseph F. Petrosino
- Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, TX, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Joseph M. Hyser
- Alkek Center for Metagenomic and Microbiome Research, Baylor College of Medicine, Houston, TX, USA,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA,CONTACT Joseph M. Hyser 1 Baylor Plaza, HoustonTX77030, USA
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46
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Faucher MA, Greathouse KL, Hastings-Tolsma M, Padgett RN, Sakovich K, Choudhury A, Sheikh A, Ajami NJ, Petrosino JF. Exploration of the Vaginal and Gut Microbiome in African American Women by Body Mass Index, Class of Obesity, and Gestational Weight Gain: A Pilot Study. Am J Perinatol 2020; 37:1160-1172. [PMID: 31242511 DOI: 10.1055/s-0039-1692715] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
OBJECTIVE This study determines the differences in the distal gut and vaginal microbiome in African American (AA) women by prepregnancy body mass index and gestational weight gain (GWG) comparing women with and without obesity and by obesity class. STUDY DESIGN We prospectively sampled the vaginal and distal gut microbiome in pregnant AA women at two time points during pregnancy. Samples were analyzed using high-throughput sequencing of the V4 region of the 16S ribosomal ribonucleic acid gene. RESULTS Distinct differences in vaginal and distal gut α-diversity were observed at time point 1 between women with and without obesity by total GWG. Significant differences in distal gut β-diversity were also found at time point 1 in obese women by GWG. Within the Bacteroides genus, a significant association was observed by total GWG among obese women which was absent in nonobese women. Women with class III obesity who experienced low GWG had the lowest abundance of distal gut Bacteroides and appreciably higher relative abundance of a consortia of vaginal taxa including Atopobium, Gardnerella, Prevotella, and Sneathia. CONCLUSION These results contribute new evidence showing that GWG in combination with obesity and obesity class is associated with an altered distal gut and vaginal composition early in pregnancy among AA women.
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Affiliation(s)
- Mary Ann Faucher
- Louise Herrington School of Nursing, Midwifery Specialty, Baylor University, Dallas, Texas
| | | | - Marie Hastings-Tolsma
- Louise Herrington School of Nursing, Midwifery Specialty, Baylor University, Dallas, Texas
| | | | - Kimberly Sakovich
- Women's Health Care, MacArthur Obstetrics and Gynecology, Irving, Texas
| | | | - Aadil Sheikh
- Department of Biology, Baylor University, Waco, Texas
| | - Nadim J Ajami
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Texas Medical Center, Houston, Texas
| | - Joseph F Petrosino
- The Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Texas Medical Center, Houston, Texas
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Paul AA, Hoffman KL, Hagan JL, Sampath V, Petrosino JF, Pammi M. Fungal cutaneous microbiome and host determinants in preterm and term neonates. Pediatr Res 2020; 88:225-233. [PMID: 31816621 DOI: 10.1038/s41390-019-0719-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND The neonatal cutaneous mycobiome has not been characterized in preterm infants. Invasive fungal infections in preterm neonates are associated with high mortality. The immaturity of the preterm skin predisposes neonates to invasive infection by skin colonizers. We report the clinical and host determinants that influence the skin mycobiome. METHODS Skin swabs from the antecubital fossa, forehead, and gluteal region of 15 preterm and 15 term neonates were obtained during the first 5 weeks of life. The mycobiome was sequenced using the conserved pan-fungal ITS2 region. Blood samples were used to genotype immune modulating genes. Clinical metadata was collected to determine the clinical predictors of the abundance and diversity of the skin mycobiome. RESULTS The neonatal mycobiome is characterized by few taxa. Alpha diversity of the mycobiome is influenced by antibiotic exposure, the forehead body site, and the neonatal intensive care unit (NICU) environment. Beta diversity varies with mode of delivery, diet, and body site. The host determinants of the cutaneous microbiome include single-nucleotide polymorphisms in TLR4, NLRP3,CARD8, and NOD2. CONCLUSION The neonatal cutaneous mycobiome is composed of few genera and is influenced by clinical factors and host genetics, the understanding of which will inform preventive strategies against invasive fungal infections.
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Affiliation(s)
- Anshu A Paul
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Kristi L Hoffman
- Alkek Center for Microbiome and Metagenomics Research, Baylor College of Medicine, Houston, TX, USA
| | - Joseph L Hagan
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Venkatesh Sampath
- Department of Pediatrics, Section: Neonatology, Children's Mercy Hospital, University of Missouri, Kansas City, MO, USA
| | - Joseph F Petrosino
- Alkek Center for Microbiome and Metagenomics Research, Baylor College of Medicine, Houston, TX, USA
| | - Mohan Pammi
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
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48
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Lindfors K, Lin J, Lee HS, Hyöty H, Nykter M, Kurppa K, Liu E, Koletzko S, Rewers M, Hagopian W, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Petrosino JF, Lloyd RE, Agardh D. Metagenomics of the faecal virome indicate a cumulative effect of enterovirus and gluten amount on the risk of coeliac disease autoimmunity in genetically at risk children: the TEDDY study. Gut 2020; 69:1416-1422. [PMID: 31744911 PMCID: PMC7234892 DOI: 10.1136/gutjnl-2019-319809] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 01/27/2023]
Abstract
OBJECTIVE Higher gluten intake, frequent gastrointestinal infections and adenovirus, enterovirus, rotavirus and reovirus have been proposed as environmental triggers for coeliac disease. However, it is not known whether an interaction exists between the ingested gluten amount and viral exposures in the development of coeliac disease. This study investigated whether distinct viral exposures alone or together with gluten increase the risk of coeliac disease autoimmunity (CDA) in genetically predisposed children. DESIGN The Environmental Determinants of Diabetes in the Young study prospectively followed children carrying the HLA risk haplotypes DQ2 and/or DQ8 and constructed a nested case-control design. From this design, 83 CDA case-control pairs were identified. Median age of CDA was 31 months. Stool samples collected monthly up to the age of 2 years were analysed for virome composition by Illumina next-generation sequencing followed by comprehensive computational virus profiling. RESULTS The cumulative number of stool enteroviral exposures between 1 and 2 years of age was associated with an increased risk for CDA. In addition, there was a significant interaction between cumulative stool enteroviral exposures and gluten consumption. The risk conferred by stool enteroviruses was increased in cases reporting higher gluten intake. CONCLUSIONS Frequent exposure to enterovirus between 1 and 2 years of age was associated with increased risk of CDA. The increased risk conferred by the interaction between enteroviruses and higher gluten intake indicate a cumulative effect of these factors in the development of CDA.
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Affiliation(s)
- Katri Lindfors
- Faculty of Medicine and Health Techology, Tampere University, Tampere, Finland
| | - Jake Lin
- Faculty of Medicine and Health Techology, Tampere University, Tampere, Finland
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Hye-Seung Lee
- Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Heikki Hyöty
- Faculty of Medicine and Health Techology, Tampere University, Tampere, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Techology, Tampere University, Tampere, Finland
| | - Kalle Kurppa
- Faculty of Medicine and Health Techology, Tampere University, Tampere, Finland
- Center for Child Health Research, Tampere University and Tampere University Hospital, Tampere, Finland
- The University Consortium of Seinäjoki, Seinäjoki, Finland
| | - Edwin Liu
- University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
- Digestive Health Institute, Children's Hospital Colorado, Aurora, United States
| | - Sibylle Koletzko
- Ludwig-Maximilians-Universitat Munchen, Munchen, Bayern, Germany
- Division of Paediatric Gastroenterology and Hepatology, Dr von Hauner Children's Hospital, Munchen, Germany
| | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Denver, Colorado, USA
| | | | - Jorma Toppari
- Research Centre for Integrative Physiology and Phamacology, Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Paediatrics, Turku University Hospital, Turku, Finland
| | - Annette-Gabriele Ziegler
- Kliikum Rechts der Isar, Technische Universität München, Munchen, Bayern, Germany
- Institute of Diabetes Research, Helmholtz Zentrum München, Germany
- Forschergruppe Diabetes e.V, Neuherberg, Germany
| | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Jeffrey P Krischer
- Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Richard E Lloyd
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Daniel Agardh
- The Diabetes and Celiac Disease Unit, Department of Clinical Sciences, Lund University, Lund, Sweden
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49
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Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. bioRxiv 2020:2020.07.27.223495. [PMID: 32766579 PMCID: PMC7402036 DOI: 10.1101/2020.07.27.223495] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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Affiliation(s)
- Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Richard Sucgang
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Vipin Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Erin Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA, 77030
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Felipe-Andres Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030
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Coy SR, Gann ER, Papoulis SE, Holder ME, Ajami NJ, Petrosino JF, Zinser ER, Van Etten JL, Wilhelm SW. SMRT Sequencing of Paramecium Bursaria Chlorella Virus-1 Reveals Diverse Methylation Stability in Adenines Targeted by Restriction Modification Systems. Front Microbiol 2020; 11:887. [PMID: 32508769 PMCID: PMC7248222 DOI: 10.3389/fmicb.2020.00887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/16/2020] [Indexed: 12/31/2022] Open
Abstract
Chloroviruses (family Phycodnaviridae) infect eukaryotic, freshwater, unicellular green algae. A unique feature of these viruses is an abundance of DNA methyltransferases, with isolates dedicating up to 4.5% of their protein coding potential to these genes. This diversity highlights just one of the long-standing values of the chlorovirus model system; where group-wide epigenomic characterization might begin to elucidate the function(s) of DNA methylation in large dsDNA viruses. We characterized DNA modifications in the prototype chlorovirus, PBCV-1, using single-molecule real time (SMRT) sequencing (aka PacBio). Results were compared to total available sites predicted in silico based on DNA sequence alone. SMRT-software detected N6-methyl-adenine (m6A) at GATC and CATG recognition sites, motifs previously shown to be targeted by PBCV-1 DNA methyltransferases M.CviAI and M. CviAII, respectively. At the same time, PacBio analyses indicated that 10.9% of the PBCV-1 genome had large interpulse duration ratio (ipdRatio) values, the primary metric for DNA modification identification. These events represent 20.6x more sites than can be accounted for by all available adenines in GATC and CATG motifs, suggesting base or backbone modifications other than methylation might be present. To define methylation stability, we cross-compared methylation status of each GATC and CATG sequence in three biological replicates and found ∼81% of sites were stably methylated, while ∼2% consistently lack methylation. The remaining 17% of sites were stochastically methylated. When methylation status was analyzed for both strands of each target, we show that palindromes existed in completely non-methylated states, fully-methylated states, or hemi-methylated states, though GATC sites more often lack methylation than CATG sequences. Given that both sequences are targeted by not just methyltransferases, but by restriction endonucleases that are together encoded by PBCV-1 as virus-originating restriction modification (RM) systems, there is strong selective pressure to modify all target sites. The finding that most instances of non-methylation are associated with hemi-methylation is congruent with observations that hemi-methylated palindromes are resistant to cleavage by restriction endonucleases. However, sites where hemi-methylation is conserved might represent a unique regulatory function for PBCV-1. This study serves as a baseline for future investigation into the epigenomics of chloroviruses and their giant virus relatives.
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Affiliation(s)
- Samantha R. Coy
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
- BioSciences at Rice, Rice University, Houston, TX, United States
| | - Eric R. Gann
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Spiridon E. Papoulis
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Michael E. Holder
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States
| | - Nadim J. Ajami
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States
| | - Erik R. Zinser
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | - James L. Van Etten
- Department of Plant Pathology and the Nebraska Center for Virology, University of Nebraska, Lincoln, NE, United States
| | - Steven W. Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, Knoxville, TN, United States
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