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Thomas DM, Knight R, Gilbert JA, Cornelis MC, Gantz MG, Burdekin K, Cummiskey K, Sumner SCJ, Pathmasiri W, Sazonov E, Gabriel KP, Dooley EE, Green MA, Pfluger A, Kleinberg S. Transforming Big Data into AI-ready data for nutrition and obesity research. Obesity (Silver Spring) 2024; 32:857-870. [PMID: 38426232 DOI: 10.1002/oby.23989] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 12/15/2023] [Accepted: 12/26/2023] [Indexed: 03/02/2024]
Abstract
OBJECTIVE Big Data are increasingly used in obesity and nutrition research to gain new insights and derive personalized guidance; however, this data in raw form are often not usable. Substantial preprocessing, which requires machine learning (ML), human judgment, and specialized software, is required to transform Big Data into artificial intelligence (AI)- and ML-ready data. These preprocessing steps are the most complex part of the entire modeling pipeline. Understanding the complexity of these steps by the end user is critical for reducing misunderstanding, faulty interpretation, and erroneous downstream conclusions. METHODS We reviewed three popular obesity/nutrition Big Data sources: microbiome, metabolomics, and accelerometry. The preprocessing pipelines, specialized software, challenges, and how decisions impact final AI- and ML-ready products were detailed. RESULTS Opportunities for advances to improve quality control, speed of preprocessing, and intelligent end user consumption were presented. CONCLUSIONS Big Data have the exciting potential for identifying new modifiable factors that impact obesity research. However, to ensure accurate interpretation of conclusions arising from Big Data, the choices involved in preparing AI- and ML-ready data need to be transparent to investigators and clinicians relying on the conclusions.
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Affiliation(s)
- Diana M Thomas
- Department of Mathematical Sciences, United States Military Academy, West Point, New York, USA
| | - Rob Knight
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California, USA
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Marilyn C Cornelis
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Marie G Gantz
- Biostatics and Epidemiology Division, Research Triangle Institute International, Research Triangle Park, North Carolina, USA
| | - Kate Burdekin
- Biostatics and Epidemiology Division, Research Triangle Institute International, Research Triangle Park, North Carolina, USA
| | - Kevin Cummiskey
- Department of Mathematical Sciences, United States Military Academy, West Point, New York, USA
| | - Susan C J Sumner
- Department of Nutrition, Nutrition Research Institute, University of North Carolina Chapel Hill, Kannapolis, North Carolina, USA
| | - Wimal Pathmasiri
- Department of Nutrition, Nutrition Research Institute, University of North Carolina Chapel Hill, Kannapolis, North Carolina, USA
| | - Edward Sazonov
- Electrical and Computer Engineering Department, The University of Alabama, Tuscaloosa, Alabama, USA
| | - Kelley Pettee Gabriel
- Department of Epidemiology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Erin E Dooley
- Department of Epidemiology, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Mark A Green
- Department of Geography & Planning, University of Liverpool, Liverpool, UK
| | - Andrew Pfluger
- Department of Geography and Environmental Engineering, United States Military Academy, West Point, New York, USA
| | - Samantha Kleinberg
- Computer Science Department, Stevens Institute of Technology, Hoboken, New Jersey, USA
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O’Dwyer DN, Kim JS, Ma SF, Ranjan P, Das P, Lipinski JH, Metcalf JD, Falkowski NR, Yow E, Anstrom K, Dickson RP, Huang Y, Gilbert JA, Martinez FJ, Noth I. Commensal Oral Microbiota, Disease Severity, and Mortality in Fibrotic Lung Disease. Am J Respir Crit Care Med 2024; 209:1101-1110. [PMID: 38051927 PMCID: PMC11092942 DOI: 10.1164/rccm.202308-1357oc] [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: 08/04/2023] [Accepted: 12/05/2023] [Indexed: 12/07/2023] Open
Abstract
Rationale: Oral microbiota associate with diseases of the mouth and serve as a source of lung microbiota. However, the role of oral microbiota in lung disease is unknown. Objectives: To determine associations between oral microbiota and disease severity and death in idiopathic pulmonary fibrosis (IPF). Methods: We analyzed 16S rRNA gene and shotgun metagenomic sequencing data of buccal swabs from 511 patients with IPF in the multicenter CleanUP-IPF (Study of Clinical Efficacy of Antimicrobial Therapy Strategy Using Pragmatic Design in IPF) trial. Buccal swabs were collected from usual care and antimicrobial cohorts. Microbiome data were correlated with measures of disease severity using principal component analysis and linear regression models. Associations between the buccal microbiome and mortality were determined using Cox additive models, Kaplan-Meier analysis, and Cox proportional hazards models. Measurements and Main Results: Greater buccal microbial diversity associated with lower FVC at baseline (mean difference, -3.60; 95% confidence interval [CI], -5.92 to -1.29% predicted FVC per 1-unit increment). The buccal proportion of Streptococcus correlated positively with FVC (mean difference, 0.80; 95% CI, 0.16 to 1.43% predicted per 10% increase) (n = 490). Greater microbial diversity was associated with an increased risk of death (hazard ratio, 1.73; 95% CI, 1.03-2.90), whereas a greater proportion of Streptococcus was associated with a reduced risk of death (HR, 0.85; 95% CI, 0.73 to 0.99). The Streptococcus genus was mainly composed of Streptococcus mitis species. Conclusions: Increasing buccal microbial diversity predicts disease severity and death in IPF. The oral commensal S. mitis spp associates with preserved lung function and improved survival.
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Affiliation(s)
- David N. O’Dwyer
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - John S. Kim
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Shwu-Fan Ma
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Piyush Ranjan
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Promi Das
- Department of Pediatrics, University of California San Diego, San Diego, California
| | - Jay H. Lipinski
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Joseph D. Metcalf
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
| | - Nicole R. Falkowski
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
| | - Eric Yow
- Department of Biostatistics, Duke University, Durham, North Carolina
| | - Kevin Anstrom
- Department of Biostatistics, University of North Carolina–Chapel Hill Gillings School of Global Public Health, Chapel Hill, North Carolina
| | - Robert P. Dickson
- Department of Medicine, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
- Weil Institute for Critical Care Research and Innovation, Ann Arbor, Michigan; and
| | - Yong Huang
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego, San Diego, California
| | | | - Imre Noth
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia
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Lie AAY, Zimmer-Faust AG, Diner RE, Kunselman E, Daniel Z, Van Artsdalen K, Salas Garcia MC, Gilbert JA, Shultz D, Chokry J, Langlois K, Smith J. Understanding the risks of co-exposures in a changing world: a case study of dual monitoring of the biotoxin domoic acid and Vibrio spp. in Pacific oyster. Environ Monit Assess 2024; 196:447. [PMID: 38607511 DOI: 10.1007/s10661-024-12614-1] [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] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 04/05/2024] [Indexed: 04/13/2024]
Abstract
Assessing the co-occurrence of multiple health risk factors in coastal ecosystems is challenging due to the complexity of multi-factor interactions and limited availability of simultaneously collected data. Understanding co-occurrence is particularly important for risk factors that may be associated with, or occur in similar environmental conditions. In marine ecosystems, the co-occurrence of harmful algal bloom toxins and bacterial pathogens within the genus Vibrio may impact both ecosystem and human health. This study examined the co-occurrence of Vibrio spp. and domoic acid (DA) produced by the harmful algae Pseudo-nitzschia by (1) analyzing existing California Department of Public Health monitoring data for V. parahaemolyticus and DA in oysters; and (2) conducting a 1-year seasonal monitoring of these risk factors across two Southern California embayments. Existing public health monitoring efforts in the state were robust for individual risk factors; however, it was difficult to evaluate the co-occurrence of these risk factors in oysters due to low number of co-monitoring instances between 2015 and 2020. Seasonal co-monitoring of DA and Vibrio spp. (V. vulnificus or V. parahaemolyticus) at two embayments revealed the co-occurrence of these health risk factors in 35% of sampled oysters in most seasons. Interestingly, both the overall detection frequency and co-occurrence of these risk factors were considerably less frequent in water samples. These findings may in part suggest the slow depuration of Vibrio spp. and DA in oysters as residual levels may be retained. This study expanded our understanding of the simultaneous presence of DA and Vibrio spp. in bivalves and demonstrates the feasibility of co-monitoring different risk factors from the same sample. Individual programs monitoring for different risk factors from the same sample matrix may consider combining efforts to reduce cost, streamline the process, and better understand the prevalence of co-occurring health risk factors.
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Affiliation(s)
- Alle A Y Lie
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA.
| | - Amity G Zimmer-Faust
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
- The Nature Conservancy, Arlington, VA, USA
| | - Rachel E Diner
- University of California, Scripps Institute of Oceanography, La Jolla, San Diego, CA, USA
- University of Memphis, Memphis, TN, USA
| | - Emily Kunselman
- University of California, Scripps Institute of Oceanography, La Jolla, San Diego, CA, USA
| | - Zachary Daniel
- University of California, Scripps Institute of Oceanography, La Jolla, San Diego, CA, USA
| | - Kathryn Van Artsdalen
- University of California, Scripps Institute of Oceanography, La Jolla, San Diego, CA, USA
| | - Mariana C Salas Garcia
- University of California, Scripps Institute of Oceanography, La Jolla, San Diego, CA, USA
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, USA
| | - Jack A Gilbert
- University of California, Scripps Institute of Oceanography, La Jolla, San Diego, CA, USA
- Department of Pediatrics, University of California, La Jolla, San Diego, CA, USA
| | - Dana Shultz
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - Jeff Chokry
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - Kylie Langlois
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
| | - Jayme Smith
- Southern California Coastal Water Research Project, Costa Mesa, CA, USA
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4
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Gilbert JA, Alverdy J. Where do the pathogens that cause surgical site infections come from? Sci Transl Med 2024; 16:eado1449. [PMID: 38598617 DOI: 10.1126/scitranslmed.ado1449] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/20/2024] [Indexed: 04/12/2024]
Abstract
A study from Long et al. shows that many pathogens that cause surgical site infections during spine surgery come from the patient's own microbiome, suggesting a paradigm shift in the understanding of surgical site infections that questions the effectiveness of current enhanced sterility and antibiotic protocols.
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Affiliation(s)
- Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, Microbiome and Metagenomics Center, UC San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - John Alverdy
- Department of Surgery, University of Chicago, 5801 S. Ellis Avenue, Chicago, IL 60637, USA
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Brennan C, Chan K, Kumar T, Maissy E, Brubaker L, Dothard MI, Gilbert JA, Gilbert KE, Lewis AL, Thackray VG, Zarrinpar A, Knight R. Harnessing the power within: engineering the microbiome for enhanced gynecologic health. Reprod Fertil 2024; 5:e230060. [PMID: 38513356 PMCID: PMC11046331 DOI: 10.1530/raf-23-0060] [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: 12/28/2023] [Accepted: 03/18/2024] [Indexed: 03/23/2024] Open
Abstract
Graphical abstract Abstract Although numerous studies have demonstrated the impact of microbiome manipulation on human health, research on the microbiome's influence on female health remains relatively limited despite substantial disease burden. In light of this, we present a selected review of clinical trials and preclinical studies targeting both the vaginal and gut microbiomes for the prevention or treatment of various gynecologic conditions. Specifically, we explore studies that leverage microbiota transplants, probiotics, prebiotics, diet modifications, and engineered microbial strains. A healthy vaginal microbiome for females of reproductive age consists of lactic acid-producing bacteria predominantly of the Lactobacillus genus, which serves as a protective barrier against pathogens and maintains a balanced ecosystem. The gut microbiota's production of short-chain fatty acids, metabolism of primary bile acids, and modulation of sex steroid levels have significant implications for the interplay between host and microbes throughout the body, ultimately impacting reproductive health. By harnessing interventions that modulate both the vaginal and gut microbiomes, it becomes possible to not only maintain homeostasis but also mitigate pathological conditions. While the field is still working toward making broad clinical recommendations, the current studies demonstrate that manipulating the microbiome holds great potential for addressing diverse gynecologic conditions. Lay summary Manipulating the microbiome has recently entered popular culture, with various diets thought to aid the microbes that live within us. These microbes live in different locations of our body and accordingly help us digest food, modulate our immune system, and influence reproductive health. The role of the microbes living in and influencing the female reproductive tract remains understudied despite known roles in common conditions such as vulvovaginal candidiasis (affecting 75% of females in their lifetime), bacterial vaginosis (25% of females in their lifetime), cervical HPV infection (80% of females in their lifetime), endometriosis (6-10% of females of reproductive age), and polycystic ovary syndrome (10-12% of females of reproductive age). Here, we review four different approaches used to manipulate the female reproductive tract and gastrointestinal system microbiomes: microbiota transplants, probiotics, prebiotics, and dietary interventions, and the use of engineered microbial strains. In doing so, we aim to stimulate discussion on new ways to understand and treat female reproductive health conditions.
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Affiliation(s)
- Caitriona Brennan
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Kristina Chan
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Tanya Kumar
- Medical Scientist Training Program, University of California San Diego, La Jolla, California, USA
| | - Erica Maissy
- Division of Gastroenterology, University of California San Diego, La Jolla, California, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | - Linda Brubaker
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
| | - Marisol I Dothard
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | - Jack A Gilbert
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| | - Katharine E Gilbert
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Amanda L Lewis
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
| | - Varykina G Thackray
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| | - Amir Zarrinpar
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Medical Scientist Training Program, University of California San Diego, La Jolla, California, USA
- Division of Gastroenterology, University of California San Diego, La Jolla, California, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Jennifer Moreno Department of Veterans Affairs Medical Center, La Jolla, California, USA
- Institute of Diabetes and Metabolic Health, University of California San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, California, USA
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6
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Alvernaz SA, Wenzel ES, Nagelli U, Pezley LB, LaBomascus B, Gilbert JA, Maki PM, Tussing-Humphreys L, Peñalver Bernabé B. Inflammatory Dietary Potential Is Associated with Vitamin Depletion and Gut Microbial Dysbiosis in Early Pregnancy. Nutrients 2024; 16:935. [PMID: 38612969 PMCID: PMC11013194 DOI: 10.3390/nu16070935] [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: 02/20/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/14/2024] Open
Abstract
Pregnancy alters many physiological systems, including the maternal gut microbiota. Diet is a key regulator of this system and can alter the host immune system to promote inflammation. Multiple perinatal disorders have been associated with inflammation, maternal metabolic alterations, and gut microbial dysbiosis, including gestational diabetes mellitus, pre-eclampsia, preterm birth, and mood disorders. However, the effects of high-inflammatory diets on the gut microbiota during pregnancy have yet to be fully explored. We aimed to address this gap using a system-based approach to characterize associations among dietary inflammatory potential, a measure of diet quality, and the gut microbiome during pregnancy. Forty-seven pregnant persons were recruited prior to 16 weeks of gestation. Participants completed a food frequency questionnaire (FFQ) and provided fecal samples. Dietary inflammatory potential was assessed using the Dietary Inflammatory Index (DII) from the FFQ data. Fecal samples were analyzed using 16S rRNA amplicon sequencing. Differential taxon abundances with respect to the DII score were identified, and the microbial metabolic potential was predicted using PICRUSt2. Inflammatory diets were associated with decreased vitamin and mineral intake and a dysbiotic gut microbiota structure and predicted metabolism. Gut microbial compositional differences revealed a decrease in short-chain fatty acid producers such as Faecalibacterium, and an increase in predicted vitamin B12 synthesis, methylglyoxal detoxification, galactose metabolism, and multidrug efflux systems in pregnant individuals with increased DII scores. Dietary inflammatory potential was associated with a reduction in the consumption of vitamins and minerals and predicted gut microbiota metabolic dysregulation.
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Affiliation(s)
- Suzanne A. Alvernaz
- Department of Biomedical Engineering, University of Illinois, Chicago, IL 60607, USA; (S.A.A.); (U.N.)
| | - Elizabeth S. Wenzel
- Department of Psychology, University of Illinois, Chicago, IL 60607, USA; (E.S.W.); (P.M.M.)
| | - Unnathi Nagelli
- Department of Biomedical Engineering, University of Illinois, Chicago, IL 60607, USA; (S.A.A.); (U.N.)
| | - Lacey B. Pezley
- Department of Kinesiology and Nutrition, University of Illinois, Chicago, IL 60612, USA; (L.B.P.); (B.L.); (L.T.-H.)
| | - Bazil LaBomascus
- Department of Kinesiology and Nutrition, University of Illinois, Chicago, IL 60612, USA; (L.B.P.); (B.L.); (L.T.-H.)
| | - Jack A. Gilbert
- Department of Pediatrics, University of California, San Diego, CA 92093, USA;
- Scripps Oceanographic Institute, University of California, San Diego, CA 92037, USA
| | - Pauline M. Maki
- Department of Psychology, University of Illinois, Chicago, IL 60607, USA; (E.S.W.); (P.M.M.)
- Department of Psychiatry, University of Illinois, Chicago, IL 60612, USA
- Department of Obstetrics and Gynecology, University of Illinois, Chicago, IL 60612, USA
| | - Lisa Tussing-Humphreys
- Department of Kinesiology and Nutrition, University of Illinois, Chicago, IL 60612, USA; (L.B.P.); (B.L.); (L.T.-H.)
| | - Beatriz Peñalver Bernabé
- Department of Biomedical Engineering, University of Illinois, Chicago, IL 60607, USA; (S.A.A.); (U.N.)
- Center for Bioinformatics and Quantitative Biology, University of Illinois, Chicago, IL 60612, USA
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Choo-Kang C, Reese TO, Micklesfield LK, Bovet P, Bedu-Addo K, Forrester T, Gilbert JA, Goedecke JH, Plange-Rhule J, Lambert EV, Layden BT, Rae DE, Viswanathan B, Luke A, Dugas L. Silhouette showcards confirm altered obesity-associated body image perception in international cohort study of African-origin populations. BMJ Open 2024; 14:e065498. [PMID: 38458795 DOI: 10.1136/bmjopen-2022-065498] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/10/2024] Open
Abstract
OBJECTIVES Given the increasing prevalence of obesity and need for effective interventions, there is a growing interest in understanding how an individual's body image can inform obesity prevention and management. This study's objective was to examine the use of silhouette showcards to measure body size perception compared with measured body mass index, and assess body size dissatisfaction, in three different African-origin populations spanning the epidemiological transition. An ancillary objective was to investigate associations between body size perception and dissatisfaction with diabetes and hypertension. SETTING Research visits were completed in local research clinics in respective countries. PARTICIPANTS Seven hundred and fifty-one African-origin participants from the USA and the Republic of Seychelles (both high-income countries), and Ghana (low/middle-income country). PRIMARY AND SECONDARY OUTCOME MEASURES Silhouette showcards were used to measure perceived body size and body size dissatisfaction. Objectively measured body size was measured using a scale and stadiometer. Diabetes was defined as fasting blood glucose ≥126 mg/dL and hypertension was defined as ≥130 mm Hg/80 mm Hg. RESULTS Most women and men from the USA and Seychelles had 'Perceived minus Actual weight status Discrepancy' scores less than 0, meaning they underestimated their actual body size. Similarly, most overweight or obese men and women also underestimated their body size, while normal weight men and women were accurately able to estimate their body size. Finally, participants with diabetes were able to accurately estimate their body size and similarly desired a smaller body size. CONCLUSIONS This study highlights that overweight and obese women and men from countries spanning the epidemiological transition were unable to accurately perceive their actual body size. Understanding people's perception of their body size is critical to implementing successful obesity prevention programmes across the epidemiological transition.
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Affiliation(s)
- Candice Choo-Kang
- Public Health Scienes, Loyola University Chicago, Maywood, Illinois, USA
| | - Tyler O Reese
- Department of Medicine, University of Colorado Denver School of Medicine, Aurora, Colorado, USA
| | - Lisa K Micklesfield
- SAMRC/Wits Developmental Pathways for Health Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg-Braamfontein, Gauteng, South Africa
| | - Pascal Bovet
- University Center for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
- Ministry of Health, Lisbon, Portugal
| | - Kweku Bedu-Addo
- Department of Physiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Terrence Forrester
- Solutions for Developing Countries, The University of the West Indies, Kingston, Jamaica
| | - Jack A Gilbert
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Julia H Goedecke
- Non-Communicable Diseases Research Unit, South African Medical Research Council, Cape Town, South Africa
| | - Jacob Plange-Rhule
- Department of Physiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Estelle V Lambert
- Health through Physical Activity, Lifestyle and Sport Research Centre, University of Cape Town, Rondebosch, South Africa
| | - Brian T Layden
- Division of Endocrinology, Diabetes, and Metabolism, University of Illinois Chicago, Chicago, Illinois, USA
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
| | - Dale E Rae
- Health through Physical Activity, Lifestyle and Sport Research Centre, University of Cape Town, Rondebosch, South Africa
| | - Bharathi Viswanathan
- Unit for Prevention and Control of Cardiovascular Disease, Republic of Seychelles Ministry of Health, Mont Fleuri, Seychelles
| | - Amy Luke
- Public Health Sciences, Loyola University Chicago, Chicago, Illinois, USA
| | - Lara Dugas
- Public Health Sciences, Loyola University Chicago, Chicago, Illinois, USA
- Division of Epidemiology & Biostatistics, University of Cape Town, Rondebosch, South Africa
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8
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Bosch ME, Dodiya HB, Michalkiewicz J, Lee C, Shaik SM, Weigle IQ, Zhang C, Osborn J, Nambiar A, Patel P, Parhizkar S, Zhang X, Laury ML, Mondal P, Gomm A, Schipma MJ, Mallah D, Butovsky O, Chang EB, Tanzi RE, Gilbert JA, Holtzman DM, Sisodia SS. Sodium oligomannate alters gut microbiota, reduces cerebral amyloidosis and reactive microglia in a sex-specific manner. Mol Neurodegener 2024; 19:18. [PMID: 38365827 PMCID: PMC10874048 DOI: 10.1186/s13024-023-00700-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/21/2023] [Indexed: 02/18/2024] Open
Abstract
It has recently become well-established that there is a connection between Alzheimer's disease pathology and gut microbiome dysbiosis. We have previously demonstrated that antibiotic-mediated gut microbiota perturbations lead to attenuation of Aβ deposition, phosphorylated tau accumulation, and disease-associated glial cell phenotypes in a sex-dependent manner. In this regard, we were intrigued by the finding that a marine-derived oligosaccharide, GV-971, was reported to alter gut microbiota and reduce Aβ amyloidosis in the 5XFAD mouse model that were treated at a point when Aβ burden was near plateau levels. Utilizing comparable methodologies, but with distinct technical and temporal features, we now report on the impact of GV-971 on gut microbiota, Aβ amyloidosis and microglial phenotypes in the APPPS1-21 model, studies performed at the University of Chicago, and independently in the 5X FAD model, studies performed at Washington University, St. Louis.Methods To comprehensively characterize the effects of GV-971 on the microbiota-microglia-amyloid axis, we conducted two separate investigations at independent institutions. There was no coordination of the experimental design or execution between the two laboratories. Indeed, the two laboratories were not aware of each other's experiments until the studies were completed. Male and female APPPS1-21 mice were treated daily with 40, 80, or 160 mg/kg of GV-971 from 8, when Aβ burden was detectable upto 12 weeks of age when Aβ burden was near maximal levels. In parallel, and to corroborate existing published studies and further investigate sex-related differences, male and female 5XFAD mice were treated daily with 100 mg/kg of GV-971 from 7 to 9 months of age when Aβ burden was near peak levels. Subsequently, the two laboratories independently assessed amyloid-β deposition, metagenomic, and neuroinflammatory profiles. Finally, studies were initiated at the University of Chicago to evaluate the metabolites in cecal tissue from vehicle and GV-971-treated 5XFAD mice.Results These studies showed that independent of the procedural differences (dosage, timing and duration of treatment) between the two laboratories, cerebral amyloidosis was reduced primarily in male mice, independent of strain. We also observed sex-specific microbiota differences following GV-971 treatment. Interestingly, GV-971 significantly altered multiple overlapping bacterial species at both institutions. Moreover, we discovered that GV-971 significantly impacted microbiome metabolism, particularly by elevating amino acid production and influencing the tryptophan pathway. The metagenomics and metabolomics changes correspond with notable reductions in peripheral pro-inflammatory cytokine and chemokine profiles. Furthermore, GV-971 treatment dampened astrocyte and microglia activation, significantly decreasing plaque-associated reactive microglia while concurrently increasing homeostatic microglia only in male mice. Bulk RNAseq analysis unveiled sex-specific changes in cerebral cortex transcriptome profiles, but most importantly, the transcriptome changes in the GV-971-treated male group revealed the involvement of microglia and inflammatory responses.Conclusions In conclusion, these studies demonstrate the connection between the gut microbiome, neuroinflammation, and Alzheimer's disease pathology while highlighting the potential therapeutic effect of GV-971. GV-971 targets the microbiota-microglia-amyloid axis, leading to the lowering of plaque pathology and neuroinflammatory signatures in a sex-dependent manner when given at the onset of Aβ deposition or when given after Aβ deposition is already at higher levels.
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Affiliation(s)
- Megan E Bosch
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, Washington University in St. Louis, St. Louis, USA
| | - Hemraj B Dodiya
- Department of Neurobiology, University of Chicago, Chicago, USA
| | | | - Choonghee Lee
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, Washington University in St. Louis, St. Louis, USA
| | - Shabana M Shaik
- Department of Neurobiology, University of Chicago, Chicago, USA
| | - Ian Q Weigle
- Department of Neurobiology, University of Chicago, Chicago, USA
| | - Can Zhang
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jack Osborn
- Department of Neurobiology, University of Chicago, Chicago, USA
| | - Aishwarya Nambiar
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, Washington University in St. Louis, St. Louis, USA
| | - Priyam Patel
- Center for Genetic Medicine, Northwestern University, Chicago, USA
| | - Samira Parhizkar
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, Washington University in St. Louis, St. Louis, USA
| | - Xiaoqiong Zhang
- Department of Neurobiology, University of Chicago, Chicago, USA
| | - Marie L Laury
- Genome Technology Access Center, Washington University in St. Louis, St. Louis, USA
| | - Prasenjit Mondal
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ashley Gomm
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Dania Mallah
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Oleg Butovsky
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Eugene B Chang
- Department Medicine, Section of Gastroenterology, Hepatology, and Nutrition, The University of Chicago, Chicago, USA
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, UCSD, San Diego, USA
| | - David M Holtzman
- Department of Neurology, Hope Center for Neurological Disorders, Knight Alzheimer's Disease Research Center, Washington University in St. Louis, St. Louis, USA.
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Linnehan BK, Kodera SM, Allard SM, Brodie EC, Allaband C, Knight R, Lutz HL, Carroll MC, Meegan JM, Jensen ED, Gilbert JA. Evaluation of the safety and efficacy of fecal microbiota transplantations in bottlenose dolphins (Tursiops truncatus) using metagenomic sequencing. J Appl Microbiol 2024; 135:lxae026. [PMID: 38305096 PMCID: PMC10853691 DOI: 10.1093/jambio/lxae026] [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: 11/09/2023] [Revised: 12/28/2023] [Accepted: 01/31/2024] [Indexed: 02/03/2024]
Abstract
AIMS Gastrointestinal disease is a leading cause of morbidity in bottlenose dolphins (Tursiops truncatus) under managed care. Fecal microbiota transplantation (FMT) holds promise as a therapeutic tool to restore gut microbiota without antibiotic use. This prospective clinical study aimed to develop a screening protocol for FMT donors to ensure safety, determine an effective FMT administration protocol for managed dolphins, and evaluate the efficacy of FMTs in four recipient dolphins. METHODS AND RESULTS Comprehensive health monitoring was performed on donor and recipient dolphins. Fecal samples were collected before, during, and after FMT therapy. Screening of donor and recipient fecal samples was accomplished by in-house and reference lab diagnostic tests. Shotgun metagenomics was used for sequencing. Following FMT treatment, all four recipient communities experienced engraftment of novel microbial species from donor communities. Engraftment coincided with resolution of clinical signs and a sustained increase in alpha diversity. CONCLUSION The donor screening protocol proved to be safe in this study and no adverse effects were observed in four recipient dolphins. Treatment coincided with improvement in clinical signs.
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Affiliation(s)
| | - Sho M Kodera
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
| | - Sarah M Allard
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, United States
| | - Erin C Brodie
- National Marine Mammal Foundation, San Diego, CA 92106, United States
| | - Celeste Allaband
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, United States
| | - Rob Knight
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, United States
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA 92093, United States
- Department of Medicine, University of California San Diego, La Jolla, CA 92161, United States
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, United States
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, United States
| | - Holly L Lutz
- Department of Immunology and Microbiology, Scripps Research Institute, La Jolla, CA 92037, United States
| | | | - Jennifer M Meegan
- National Marine Mammal Foundation, San Diego, CA 92106, United States
| | - Eric D Jensen
- U.S. Navy Marine Mammal Program, Naval Information Warfare Center Pacific, San Diego, CA 92106, United States
| | - Jack A Gilbert
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, United States
- Center for Microbiome Innovation, Joan and Irwin Jacobs School of Engineering, University of California San Diego, La Jolla, CA 92093, United States
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Alvernaz SA, Wenzel ES, Nagelli U, Pezley LB, LaBomascus B, Gilbert JA, Maki PM, Tussing-Humphreys L, Peñalver Bernabé B. Inflammatory dietary potential is associated with vitamin depletion and gut microbial dysbiosis in early pregnancy. medRxiv 2024:2023.12.02.23299325. [PMID: 38076865 PMCID: PMC10705629 DOI: 10.1101/2023.12.02.23299325] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Background Pregnancy alters many physiological systems, including the maternal gut microbiota. Diet is a key regulator of this system and can alter the host immune system to promote inflammation. Multiple perinatal disorders have been associated with inflammation, maternal metabolic alterations, and gut microbial dysbiosis, including gestational diabetes mellitus, preeclampsia, preterm birth, and mood disorders. However, the effects of high inflammatory diets on the gut microbiota during pregnancy have yet to be fully explored. Objective To use a systems-based approach to characterize associations among dietary inflammatory potential, a measure of diet quality, and the gut microbiome during pregnancy. Methods Forty-nine pregnant persons were recruited prior to 16 weeks of gestation. Participants completed a food frequency questionnaire (FFQ) and provided fecal samples. Dietary inflammatory potential was assessed using the Dietary Inflammatory Index (DII) from FFQ data. Fecal samples were analyzed using 16S rRNA amplicon sequencing. Differential taxon abundance with respect to DII score were identified, and microbial metabolic potential was predicted using PICRUSt2. Results Inflammatory diets were associated with decreased vitamin and mineral intake and dysbiotic gut microbiota structure and predicted metabolism. Gut microbial compositional differences revealed a decrease in short chain fatty acid producers such as Faecalibacterium, and an increase in predicted vitamin B12 synthesis, methylglyoxal detoxification, galactose metabolism and multi drug efflux systems in pregnant individuals with increased DII scores. Conclusions Dietary inflammatory potential was associated with a reduction in the consumption of vitamins & minerals and predicted gut microbiota metabolic dysregulation.
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Affiliation(s)
- Suzanne A. Alvernaz
- Department of Biomedical Engineering, University of Illinois, Chicago, IL, USA
| | | | - Unnathi Nagelli
- Department of Biomedical Engineering, University of Illinois, Chicago, IL, USA
| | - Lacey B. Pezley
- Department of Kinesiology and Nutrition, University of Illinois, Chicago, IL, USA
| | - Bazil LaBomascus
- Department of Kinesiology and Nutrition, University of Illinois, Chicago, IL, USA
| | - Jack A. Gilbert
- Department of Pediatrics, University of California, San Diego, CA, USA
- Scripps Oceanographic Institute, University of California, San Diego, CA, USA
| | - Pauline M. Maki
- Department of Psychology, University of Illinois, Chicago, IL, USA
- Department of Psychiatry, University of Illinois, Chicago, IL, USA
- Department of Obstetrics and Gynecology, University of Illinois, Chicago, IL, USA
| | | | - Beatriz Peñalver Bernabé
- Department of Biomedical Engineering, University of Illinois, Chicago, IL, USA
- Center for Bioinformatics and Quantitative Biology, University of Illinois, Chicago, IL, USA
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11
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Gottel NR, Hill MS, Neal MJ, Allard SM, Zengler K, Gilbert JA. Biocontrol in built environments to reduce pathogen exposure and infection risk. ISME J 2024; 18:wrad024. [PMID: 38365248 PMCID: PMC10848226 DOI: 10.1093/ismejo/wrad024] [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] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/27/2023] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
The microbiome of the built environment comprises bacterial, archaeal, fungal, and viral communities associated with human-made structures. Even though most of these microbes are benign, antibiotic-resistant pathogens can colonize and emerge indoors, creating infection risk through surface transmission or inhalation. Several studies have catalogued the microbial composition and ecology in different built environment types. These have informed in vitro studies that seek to replicate the physicochemical features that promote pathogenic survival and transmission, ultimately facilitating the development and validation of intervention techniques used to reduce pathogen accumulation. Such interventions include using Bacillus-based cleaning products on surfaces or integrating bacilli into printable materials. Though this work is in its infancy, early research suggests the potential to use microbial biocontrol to reduce hospital- and home-acquired multidrug-resistant infections. Although these techniques hold promise, there is an urgent need to better understand the microbial ecology of built environments and to determine how these biocontrol solutions alter species interactions. This review covers our current understanding of microbial ecology of the built environment and proposes strategies to translate that knowledge into effective biocontrol of antibiotic-resistant pathogens.
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Affiliation(s)
- Neil R Gottel
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
| | - Megan S Hill
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Maxwell J Neal
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, United States
| | - Sarah M Allard
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Karsten Zengler
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, United States
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, United States
| | - Jack A Gilbert
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, United States
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, United States
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12
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Ochman H, Quandt EM, Gottell N, Gilbert JA. Examining the taxonomic distribution of tetracycline resistance in a wastewater plant. Sustain Microbiol 2024; 1:qvad003. [PMID: 38317688 PMCID: PMC10840452 DOI: 10.1093/sumbio/qvad003] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 12/15/2023] [Accepted: 01/16/2024] [Indexed: 02/07/2024]
Abstract
Microbial communities serve as reservoirs of antibiotic resistance genes (ARGs) and facilitate the dissemination of these genes to bacteria that infect humans. Relatively little is known about the taxonomic distribution of bacteria harboring ARGs in these reservoirs and the avenues of transmission due to the technical hurdles associated with characterizing the contents of complex microbial populations and the assignment of genes to particular genomes. Focusing on the array of tetracycline resistance (Tcr) genes in the primary and secondary phases of wastewater treatment, 17 of the 22 assayed Tcr genes were detected in at least one sample. We then applied emulsion, paired isolation, and concatenation PCR (epicPCR) to link tetracycline resistance genes to specific bacterial hosts. Whereas Tcr genes tend to vary in their distributions among bacterial taxa according to their modes of action, there were numerous instances in which a particular Tcr gene was associated with a host that was distantly related to all other bacteria bearing the same gene, including several hosts not previously identified. Tcr genes are far less host-restricted than previously assumed, indicating that complex microbial communities serve as settings where ARGs are spread among divergent bacterial phyla.
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Affiliation(s)
- Howard Ochman
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, United States
| | - Erik M Quandt
- Department of Molecular Biosciences, University of Texas, Austin, TX 78712, United States
| | - Neil Gottell
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, United States
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Gilbert JA. 2023 Acknowledgment of mSystems Ad Hoc Reviewers. mSystems 2023; 8:e0118923. [PMID: 38126780 DOI: 10.1128/msystems.01189-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Affiliation(s)
- Jack A Gilbert
- University of California San Diego School of Medicine, La Jolla, California, USA
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14
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Hill MS, Gilbert JA. Microbiology of the built environment: harnessing human-associated built environment research to inform the study and design of animal nests and enclosures. Microbiol Mol Biol Rev 2023; 87:e0012121. [PMID: 38047636 PMCID: PMC10732082 DOI: 10.1128/mmbr.00121-21] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
SUMMARYOver the past decade, hundreds of studies have characterized the microbial communities found in human-associated built environments (BEs). These have focused primarily on how the design and use of our built spaces have shaped human-microbe interactions and how the differential selection of certain taxa or genetic traits has influenced health outcomes. It is now known that the more removed humans are from the natural environment, the greater the risk for the development of autoimmune and allergic diseases, and that indoor spaces can be harsh, selective environments that can increase the emergence of antimicrobial-resistant and virulent phenotypes in surface-bound communities. However, despite the abundance of research that now points to the importance of BEs in determining human-microbe interactions, only a fraction of non-human animal structures have been comparatively explored. It is here, in the context of human-associated BE research, that we consider the microbial ecology of animal-built natural nests and burrows, as well as artificial enclosures, and point to areas of primary interest for future research.
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Affiliation(s)
- Megan S. Hill
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, California, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, California, USA
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
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Gilbert JA, Dothard M. Guest editorial from The BMS Annual Lecture 2023. Post Reprod Health 2023; 29:187-189. [PMID: 38059588 DOI: 10.1177/20533691231217150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Affiliation(s)
- Jack A Gilbert
- Biomedical Sciences Graduate Program and Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Scripps Institution Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Marisol Dothard
- Biomedical Sciences Graduate Program and Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
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Tropini C, Finlay BB, Nichter M, Melby MK, Metcalf JL, Dominguez-Bello MG, Zhao L, McFall-Ngai MJ, Geva-Zatorsky N, Amato KR, Undurraga EA, Poinar HN, Gilbert JA. Time to rethink academic publishing: the peer reviewer crisis. mBio 2023; 14:e0109123. [PMID: 37975666 PMCID: PMC10746150 DOI: 10.1128/mbio.01091-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023] Open
Abstract
There is concern that the time taken to publish academic papers in microbiological science has significantly increased in recent years. While the data do not specifically support this, evidence suggests that editors are having to invite more and more reviewers to identify those willing to perform peer review.
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Affiliation(s)
- Carolina Tropini
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada
| | - B. Brett Finlay
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Biochemistry and Microbiology and the Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mark Nichter
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- School of Anthropology, University of Arizona, Tucson, Arizona, USA
| | - Melissa K. Melby
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Department of Anthropology, University of Delaware, Newark, Delaware, USA
| | - Jessica L. Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Maria Gloria Dominguez-Bello
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
- Department of Anthropolog, Rutgers University, New Brunswick, New Jersey, USA
| | - Liping Zhao
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Margaret J. McFall-Ngai
- Carnegie Institution for Science, California Institute of Technology, Pasadena, California, USA
| | - Naama Geva-Zatorsky
- Department of Cell Biology and Cancer Science, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Rappaport Technion Integrated Cancer Center (RTICC), Haifa, Israel
| | - Katherine R. Amato
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Department of Anthropology, Northwestern University, Evanston, Illinois, USA
| | - Eduardo A. Undurraga
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Escuela de Gobierno, Pontificia Universidad Católica de Chile, Santiago, Región Metropolitana, Chile
- Research Center for Integrated Disaster Risk Management (CIGIDEN), Santiago, Región Metropolitana, Chile
| | - Hendrik N. Poinar
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
- Departments of Anthropology and Biochemistry, McMaster University, Hamilton, Ontario, Canada
| | - Jack A. Gilbert
- Department of Pediatrics, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
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Vargas-Robles D, Romaguera J, Alvarado-Velez I, Tosado-Rodríguez E, Dominicci-Maura A, Sanchez M, Wiggin KJ, Martinez-Ferrer M, Gilbert JA, Forney LJ, Godoy-Vitorino F. The cervical microbiota of Hispanics living in Puerto Rico is nonoptimal regardless of HPV status. mSystems 2023; 8:e0035723. [PMID: 37534938 PMCID: PMC10469956 DOI: 10.1128/msystems.00357-23] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/26/2023] [Indexed: 08/04/2023] Open
Abstract
The cervicovaginal microbiota is influenced by host physiology, immunology, lifestyle, and ethnicity. We hypothesized that there would be differences in the cervicovaginal microbiota among pregnant, nonpregnant, and menopausal women living in Puerto Rico (PR) with and without human papillomavirus (HPV) infection and cervical cancer. We specifically wanted to determine if the microbiota is associated with variations in cervical cytology. A total of 294 women, including reproductive-age nonpregnant (N = 196), pregnant (N = 37), and menopausal (N = 61) women, were enrolled. The cervicovaginal bacteria were characterized by 16S rRNA amplicon sequencing, the HPV was genotyped with SPF10-LiPA, and cervical cytology was quantified. High-risk HPV (HR-HPV, 67.3%) was prevalent, including genotypes not covered by the 9vt HPV vaccine. Cervical lesions (34%) were also common. The cervical microbiota was dominated by Lactobacillus iners. Pregnant women in the second and third trimesters exhibited a decrease in diversity and abundance of microbes associated with bacterial vaginosis. Women in menopause had greater alpha diversity, a greater proportion of facultative and strictly anaerobic bacteria, and higher cervicovaginal pH than premenopausal women. Cervical lesions were associated with greater alpha diversity. However, no significant associations between the microbiota and HPV infection (HR or LR-HPV types) were found. The cervicovaginal microbiota of women living in Puerto Rican were either dominated by L. iners or diverse microbial communities regardless of a woman's physiological stage. We postulate that the microbiota and the high prevalence of HR-HPV increase the risk of cervical lesions among women living in PR. IMPORTANCE In the enclosed manuscript, we provide the first in-depth characterization of the cervicovaginal microbiota of Hispanic women living in Puerto Rico (PR), using a 16S rRNA approach, and include women of different physiological stages. Surprisingly we found that high-risk HPV was ubiquitous with a prevalence of 67.3%, including types not covered by the 9vt HPV vaccine. We also found highly diverse microbial communities across women groups-with a reduction in pregnant women, but dominated by nonoptimal Lactobacillus iners. Additionally, we found vaginosis-associated bacteria as Dialister spp., Gardnerella spp., Clostridium, or Prevotella among most women. We believe this is a relevant and timely article expanding knowledge on the cervicovaginal microbiome of PR women, where we postulate that these highly diverse communities are conducive to cervical disease.
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Affiliation(s)
- Daniela Vargas-Robles
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, Medical Sciences Campus, San Juan, Puerto Rico
| | - Josefina Romaguera
- Department of Obstetrics and Gynecology, University of Puerto Rico School of Medicine, Medical Sciences Campus, San Juan, Puerto Rico
| | - Ian Alvarado-Velez
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, Medical Sciences Campus, San Juan, Puerto Rico
| | - Eduardo Tosado-Rodríguez
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, Medical Sciences Campus, San Juan, Puerto Rico
| | - Anelisse Dominicci-Maura
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, Medical Sciences Campus, San Juan, Puerto Rico
| | - Maria Sanchez
- University of Puerto Rico Comprehensive Cancer Center, San Juan, Puerto Rico
| | - Kara J. Wiggin
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | | | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Larry J. Forney
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, USA
| | - Filipa Godoy-Vitorino
- Department of Microbiology and Medical Zoology, University of Puerto Rico School of Medicine, Medical Sciences Campus, San Juan, Puerto Rico
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18
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Ecklu-Mensah G, Choo-Kang C, Maseng MG, Donato S, Bovet P, Viswanathan B, Bedu-Addo K, Plange-Rhule J, Oti Boateng P, Forrester TE, Williams M, Lambert EV, Rae D, Sinyanya N, Luke A, Layden BT, O'Keefe S, Gilbert JA, Dugas LR. Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: the METS-microbiome study. Nat Commun 2023; 14:5160. [PMID: 37620311 PMCID: PMC10449869 DOI: 10.1038/s41467-023-40874-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [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: 04/07/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023] Open
Abstract
The relationship between microbiota, short chain fatty acids (SCFAs), and obesity remains enigmatic. We employ amplicon sequencing and targeted metabolomics in a large (n = 1904) African origin cohort from Ghana, South Africa, Jamaica, Seychelles, and the US. Microbiota diversity and fecal SCFAs are greatest in Ghanaians, and lowest in Americans, representing each end of the urbanization spectrum. Obesity is significantly associated with a reduction in SCFA concentration, microbial diversity, and SCFA synthesizing bacteria, with country of origin being the strongest explanatory factor. Diabetes, glucose state, hypertension, obesity, and sex can be accurately predicted from the global microbiota, but when analyzed at the level of country, predictive accuracy is only universally maintained for sex. Diabetes, glucose, and hypertension are only predictive in certain low-income countries. Our findings suggest that adiposity-related microbiota differences differ between low-to-middle-income compared to high-income countries. Further investigation is needed to determine the factors driving this association.
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Affiliation(s)
- Gertrude Ecklu-Mensah
- Department of Pediatrics, Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Candice Choo-Kang
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA
| | - Maria Gjerstad Maseng
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Dep. of Gastroenterology, Oslo University Hospital, Oslo, Norway
- Bio-Me, Oslo, Norway
| | - Sonya Donato
- Department of Pediatrics, Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Pascal Bovet
- University Center for Primary Care and Public Health (Unisanté), Lausanne University Hospital, Lausanne, Switzerland
- Ministry of Health, Victoria, Republic of Seychelles
| | | | - Kweku Bedu-Addo
- Department of Physiology, SMS, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Jacob Plange-Rhule
- Department of Physiology, SMS, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Prince Oti Boateng
- Department of Physiology, SMS, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Terrence E Forrester
- Solutions for Developing Countries, University of the West Indies, Mona, Kingston, Jamaica
| | - Marie Williams
- Solutions for Developing Countries, University of the West Indies, Mona, Kingston, Jamaica
| | - Estelle V Lambert
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Dale Rae
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Nandipha Sinyanya
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Amy Luke
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA
| | - Brian T Layden
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL, USA
| | - Stephen O'Keefe
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jack A Gilbert
- Department of Pediatrics, Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
| | - Lara R Dugas
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA.
- Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
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19
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Diner RE, Zimmer-Faust A, Cooksey E, Allard S, Kodera SM, Kunselman E, Garodia Y, Verhougstraete MP, Allen AE, Griffith J, Gilbert JA. Host and Water Microbiota Are Differentially Linked to Potential Human Pathogen Accumulation in Oysters. Appl Environ Microbiol 2023; 89:e0031823. [PMID: 37318344 PMCID: PMC10370324 DOI: 10.1128/aem.00318-23] [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: 02/28/2023] [Accepted: 05/13/2023] [Indexed: 06/16/2023] Open
Abstract
Oysters play an important role in coastal ecology and are a globally popular seafood source. However, their filter-feeding lifestyle enables coastal pathogens, toxins, and pollutants to accumulate in their tissues, potentially endangering human health. While pathogen concentrations in coastal waters are often linked to environmental conditions and runoff events, these do not always correlate with pathogen concentrations in oysters. Additional factors related to the microbial ecology of pathogenic bacteria and their relationship with oyster hosts likely play a role in accumulation but are poorly understood. In this study, we investigated whether microbial communities in water and oysters were linked to accumulation of Vibrio parahaemolyticus, Vibrio vulnificus, or fecal indicator bacteria. Site-specific environmental conditions significantly influenced microbial communities and potential pathogen concentrations in water. Oyster microbial communities, however, exhibited less variability in microbial community diversity and accumulation of target bacteria overall and were less impacted by environmental differences between sites. Instead, changes in specific microbial taxa in oyster and water samples, particularly in oyster digestive glands, were linked to elevated levels of potential pathogens. For example, increased levels of V. parahaemolyticus were associated with higher relative abundances of cyanobacteria, which could represent an environmental vector for Vibrio spp. transport, and with decreased relative abundance of Mycoplasma and other key members of the oyster digestive gland microbiota. These findings suggest that host and microbial factors, in addition to environmental variables, may influence pathogen accumulation in oysters. IMPORTANCE Bacteria in the marine environment cause thousands of human illnesses annually. Bivalves are a popular seafood source and are important in coastal ecology, but their ability to concentrate pathogens from the water can cause human illness, threatening seafood safety and security. To predict and prevent disease, it is critical to understand what causes pathogenic bacteria to accumulate in bivalves. In this study, we examined how environmental factors and host and water microbial communities were linked to potential human pathogen accumulation in oysters. Oyster microbial communities were more stable than water communities, and both contained the highest concentrations of Vibrio parahaemolyticus at sites with warmer temperatures and lower salinities. High oyster V. parahaemolyticus concentrations corresponded with abundant cyanobacteria, a potential vector for transmission, and a decrease in potentially beneficial oyster microbes. Our study suggests that poorly understood factors, including host and water microbiota, likely play a role in pathogen distribution and pathogen transmission.
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Affiliation(s)
- Rachel E. Diner
- University of California, San Diego, Department of Pediatrics, La Jolla, California, USA
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California, USA
| | - Amy Zimmer-Faust
- Southern California Coastal Water Research Project, Microbiology Group, Costa Mesa, California, USA
| | - Emily Cooksey
- Environment, Exposure Science and Risk Assessment Center, University of Arizona Mel and Enid Zuckerman College of Public Health, Tucson, Arizona, USA
| | - Sarah Allard
- University of California, San Diego, Department of Pediatrics, La Jolla, California, USA
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California, USA
| | - Sho M. Kodera
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California, USA
| | - Emily Kunselman
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California, USA
| | - Yash Garodia
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California, USA
| | - Marc P. Verhougstraete
- Environment, Exposure Science and Risk Assessment Center, University of Arizona Mel and Enid Zuckerman College of Public Health, Tucson, Arizona, USA
| | - Andrew E. Allen
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California, USA
- J. Craig Venter Institute, Environmental and Microbial Genomics Group, La Jolla, California, USA
| | - John Griffith
- Southern California Coastal Water Research Project, Microbiology Group, Costa Mesa, California, USA
| | - Jack A. Gilbert
- University of California, San Diego, Department of Pediatrics, La Jolla, California, USA
- University of California, San Diego, Scripps Institution of Oceanography, La Jolla, California, USA
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20
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Morton JT, Jin DM, Mills RH, Shao Y, Rahman G, McDonald D, Zhu Q, Balaban M, Jiang Y, Cantrell K, Gonzalez A, Carmel J, Frankiensztajn LM, Martin-Brevet S, Berding K, Needham BD, Zurita MF, David M, Averina OV, Kovtun AS, Noto A, Mussap M, Wang M, Frank DN, Li E, Zhou W, Fanos V, Danilenko VN, Wall DP, Cárdenas P, Baldeón ME, Jacquemont S, Koren O, Elliott E, Xavier RJ, Mazmanian SK, Knight R, Gilbert JA, Donovan SM, Lawley TD, Carpenter B, Bonneau R, Taroncher-Oldenburg G. Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles. Nat Neurosci 2023:10.1038/s41593-023-01361-0. [PMID: 37365313 DOI: 10.1038/s41593-023-01361-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/13/2023] [Indexed: 06/28/2023]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by heterogeneous cognitive, behavioral and communication impairments. Disruption of the gut-brain axis (GBA) has been implicated in ASD although with limited reproducibility across studies. In this study, we developed a Bayesian differential ranking algorithm to identify ASD-associated molecular and taxa profiles across 10 cross-sectional microbiome datasets and 15 other datasets, including dietary patterns, metabolomics, cytokine profiles and human brain gene expression profiles. We found a functional architecture along the GBA that correlates with heterogeneity of ASD phenotypes, and it is characterized by ASD-associated amino acid, carbohydrate and lipid profiles predominantly encoded by microbial species in the genera Prevotella, Bifidobacterium, Desulfovibrio and Bacteroides and correlates with brain gene expression changes, restrictive dietary patterns and pro-inflammatory cytokine profiles. The functional architecture revealed in age-matched and sex-matched cohorts is not present in sibling-matched cohorts. We also show a strong association between temporal changes in microbiome composition and ASD phenotypes. In summary, we propose a framework to leverage multi-omic datasets from well-defined cohorts and investigate how the GBA influences ASD.
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Affiliation(s)
- James T Morton
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
- Biostatistics & Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Dong-Min Jin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | | | - Yan Shao
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Gibraan Rahman
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, USA
| | - Metin Balaban
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA
| | - Yueyu Jiang
- Department of Electrical and Computer Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Kalen Cantrell
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Antonio Gonzalez
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Julie Carmel
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | | | - Sandra Martin-Brevet
- Laboratory for Research in Neuroimaging, Centre for Research in Neurosciences, Department of Clinical Neurosciences, Centre Hospitalier Universitaire Vaudois, University of Lausanne, Lausanne, Switzerland
| | - Kirsten Berding
- Division of Nutritional Sciences, University of Illinois, Urbana, IL, USA
| | - Brittany D Needham
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - María Fernanda Zurita
- Microbiology Institute and Health Science College, Universidad San Francisco de Quito, Quito, Ecuador
| | - Maude David
- Departments of Microbiology & Pharmaceutical Sciences, Oregon State University, Corvallis, OR, USA
| | - Olga V Averina
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Alexey S Kovtun
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Antonio Noto
- Department of Biomedical Sciences, School of Medicine, University of Cagliari, Cagliari, Italy
| | - Michele Mussap
- Laboratory Medicine, Department of Surgical Sciences, School of Medicine, University of Cagliari, Cagliari, Italy
| | - Mingbang Wang
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China
- Microbiome Therapy Center, South China Hospital, Health Science Center, Shenzhen University, Shenzhen, China
| | - Daniel N Frank
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ellen Li
- Department of Medicine, Division of Gastroenterology and Hepatology, Stony Brook University, Stony Brook, NY, USA
| | - Wenhao Zhou
- Shanghai Key Laboratory of Birth Defects, Division of Neonatology, Children's Hospital of Fudan University, National Center for Children's Health, Shanghai, China
| | - Vassilios Fanos
- Neonatal Intensive Care Unit and Neonatal Pathology, Department of Surgical Sciences, School of Medicine, University of Cagliari, Cagliari, Italy
| | - Valery N Danilenko
- Vavilov Institute of General Genetics Russian Academy of Sciences, Moscow, Russia
| | - Dennis P Wall
- Pediatrics (Systems Medicine), Biomedical Data Science, and Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Paúl Cárdenas
- Institute of Microbiology, COCIBA, Universidad San Francisco de Quito, Quito, Ecuador
| | - Manuel E Baldeón
- Facultad de Ciencias Médicas, de la Salud y la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
| | - Sébastien Jacquemont
- Sainte Justine Hospital Research Center, Montréal, QC, Canada
- Department of Pediatrics, Université de Montréal, Montréal, QC, Canada
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Evan Elliott
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
- The Leslie and Susan Gonda Multidisciplinary Brain Research Center, Bar Ilan University, Ramat Gan, Israel
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA
| | - Sarkis K Mazmanian
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California, San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Jack A Gilbert
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Sharon M Donovan
- Division of Nutritional Sciences, University of Illinois, Urbana, IL, USA
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Bob Carpenter
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
- Prescient Design, a Genentech Accelerator, New York, NY, USA
| | - Gaspar Taroncher-Oldenburg
- Gaspar Taroncher Consulting, Philadelphia, PA, USA.
- Simons Foundation Autism Research Initiative, Simons Foundation, New York, NY, USA.
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21
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Roche KE, Bjork JR, Dasari MR, Grieneisen L, Jansen D, Gould TJ, Gesquiere LR, Barreiro LB, Alberts SC, Blekhman R, Gilbert JA, Tung J, Mukherjee S, Archie EA. Universal gut microbial relationships in the gut microbiome of wild baboons. eLife 2023; 12:e83152. [PMID: 37158607 PMCID: PMC10292843 DOI: 10.7554/elife.83152] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 09/01/2022] [Accepted: 05/08/2023] [Indexed: 05/10/2023] Open
Abstract
Ecological relationships between bacteria mediate the services that gut microbiomes provide to their hosts. Knowing the overall direction and strength of these relationships is essential to learn how ecology scales up to affect microbiome assembly, dynamics, and host health. However, whether bacterial relationships are generalizable across hosts or personalized to individual hosts is debated. Here, we apply a robust, multinomial logistic-normal modeling framework to extensive time series data (5534 samples from 56 baboon hosts over 13 years) to infer thousands of correlations in bacterial abundance in individual baboons and test the degree to which bacterial abundance correlations are 'universal'. We also compare these patterns to two human data sets. We find that, most bacterial correlations are weak, negative, and universal across hosts, such that shared correlation patterns dominate over host-specific correlations by almost twofold. Further, taxon pairs that had inconsistent correlation signs (either positive or negative) in different hosts always had weak correlations within hosts. From the host perspective, host pairs with the most similar bacterial correlation patterns also had similar microbiome taxonomic compositions and tended to be genetic relatives. Compared to humans, universality in baboons was similar to that in human infants, and stronger than one data set from human adults. Bacterial families that showed universal correlations in human infants were often universal in baboons. Together, our work contributes new tools for analyzing the universality of bacterial associations across hosts, with implications for microbiome personalization, community assembly, and stability, and for designing microbiome interventions to improve host health.
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Affiliation(s)
- Kimberly E Roche
- Program in Computational Biology and Bioinformatics, Duke UniversityDurhamUnited States
| | - Johannes R Bjork
- University of Groningen and University Medical Center Groningen, Department of Gastroenterology and HepatologyGroningenNetherlands
- University of Groningen and University Medical Center Groningen, Department of GeneticsGroningenNetherlands
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
| | - Mauna R Dasari
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
| | - Laura Grieneisen
- Department of Biology, University of British Columbia-Okanagan CampusKelownaCanada
| | - David Jansen
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
| | - Trevor J Gould
- Department of Ecology, Evolution, and Behavior, University of MinnesotaMinneapolisUnited States
| | | | - Luis B Barreiro
- Committee on Genetics, Genomics, and Systems Biology, University of ChicagoChicagoUnited States
- Section of Genetic Medicine, Department of Medicine, University of ChicagoChicagoUnited States
- Committee on Immunology, University of ChicagoChicagoUnited States
| | - Susan C Alberts
- Department of Biology, Duke UniversityDurhamUnited States
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Duke University Population Research Institute, Duke UniversityDurhamUnited States
| | - Ran Blekhman
- Section of Genetic Medicine, Department of Medicine, University of ChicagoChicagoUnited States
| | - Jack A Gilbert
- Department of Pediatrics and the Scripps Institution of Oceanography, University of California, San DiegoSan DiegoUnited States
| | - Jenny Tung
- Department of Biology, Duke UniversityDurhamUnited States
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Duke University Population Research Institute, Duke UniversityDurhamUnited States
- Department of Primate Behavior and Evolution, Max Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Sayan Mukherjee
- Program in Computational Biology and Bioinformatics, Duke UniversityDurhamUnited States
- Departments of Statistical Science, Mathematics, Computer Science, and Bioinformatics & Biostatistics, Duke UniversityDurhamUnited States
- Center for Scalable Data Analytics and Artificial Intelligence, University of LeipzigLeipzigGermany
- Max Plank Institute for Mathematics in the Natural SciencesLeipzigGermany
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre DameNotre DameUnited States
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22
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Abstract
The sex steroid hormone estrogen plays a number of regulatory roles in female development. During menopause, estrogen synthesis in the ovaries decreases, which results in adverse physiological remodeling and increased risk of disease. Reduced bone density, changes in the community composition profiles of the gut and vaginal microbiome, mood swings and changes in the vaginal environment are to be expected during this time. To alleviate these changes, postmenopausal women can be prescribed hormone replacement therapy (HRT) through the use of exogenous estradiol, often in conjunction with progestin treatment, which re-induces estrogenic action throughout the body. The microbiome and estrogen have a bidirectional, regulatory relationship in the gut, while in the vaginal environment estrogen works indirectly on the microbiome through restoring the vaginal tissue environment that leads to microbial homeostasis. This review discusses what is known about how the gut and vaginal microbiomes of postmenopausal women are responding to HRT, and the potential future of microbe-based therapeutics for symptoms of menopause.
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Affiliation(s)
- M I Dothard
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - S M Allard
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - J A Gilbert
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
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23
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Ecklu-Mensah G, Choo-Kang C, Gjerstad Maseng M, Donato S, Bovet P, Bedu-Addo K, Plange-Rhule J, Forrester TE, Lambert EV, Rae D, Luke A, Layden BT, O’Keefe S, Gilbert JA, Dugas LR. Gut microbiota and fecal short chain fatty acids differ with adiposity and country of origin: The METS-Microbiome Study. bioRxiv 2023:2023.03.21.533195. [PMID: 36993742 PMCID: PMC10055249 DOI: 10.1101/2023.03.21.533195] [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: 03/31/2023]
Abstract
The relationship between the gut microbiota, short chain fatty acid (SCFA) metabolism, and obesity remains unclear due to conflicting reports from studies with limited statistical power. Additionally, this association has rarely been explored in large scale diverse populations. Here, we investigated associations between fecal microbial composition, predicted metabolic potential, SCFA concentrations, and obesity in a large ( N = 1,934) adult cohort of African-origin spanning the epidemiologic transition, from Ghana, South Africa, Jamaica, Seychelles, and the United States (US). The greatest gut microbiota diversity and total fecal SCFA concentration was found in the Ghanaian population, while the lowest levels were found in the US population, respectively representing the lowest and the highest end of the epidemiologic transition spectrum. Country-specific bacterial taxa and predicted-functional pathways were observed, including an increased prevalence of Prevotella , Butyrivibrio , Weisella and Romboutsia in Ghana and South Africa, while Bacteroides and Parabacteroides were enriched in Jamaican and the US populations. Importantly, 'VANISH' taxa, including Butyricicoccus and Succinivibrio , were significantly enriched in the Ghanaian cohort, reflecting the participants' traditional lifestyles. Obesity was significantly associated with lower SCFA concentrations, a decrease in microbial richness, and dissimilarities in community composition, and reduction in the proportion of SCFA synthesizing bacteria including Oscillospira , Christensenella , Eubacterium , Alistipes , Clostridium and Odoribacter . Further, the predicted proportions of genes in the lipopolysaccharide (LPS) synthesis pathway were enriched in obese individuals, while genes associated with butyrate synthesis via the dominant pyruvate pathway were significantly reduced in obese individuals. Using machine learning, we identified features predictive of metabolic state and country of origin. Country of origin could accurately be predicted by the fecal microbiota (AUC = 0.97), whereas obesity could not be predicted as accurately (AUC = 0.65). Participant sex (AUC = 0.75), diabetes status (AUC = 0.63), hypertensive status (AUC = 0.65), and glucose status (AUC = 0.66) could all be predicted with different success. Interestingly, within country, the predictive accuracy of the microbiota for obesity was inversely correlated to the epidemiological transition, being greatest in Ghana (AUC = 0.57). Collectively, our findings reveal profound variation in the gut microbiota, inferred functional pathways, and SCFA synthesis as a function of country of origin. While obesity could be predicted accurately from the microbiota, the variation in accuracy in parallel with the epidemiological transition suggests that differences in the microbiota between obesity and non-obesity may be larger in low-to-middle countries compared to high-income countries. Further examination of independent study populations using multi-omic approaches will be necessary to determine the factors that drive this association.
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Affiliation(s)
| | - Candice Choo-Kang
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA
| | - Maria Gjerstad Maseng
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Dep. of Gastroenterology, Oslo University Hospital, Oslo, Norway
- Bio-Me, Oslo, Norway
| | - Sonya Donato
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pascal Bovet
- University Center for Primary Care and Public Health (Unisanté), Lausanne, Switzerland& Ministry of Health, Republic of Seychelles Department of Physiology, SMS
| | - Kweku Bedu-Addo
- Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Terrence E. Forrester
- Solutions for Developing Countries, University of the West Indies, Mona, Kingston, Jamaica
| | - Estelle V. Lambert
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Dale Rae
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Amy Luke
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA
| | - Brian T. Layden
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, USA
| | | | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Lara R. Dugas
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, USA
- Division of Epidemiology and Biostatistics, School of Public Health, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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24
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Sah GP, Kovalick G, Chopyk J, Kuo P, Huang L, Ghatbale P, Das P, Realegeno S, Knight R, Gilbert JA, Pride DT. Characterization of SARS-CoV-2 Distribution and Microbial Succession in a Clinical Microbiology Testing Facility during the SARS-CoV-2 Pandemic. Microbiol Spectr 2023; 11:e0450922. [PMID: 36916973 PMCID: PMC10100919 DOI: 10.1128/spectrum.04509-22] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 02/11/2023] [Indexed: 03/15/2023] Open
Abstract
The exchange of microbes between humans and the built environment is a dynamic process that has significant impact on health. Most studies exploring the microbiome of the built environment have been predicated on improving our understanding of pathogen emergence, persistence, and transmission. Previous studies have demonstrated that SARS-CoV-2 presence significantly correlates with the proportional abundance of specific bacteria on surfaces in the built environment. However, in these studies, SARS-CoV-2 originated from infected patients. Here, we perform a similar assessment for a clinical microbiology lab while staff were handling SARS-CoV-2 infected samples. The goal of this study was to understand the distribution and dynamics of microbial population on various surfaces within different sections of a clinical microbiology lab during a short period of 2020 Coronavirus disease (COVID-19) pandemic. We sampled floors, benches, and sinks in 3 sections (bacteriology, molecular microbiology, and COVID) of an active clinical microbiology lab over a 3-month period. Although floor samples harbored SARS-CoV-2, it was rarely identified on other surfaces, and bacterial diversity was significantly greater on floors than sinks and benches. The floors were primarily colonized by bacteria common to natural environments (e.g., soils), and benchtops harbored a greater proportion of human-associated microbes, including Staphylococcus and Streptococcus. Finally, we show that the microbial composition of these surfaces did not change over time and remained stable. Despite finding viruses on the floors, no lab-acquired infections were reported during the study period, which suggests that lab safety protocols and sanitation practices were sufficient to prevent pathogen exposures. IMPORTANCE For decades, diagnostic clinical laboratories have been an integral part of the health care systems that perform diagnostic tests on patient's specimens in bulk on a regular basis. Understanding their microbiota should assist in designing and implementing disinfection, and cleaning regime in more effective way. To our knowledge, there is a lack of information on the composition and dynamics of microbiota in the clinical laboratory environments, and, through this study, we have tried to fill that gap. This study has wider implications as understanding the makeup of microbes on various surfaces within clinical laboratories could help identify any pathogenic bacterial taxa that could have colonized these surfaces, and might act as a potential source of laboratory-acquired infections. Mapping the microbial community within these built environments may also be critical in assessing the reliability of laboratory safety and sanitation practices to lower any potential risk of exposures to health care workers.
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Affiliation(s)
- Govind Prasad Sah
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Grace Kovalick
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Jessica Chopyk
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Peiting Kuo
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Lina Huang
- Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Pooja Ghatbale
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Promi Das
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
| | - Susan Realegeno
- Department of Pathology, University of California San Diego, San Diego, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
- Department of Bioengineering, University of California San Diego, San Diego, California, USA
- Department of Computer Science & Engineering, University of California San Diego, San Diego, California, USA
| | - Jack A. Gilbert
- Department of Pediatrics, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
- Scripps Institution of Oceanography and Department of Pediatrics, University of California San Diego, San Diego, California, USA
| | - David T. Pride
- Department of Pathology, University of California San Diego, San Diego, California, USA
- Department of Medicine, University of California San Diego, San Diego, California, USA
- Center for Microbiome Innovation, University of California San Diego, San Diego, California, USA
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25
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Srinath A, Xie B, Li Y, Sone JY, Romanos S, Chen C, Sharma A, Polster S, Dorrestein PC, Weldon KC, DeBiasse D, Moore T, Lightle R, Koskimäki J, Zhang D, Stadnik A, Piedad K, Hagan M, Shkoukani A, Carrión-Penagos J, Bi D, Shen L, Shenkar R, Ji Y, Sidebottom A, Pamer E, Gilbert JA, Kahn ML, D'Souza M, Sulakhe D, Awad IA, Girard R. Plasma metabolites with mechanistic and clinical links to the neurovascular disease cavernous angioma. Commun Med (Lond) 2023; 3:35. [PMID: 36869161 PMCID: PMC9984539 DOI: 10.1038/s43856-023-00265-1] [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] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/20/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Cavernous angiomas (CAs) affect 0.5% of the population, predisposing to serious neurologic sequelae from brain bleeding. A leaky gut epithelium associated with a permissive gut microbiome, was identified in patients who develop CAs, favoring lipid polysaccharide producing bacterial species. Micro-ribonucleic acids along with plasma levels of proteins reflecting angiogenesis and inflammation were also previously correlated with CA and CA with symptomatic hemorrhage. METHODS The plasma metabolome of CA patients and CA patients with symptomatic hemorrhage was assessed using liquid-chromatography mass spectrometry. Differential metabolites were identified using partial least squares-discriminant analysis (p < 0.05, FDR corrected). Interactions between these metabolites and the previously established CA transcriptome, microbiome, and differential proteins were queried for mechanistic relevance. Differential metabolites in CA patients with symptomatic hemorrhage were then validated in an independent, propensity matched cohort. A machine learning-implemented, Bayesian approach was used to integrate proteins, micro-RNAs and metabolites to develop a diagnostic model for CA patients with symptomatic hemorrhage. RESULTS Here we identify plasma metabolites, including cholic acid and hypoxanthine distinguishing CA patients, while arachidonic and linoleic acids distinguish those with symptomatic hemorrhage. Plasma metabolites are linked to the permissive microbiome genes, and to previously implicated disease mechanisms. The metabolites distinguishing CA with symptomatic hemorrhage are validated in an independent propensity-matched cohort, and their integration, along with levels of circulating miRNAs, enhance the performance of plasma protein biomarkers (up to 85% sensitivity and 80% specificity). CONCLUSIONS Plasma metabolites reflect CAs and their hemorrhagic activity. A model of their multiomic integration is applicable to other pathologies.
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Affiliation(s)
- Abhinav Srinath
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Bingqing Xie
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Ying Li
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
- Department of Neurosurgery, First Affiliated Hospital of Harbin Medical University, 150001, Harbin, Heilongjiang, China
| | - Je Yeong Sone
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Sharbel Romanos
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Chang Chen
- Bioinformatics Core, Center for Research Informatics, The University of Chicago, Chicago, IL, 60637, USA
| | - Anukriti Sharma
- Department of Surgery, The University of Chicago, 5841 S. Maryland Avenue, Chicago, IL, 60637, USA
- Department of Pediatrics, The University of California San Diego and Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Sean Polster
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Pieter C Dorrestein
- Department of Pediatrics, The University of California San Diego and Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Pharmacology, The University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Kelly C Weldon
- Department of Pediatrics, The University of California San Diego and Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Dorothy DeBiasse
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Thomas Moore
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Rhonda Lightle
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Janne Koskimäki
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Dongdong Zhang
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Agnieszka Stadnik
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Kristina Piedad
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Matthew Hagan
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Abdallah Shkoukani
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Julián Carrión-Penagos
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Dehua Bi
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Le Shen
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
- Department of Surgery, The University of Chicago, 5841 S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Robert Shenkar
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
| | - Yuan Ji
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Ashley Sidebottom
- Host-Microbe Metabolomics Facility, Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Eric Pamer
- Host-Microbe Metabolomics Facility, Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Jack A Gilbert
- Department of Surgery, The University of Chicago, 5841 S. Maryland Avenue, Chicago, IL, 60637, USA
- Department of Pediatrics, The University of California San Diego and Scripps Institution of Oceanography, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Mark L Kahn
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, PA, 19104, USA
| | - Mark D'Souza
- Host-Microbe Metabolomics Facility, Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Dinanath Sulakhe
- Host-Microbe Metabolomics Facility, Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Issam A Awad
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA.
| | - Romuald Girard
- Neurovascular Surgery Program, Department of Neurological Surgery, The University of Chicago, 5841S. Maryland Avenue, Chicago, IL, 60637, USA
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Gilbert JA, Newton ILG, Reguera G. Recognizing the Contribution of Data: The Use of Companion Articles To Highlight Novel Resources in Microbiology Research. Appl Environ Microbiol 2023; 89:e0215322. [PMID: 36656005 PMCID: PMC9973031 DOI: 10.1128/aem.02153-22] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
As part of society-wide efforts to promote open access in science, the American Society for Microbiology journals are piloting the publication of companion articles highlighting rigorous data resources. The simultaneous publication of original research and data resource articles will increase awareness of, and access to, verified data sets that are critical to scientific progress. Companion articles in Microbiology Resource Announcements and two research journals, mSystems and Applied and Environmental Microbiology, will serve as an initial experiment to promote open and reproducible science.
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Affiliation(s)
- Jack A. Gilbert
- University of California, San Diego School of Medicine, La Jolla, California, USA
| | | | - Gemma Reguera
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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27
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Kodera SM, Sharma A, Martino C, Dsouza M, Grippo M, Lutz HL, Knight R, Gilbert JA, Negri C, Allard SM. Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades. Environ Microbiome 2023; 18:10. [PMID: 36805022 PMCID: PMC9938989 DOI: 10.1186/s40793-023-00470-4] [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] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Microorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013-2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention. RESULTS Examinations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality. CONCLUSIONS This study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed.
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Affiliation(s)
- Sho M Kodera
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Anukriti Sharma
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Cameron Martino
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
| | | | - Mark Grippo
- Environmental Science Division, Argonne National Laboratory, University of Chicago, Lemont, IL, USA
| | - Holly L Lutz
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Jack A Gilbert
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Cristina Negri
- Environmental Science Division, Argonne National Laboratory, University of Chicago, Lemont, IL, USA.
| | - Sarah M Allard
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
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28
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Peñalver Bernabé B, Maki PM, Cunningham JL, Eisenlohr-Moul T, Tussing-Humphreys L, Carroll IM, Meltzer-Brody S, Gilbert JA, Kimmel M. Interactions between perceived stress and microbial-host immune components: two demographically and geographically distinct pregnancy cohorts. Transl Psychiatry 2023; 13:3. [PMID: 36609477 PMCID: PMC9822983 DOI: 10.1038/s41398-022-02276-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 11/18/2022] [Accepted: 11/30/2022] [Indexed: 01/09/2023] Open
Abstract
Higher stress during pregnancy associates with negative outcomes and elevated inflammation. The gut microbiota, reflecting environment and social interactions, alongside host immune responses have the potential to better understand perceived stress and identify when stress is excessive in pregnancy. Two U.S. cohorts of 84 pregnant individuals, composed of urban women of color and suburban white women, completed the Perceived Stress Scale-10 (PSS-10) and provided fecal and blood samples at two time points. Confirmatory Factor Analysis assessed the robustness of a two-factor PSS-10 model (Emotional Distress/ED and Self-Efficacy/SE). Gut microbiota composition was measured by 16 S rRNA amplicon sequencing and the immune system activity was assessed with a panel of 21 T-cell related cytokines and chemokines. ED levels were higher in the suburban compared to the urban cohort, but levels of SE were similar. ED and SE levels were associated with distinct taxonomical signatures and the gut microbiota data improved the prediction of SE levels compared with models based on socio-demographic characteristics alone. Integration of self-reported symptoms, microbial and immune information revealed a possible mediation effect of Bacteroides uniformis between the immune system (through CXCL11) and SE. The study identified links between distinct taxonomical and immunological signatures with perceived stress. The data are congruent with a model where gut microbiome and immune factors, both impacting and reflecting factors such as close social relationships and dietary fiber, may modulate neural plasticity resulting in increased SE during pregnancy. The predictive value of these peripheral markers merit further study.
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Affiliation(s)
- Beatriz Peñalver Bernabé
- Department of Biomedical Engineering, College of Engineering and Medicine, University of Illinois Chicago, Chicago, IL, USA. .,Center of Bioinformatics and Quantitative Biology, University of Illinois Chicago, Chicago, IL, USA.
| | - Pauline M. Maki
- grid.185648.60000 0001 2175 0319Department of Psychology, College of Medicine, University of Illinois Chicago, Chicago, IL USA ,grid.185648.60000 0001 2175 0319Department of Psychiatry, College of Medicine, University of Illinois Chicago, Chicago, IL USA ,grid.185648.60000 0001 2175 0319Department of Obstetrics and Gynecology, College of Medicine, University of Illinois Chicago, Chicago, IL USA
| | - Janet L. Cunningham
- grid.8993.b0000 0004 1936 9457Department of Medical Sciences, Psychiatry, Uppsala University, Uppsala, Sweden
| | - Tory Eisenlohr-Moul
- grid.185648.60000 0001 2175 0319Department of Psychology, College of Medicine, University of Illinois Chicago, Chicago, IL USA ,grid.185648.60000 0001 2175 0319Department of Psychiatry, College of Medicine, University of Illinois Chicago, Chicago, IL USA
| | - Lisa Tussing-Humphreys
- grid.185648.60000 0001 2175 0319Department of Kinesiology and Nutrition, College of Applied Health Sciences, University of Illinois Chicago, Chicago, IL USA
| | - Ian M. Carroll
- grid.410711.20000 0001 1034 1720Department of Nutrition, School of Public Health, University of North Carolina, Chapel Hill, NC USA
| | - Samantha Meltzer-Brody
- grid.410711.20000 0001 1034 1720Department of Psychiatry, University of North Carolina, Chapel Hill, NC USA
| | - Jack A. Gilbert
- grid.266100.30000 0001 2107 4242Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA USA
| | - Mary Kimmel
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA. .,Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden.
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29
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Yang T, Tedersoo L, Soltis PS, Soltis DE, Sun M, Ma Y, Ni Y, Liu X, Fu X, Shi Y, Lin HY, Zhao YP, Fu C, Dai CC, Gilbert JA, Chu H. Plant and fungal species interactions differ between aboveground and belowground habitats in mountain forests of eastern China. Sci China Life Sci 2022; 66:1134-1150. [PMID: 36462107 DOI: 10.1007/s11427-022-2174-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/22/2022] [Indexed: 12/04/2022]
Abstract
Plant and fungal species interactions drive many essential ecosystem properties and processes; however, how these interactions differ between aboveground and belowground habitats remains unclear at large spatial scales. Here, we surveyed 494 pairwise fungal communities in leaves and soils by Illumina sequencing, which were associated with 55 woody plant species across more than 2,000-km span of mountain forests in eastern China. The relative contributions of plant, climate, soil and space to the variation of fungal communities were assessed, and the plant-fungus network topologies were inferred. Plant phylogeny was the strongest predictor for fungal community composition in leaves, accounting for 19.1% of the variation. In soils, plant phylogeny, climatic factors and soil properties explained 9.2%, 9.0% and 8.7% of the variation in soil fungal community, respectively. The plant-fungus networks in leaves exhibited significantly higher specialization, modularity and robustness (resistance to node loss), but less complicated topology (e.g., significantly lower linkage density and mean number of links) than those in soils. In addition, host/fungus preference combinations and key species, such as hubs and connectors, in bipartite networks differed strikingly between aboveground and belowground samples. The findings provide novel insights into cross-kingdom (plant-fungus) species co-occurrence at large spatial scales. The data further suggest that community shifts of trees due to climate change or human activities will impair aboveground and belowground forest fungal diversity in different ways.
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Affiliation(s)
- Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Leho Tedersoo
- Mycology and Microbiology Center, University of Tartu, Tartu, 50409, Estonia
- College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, 32611, USA
| | - Miao Sun
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuying Ma
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xu Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Fu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Han-Yang Lin
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yun-Peng Zhao
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chengxin Fu
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, 210003, China
| | - Jack A Gilbert
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, 92093, USA
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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30
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Bernabé BP, Maki PM, Dowty SM, Salas MLC, Shah Z, Gilbert JA. Correction to: Precision medicine in perinatal depression in light of the human microbiome. Psychopharmacology (Berl) 2022; 239:2367. [PMID: 35303139 DOI: 10.1007/s00213-022-06102-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Beatriz Peñalver Bernabé
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States.
| | - Pauline M Maki
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA.,Department of Psychology, University of Illinois at Chicago, Chicago, IL, USA.,Department of Obstetrics and Gynecology, University of Illinois at Chicago, Chicago, IL, USA
| | - Shannon M Dowty
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
| | - Mariana Lauren Cralle Salas
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States.,University of Massachusetts Medical School, Worcester, MA, USA
| | - Zainab Shah
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
| | - Jack A Gilbert
- Scripts Oceanographic Institute, University of California San Diego, La Jolla, CA, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
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31
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Reese TO, Bovet P, Choo-Kang C, Bedu-Addo K, Forrester T, Gilbert JA, Goedecke JH, Lambert EV, Layden BT, Micklesfield LK, Plange-Rhule J, Rae D, Viswanathan B, Luke A, Dugas LR. Utility of silhouette showcards to assess adiposity in three countries across the epidemiological transition. PLOS Glob Public Health 2022; 2:e0000127. [PMID: 36962336 PMCID: PMC10021870 DOI: 10.1371/journal.pgph.0000127] [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] [Received: 08/18/2021] [Accepted: 03/31/2022] [Indexed: 01/10/2023]
Abstract
The Pulvers' silhouette showcards provide a non-invasive and easy-to-use way of assessing an individual's body size perception using nine silhouette shapes. However, their utility across different populations has not been examined. This study aimed to assess: 1) the relationship between silhouette perception and measured anthropometrics, i.e., body mass index (BMI), waist circumference (WC), waist-height-ratio (WHtR), and 2) the ability to predict with silhouette showcards anthropometric adiposity measures, i.e., overweight and obesity (BMI ≥ 25 kg/m2), obesity alone (BMI ≥ 30 kg/m2), elevated WC (men ≥ 94 cm; women ≥ 80 cm), and WHtR (> 0.5) across the epidemiological transition. 751 African-origin participants, aged 20-68 years old, from the United States (US), Seychelles, and Ghana, completed anthropometrics and selected silhouettes corresponding to their perceived body size. Silhouette performance to anthropometrics was examined using a least-squares linear regression model. A receiver operator curve (ROC) was used to investigate the showcards ability to predict anthropometric adiposity measures. The relationship between silhouette ranking and BMI were similar between sexes of the same country but differed between countries: 3.65 [95% CI: 3.34-3.97] BMI units/silhouette unit in the US, 3.23 [2.93-3.74] in Seychelles, and 1.99 [1.72-2.26] in Ghana. Different silhouette cutoffs predicted obesity differently in the three countries. For example, a silhouette ≥ five had a sensitivity/specificity of 77.3%/90.6% to predict BMI ≥ 25 kg/m2 in the US, but 77.8%/85.9% in Seychelles and 84.9%/71.4% in Ghana. Ultimately, silhouettes predicted BMI, WC, and WHtR similarly within each country and sex but not across countries. Our data suggest that Pulvers' silhouette showcards may be a helpful tool to predict anthropometric and adiposity measures in different populations when direct measurement cannot be performed. However, no universal silhouette cutoff can be used for detecting overweight or obesity status, and population-specific differences may stress the need to calibrate silhouette showcards when using them as a survey tool in different countries.
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Affiliation(s)
- Tyler O. Reese
- Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, United States of America
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Pascal Bovet
- Unit for Prevention and Control of Cardiovascular Disease, Ministry of Health, Victoria, Republic of Seychelles
- University Center for Primary Care and Public Health, Lausanne, Switzerland
| | - Candice Choo-Kang
- Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Kweku Bedu-Addo
- Department of Physiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Terrence Forrester
- Solutions for Developing Countries, University of the West Indies, Mona, Kingston, Jamaica
| | - Jack A. Gilbert
- Department of Surgery, Microbiome Center, University of Chicago, Chicago, Illinois, United States of America
| | - Julia H. Goedecke
- Division of Exercise Science and Sports Medicine, Department of Human Biology, Research Centre for Health through Physical Activity, Lifestyle and Sport, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Non-Communicable Diseases Research Unit, South African Medical Research Council, Cape Town, South Africa
| | - Estelle V. Lambert
- Department of Surgery, Microbiome Center, University of Chicago, Chicago, Illinois, United States of America
| | - Brian T. Layden
- Division of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, United States of America
| | - Lisa K. Micklesfield
- Division of Exercise Science and Sports Medicine, Department of Human Biology, Research Centre for Health through Physical Activity, Lifestyle and Sport, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- SAMRC/Wits Developmental Pathways for Health Research Unit, Department of Pediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jacob Plange-Rhule
- Department of Physiology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Dale Rae
- Division of Exercise Science and Sports Medicine, Department of Human Biology, Research Centre for Health through Physical Activity, Lifestyle and Sport, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Bharathi Viswanathan
- Unit for Prevention and Control of Cardiovascular Disease, Ministry of Health, Victoria, Republic of Seychelles
| | - Amy Luke
- Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, Illinois, United States of America
| | - Lara R. Dugas
- Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, Illinois, United States of America
- Division of Exercise Science and Sports Medicine, Department of Human Biology, Research Centre for Health through Physical Activity, Lifestyle and Sport, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight R. Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy. mSystems 2022; 7:e0016722. [PMID: 35369727 PMCID: PMC9040630 DOI: 10.1128/msystems.00167-22] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 02/19/2022] [Accepted: 02/25/2022] [Indexed: 02/06/2023] Open
Abstract
We introduce the operational genomic unit (OGU) method, a metagenome analysis strategy that directly exploits sequence alignment hits to individual reference genomes as the minimum unit for assessing the diversity of microbial communities and their relevance to environmental factors. This approach is independent of taxonomic classification, granting the possibility of maximal resolution of community composition, and organizes features into an accurate hierarchy using a phylogenomic tree. The outputs are suitable for contemporary analytical protocols for community ecology, differential abundance, and supervised learning while supporting phylogenetic methods, such as UniFrac and phylofactorization, that are seldom applied to shotgun metagenomics despite being prevalent in 16S rRNA gene amplicon studies. As demonstrated in two real-world case studies, the OGU method produces biologically meaningful patterns from microbiome data sets. Such patterns further remain detectable at very low metagenomic sequencing depths. Compared with taxonomic unit-based analyses implemented in currently adopted metagenomics tools, and the analysis of 16S rRNA gene amplicon sequence variants, this method shows superiority in informing biologically relevant insights, including stronger correlation with body environment and host sex on the Human Microbiome Project data set and more accurate prediction of human age by the gut microbiomes of Finnish individuals included in the FINRISK 2002 cohort. We provide Woltka, a bioinformatics tool to implement this method, with full integration with the QIIME 2 package and the Qiita web platform, to facilitate adoption of the OGU method in future metagenomics studies. IMPORTANCE Shotgun metagenomics is a powerful, yet computationally challenging, technique compared to 16S rRNA gene amplicon sequencing for decoding the composition and structure of microbial communities. Current analyses of metagenomic data are primarily based on taxonomic classification, which is limited in feature resolution. To solve these challenges, we introduce operational genomic units (OGUs), which are the individual reference genomes derived from sequence alignment results, without further assigning them taxonomy. The OGU method advances current read-based metagenomics in two dimensions: (i) providing maximal resolution of community composition and (ii) permitting use of phylogeny-aware tools. Our analysis of real-world data sets shows that it is advantageous over currently adopted metagenomic analysis methods and the finest-grained 16S rRNA analysis methods in predicting biological traits. We thus propose the adoption of OGUs as an effective practice in metagenomic studies.
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Affiliation(s)
- Qiyun Zhu
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona, USA
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, China
| | - Antonio Gonzalez
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Imran McGrath
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Niina Haiminen
- IBM T. J. Watson Research Center, Yorktown Heights, New York, USA
| | - George Armstrong
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, California, USA
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Julian Yu
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, Arizona, USA
| | | | | | - Austin D. Swafford
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Promi Das
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Justin P. Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Franck Lejzerowicz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Aki S. Havulinna
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Guillaume Méric
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Teemu Niiranen
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
- Department of Internal Medicine, University of Turku, Turku, Finland
- Division of Medicine, Turku University Hospital, Finland
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Veikko Salomaa
- Department of Public Health and Welfare, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Ho-Cheol Kim
- IBM Almaden Research Center, San Jose, California, USA
| | - Mohit Jain
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Public Health and Primary Care, Cambridge University, Cambridge, United Kingdom
| | - Jack A. Gilbert
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
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Kodera SM, Das P, Gilbert JA, Lutz HL. Conceptual strategies for characterizing interactions in microbial communities. iScience 2022; 25:103775. [PMID: 35146390 PMCID: PMC8819398 DOI: 10.1016/j.isci.2022.103775] [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] [Indexed: 11/17/2022] Open
Abstract
Understanding the sets of inter- and intraspecies interactions in microbial communities is a fundamental goal of microbial ecology. However, the study and quantification of microbial interactions pose several challenges owing to their complexity, dynamic nature, and the sheer number of unique interactions within a typical community. To overcome such challenges, microbial ecologists must rely on various approaches to distill the system of study to a functional and conceptualizable level, allowing for a practical understanding of microbial interactions in both simplified and complex systems. This review broadly addresses the role of several conceptual approaches available for the microbial ecologist’s arsenal, examines specific tools used to accomplish such approaches, and describes how the assumptions, expectations, and philosophies underlying these tools change across scales of complexity.
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Affiliation(s)
- Sho M Kodera
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Promi Das
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Jack A Gilbert
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Holly L Lutz
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA.,Negaunee Integrative Collections Center, Field Museum of Natural History, Chicago, IL 60605, USA
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34
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Dodiya HB, Lutz HL, Weigle IQ, Patel P, Michalkiewicz J, Roman-Santiago CJ, Zhang CM, Liang Y, Srinath A, Zhang X, Xia J, Olszewski M, Zhang X, Schipma MJ, Chang EB, Tanzi RE, Gilbert JA, Sisodia SS. Gut microbiota-driven brain Aβ amyloidosis in mice requires microglia. J Exp Med 2022; 219:e20200895. [PMID: 34854884 PMCID: PMC8647415 DOI: 10.1084/jem.20200895] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [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: 05/05/2020] [Revised: 08/16/2021] [Accepted: 10/14/2021] [Indexed: 12/25/2022] Open
Abstract
We previously demonstrated that lifelong antibiotic (ABX) perturbations of the gut microbiome in male APPPS1-21 mice lead to reductions in amyloid β (Aβ) plaque pathology and altered phenotypes of plaque-associated microglia. Here, we show that a short, 7-d treatment of preweaned male mice with high-dose ABX is associated with reductions of Aβ amyloidosis, plaque-localized microglia morphologies, and Aβ-associated degenerative changes at 9 wk of age in male mice only. More importantly, fecal microbiota transplantation (FMT) from transgenic (Tg) or WT male donors into ABX-treated male mice completely restored Aβ amyloidosis, plaque-localized microglia morphologies, and Aβ-associated degenerative changes. Transcriptomic studies revealed significant differences between vehicle versus ABX-treated male mice and FMT from Tg mice into ABX-treated mice largely restored the transcriptome profiles to that of the Tg donor animals. Finally, colony-stimulating factor 1 receptor (CSF1R) inhibitor-mediated depletion of microglia in ABX-treated male mice failed to reduce cerebral Aβ amyloidosis. Thus, microglia play a critical role in driving gut microbiome-mediated alterations of cerebral Aβ deposition.
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Affiliation(s)
- Hemraj B. Dodiya
- Department of Neurobiology, The University of Chicago, Chicago, IL
| | - Holly L. Lutz
- Department of Pediatrics and Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA
| | - Ian Q. Weigle
- Department of Neurobiology, The University of Chicago, Chicago, IL
| | - Priyam Patel
- Center for Genetic Medicine, Northwestern University, Chicago, IL
| | | | | | | | - Yingxia Liang
- Department of Neurology, Harvard Medical School, Boston, MA
| | - Abhinav Srinath
- Department of Neurobiology, The University of Chicago, Chicago, IL
| | - Xulun Zhang
- Department of Neurobiology, The University of Chicago, Chicago, IL
| | - Jessica Xia
- Department of Neurobiology, The University of Chicago, Chicago, IL
| | - Monica Olszewski
- Department of Neurobiology, The University of Chicago, Chicago, IL
| | - Xiaoqiong Zhang
- Department of Neurobiology, The University of Chicago, Chicago, IL
| | | | - Eugene B. Chang
- Department of Digestive Diseases, The University of Chicago, Chicago, IL
| | | | - Jack A. Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA
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35
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Fei N, Choo-Kang C, Reutrakul S, Crowley SJ, Rae D, Bedu-Addo K, Plange-Rhule J, Forrester TE, Lambert EV, Bovet P, Riesen W, Korte W, Luke A, Layden BT, Gilbert JA, Dugas LR. Gut microbiota alterations in response to sleep length among African-origin adults. PLoS One 2021; 16:e0255323. [PMID: 34495955 PMCID: PMC8425534 DOI: 10.1371/journal.pone.0255323] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/14/2021] [Indexed: 12/15/2022] Open
Abstract
Sleep disorders are increasingly being characterized in modern society as contributing to a host of serious medical problems, including obesity and metabolic syndrome. Changes to the microbial community in the human gut have been reportedly associated with many of these cardiometabolic outcomes. In this study, we investigated the impact of sleep length on the gut microbiota in a large cohort of 655 participants of African descent, aged 25-45, from Ghana, South Africa (SA), Jamaica, and the United States (US). The sleep duration was self-reported via a questionnaire. Participants were classified into 3 sleep groups: short (<7hrs), normal (7-<9hrs), and long (≥9hrs). Forty-seven percent of US participants were classified as short sleepers and 88% of SA participants as long sleepers. Gut microbial composition analysis (16S rRNA gene sequencing) revealed that bacterial alpha diversity negatively correlated with sleep length (p<0.05). Furthermore, sleep length significantly contributed to the inter-individual beta diversity dissimilarity in gut microbial composition (p<0.01). Participants with both short and long-sleep durations exhibited significantly higher abundances of several taxonomic features, compared to normal sleep duration participants. The predicted relative proportion of two genes involved in the butyrate synthesis via lysine pathway were enriched in short sleep duration participants. Finally, co-occurrence relationships revealed by network analysis showed unique interactions among the short, normal and long duration sleepers. These results suggest that sleep length in humans may alter gut microbiota by driving population shifts of the whole microbiota and also specific changes in Exact Sequence Variants abundance, which may have implications for chronic inflammation associated diseases. The current findings suggest a possible relationship between disrupted sleep patterns and the composition of the gut microbiota. Prospective investigations in larger and more prolonged sleep researches and causally experimental studies are needed to confirm these findings, investigate the underlying mechanism and determine whether improving microbial homeostasis may buffer against sleep-related health decline in humans.
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Affiliation(s)
- Na Fei
- Microbiome Center, Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Candice Choo-Kang
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, United States of America
| | - Sirimon Reutrakul
- Department of Psychiatry & Behavioral Sciences, Biological Rhythms Research Laboratory, Rush University Medical Center, Chicago, IL, United States of America
| | - Stephanie J. Crowley
- Department of Psychiatry & Behavioral Sciences, Biological Rhythms Research Laboratory, Rush University Medical Center, Chicago, IL, United States of America
| | - Dale Rae
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Kweku Bedu-Addo
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Jacob Plange-Rhule
- Research Unit for Exercise Science and Sports Medicine, University of Cape Town, Cape Town, South Africa
| | - Terrence E. Forrester
- Solutions for Developing Countries, University of the West Indies, Mona, Kingston, Jamaica
| | - Estelle V. Lambert
- Department of Physiology, School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Pascal Bovet
- University Center for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
- Ministry of Health, Victoria, Republic of Seychelles
| | - Walter Riesen
- University Center for Primary Care and Public Health (Unisanté), Lausanne, Switzerland
- Ministry of Health, Victoria, Republic of Seychelles
| | - Wolfgang Korte
- Center for Laboratory Medicine, Canton Hospital, St. Gallen, Switzerland
| | - Amy Luke
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, United States of America
| | - Brian T. Layden
- Department of Psychiatry & Behavioral Sciences, Biological Rhythms Research Laboratory, Rush University Medical Center, Chicago, IL, United States of America
- Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois, United States of America
| | - Jack A. Gilbert
- University of California San Diego, San Diego, California, United States of America
| | - Lara R. Dugas
- Public Health Sciences, Parkinson School of Health Sciences and Public Health, Loyola University Chicago, Maywood, IL, United States of America
- Division of Epidemiology & Biostatistics, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa
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Ozen S, Lutz HL, Rivera VM, Reiff A, Batu ED, Anderson E, Salas Garcia M, Aldrovandi G, Akbaba TH, Pazarbasi İ, Bilginer Y, Balat A, Balci-Peynircioglu B, Gilbert JA, Dedeoglu F, Hausmann JS. Microbiome is not linked to clinical disease severity of familial Mediterranean fever in an international cohort of children. Clin Exp Rheumatol 2021; 39 Suppl 132:102-108. [PMID: 34251310 DOI: 10.55563/clinexprheumatol/olvbyd] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/01/2021] [Indexed: 11/13/2022]
Abstract
OBJECTIVES The severity of familial Mediterranean fever (FMF) may vary in different areas, suggesting a role for environmental factors. We analysed the composition of gut microbiota among children with FMF and healthy controls from Turkey and the USA and determined its effect on disease severity. METHODS Children with FMF with pathogenic MEFV mutations and healthy controls from Turkey and the USA were enrolled. FMF disease activity was evaluated with the Autoinflammatory Disease Activity Index (AIDAI). Gut bacterial diversity was assessed by sequencing 16S rRNA gene libraries. RESULTS We included 36 children from Turkey (28 patients with FMF, 8 healthy controls), and 21 patients and 6 controls from the USA. In the Turkish group, 28.6% of patients had severe disease, while 13.3% of US group patients had severe disease. As expected, we observed substantial differences between the gut microbiota of children from the two geographic regions, with Turkish patients and controls exhibiting higher relative abundances of Bacteriodia, while US patients and controls exhibited higher relative abundances of Clostridia. Alpha- and betadiversity did not differ significantly between FMF patients and controls, and neither was predictive of disease severity within each geographic region. We observed differences between FMF patients and controls in the relative abundance of some bacterial taxa at the amplicon sequence variant (ASV) level, but these differences received mixed statistical support. CONCLUSIONS Among an international cohort of children with FMF, we did not find a strong effect of gut microbiota composition on disease severity. Other environmental or epigenetic factors may be operative.
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Affiliation(s)
- Seza Ozen
- Department of Paediatric Rheumatology, Hacettepe University Faculty of Medicine in Ankara, Turkey.
| | - Holly L Lutz
- Department of Paediatrics, University of California San Diego, La Jolla, CA, and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | | | - Andreas Reiff
- Division of Rheumatology at CHLA, Los Angeles, CA, USA
| | - Ezgi Deniz Batu
- Department of Paediatric Rheumatology, Hacettepe University Faculty of Medicine in Ankara, Turkey
| | - Edwin Anderson
- Program in Rheumatology, Division of Immunology, Boston Children's Hospital, Boston, MA, USA
| | - Mariana Salas Garcia
- Department of Paediatrics, University of California San Diego, La Jolla, CA, and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, and Division of Rheumatology at CHLA, Los Angeles, CA, USA
| | | | | | - İlker Pazarbasi
- Department of Nutrition and Dietetics, Hacettepe University, Ankara, Turkey
| | - Yelda Bilginer
- Department of Paediatric Rheumatology, Hacettepe University Faculty of Medicine in Ankara, Turkey
| | - Ayse Balat
- Division of Nephrology and Rheumatology, Istanbul Aydin University, Istanbul, Turkey
| | | | - Jack A Gilbert
- Department of Paediatrics, University of California San Diego, La Jolla, CA, and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, and Division of Rheumatology at CHLA, Los Angeles, CA, USA
| | - Fatma Dedeoglu
- Program in Rheumatology, Division of Immunology, Boston Children's Hospital, Boston, MA, USA
| | - Jonathan S Hausmann
- Program in Rheumatology, Division of Immunology, Boston Children's Hospital, Boston, MA, and Division of Rheumatology and Clinical Immunology, Beth Israel Deaconess Medical Center, Boston, MA, USA
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Khan R, Yee AL, Gilbert JA, Haider A, Jamal SB, Muhammad F. Triclosan-containing sutures: safety and resistance issues need to be addressed prior to generalized use. Appl Nanosci 2021. [DOI: 10.1007/s13204-021-01979-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Grieneisen L, Dasari M, Gould TJ, Björk JR, Grenier JC, Yotova V, Jansen D, Gottel N, Gordon JB, Learn NH, Gesquiere LR, Wango TL, Mututua RS, Warutere JK, Siodi L, Gilbert JA, Barreiro LB, Alberts SC, Tung J, Archie EA, Blekhman R. Gut microbiome heritability is nearly universal but environmentally contingent. Science 2021; 373:181-186. [PMID: 34244407 DOI: 10.1126/science.aba5483] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 01/25/2021] [Accepted: 05/17/2021] [Indexed: 12/31/2022]
Abstract
Relatives have more similar gut microbiomes than nonrelatives, but the degree to which this similarity results from shared genotypes versus shared environments has been controversial. Here, we leveraged 16,234 gut microbiome profiles, collected over 14 years from 585 wild baboons, to reveal that host genetic effects on the gut microbiome are nearly universal. Controlling for diet, age, and socioecological variation, 97% of microbiome phenotypes were significantly heritable, including several reported as heritable in humans. Heritability was typically low (mean = 0.068) but was systematically greater in the dry season, with low diet diversity, and in older hosts. We show that longitudinal profiles and large sample sizes are crucial to quantifying microbiome heritability, and indicate scope for selection on microbiome characteristics as a host phenotype.
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Affiliation(s)
- Laura Grieneisen
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Mauna Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Trevor J Gould
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Johannes R Björk
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jean-Christophe Grenier
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada.,Research Center, Montreal Heart Institute, Montréal, Quebec H1T 1C8, Canada
| | - Vania Yotova
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada
| | - David Jansen
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Neil Gottel
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Jacob B Gordon
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Niki H Learn
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | | | - Tim L Wango
- Amboseli Baboon Research Project, Amboseli National Park, Kenya.,The Department of Veterinary Anatomy and Animal Physiology, University of Nairobi, Kenya
| | | | | | - Long'ida Siodi
- Amboseli Baboon Research Project, Amboseli National Park, Kenya
| | - Jack A Gilbert
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte Justine Research Center, Montréal, Quebec H3T 1C5, Canada.,Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Susan C Alberts
- Department of Biology, Duke University, Durham, NC 27708, USA.,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Duke Population Research Institute, Duke University, Durham, NC 27708, USA
| | - Jenny Tung
- Department of Biology, Duke University, Durham, NC 27708, USA. .,Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.,Duke Population Research Institute, Duke University, Durham, NC 27708, USA.,Canadian Institute for Advanced Research, Toronto, Ontario M5G 1M1, Canada
| | - Elizabeth A Archie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Ran Blekhman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA. .,Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, MN 55455, USA
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39
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Lutz HL, Gilbert JA, Dick CW. Associations between Afrotropical bats, eukaryotic parasites, and microbial symbionts. Mol Ecol 2021; 31:1939-1950. [PMID: 34181795 PMCID: PMC9546020 DOI: 10.1111/mec.16044] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 05/06/2021] [Accepted: 06/16/2021] [Indexed: 01/06/2023]
Abstract
Skin is the largest mammalian organ and the first defensive barrier against the external environment. The skin and fur of mammals can host a wide variety of ectoparasites, many of which are phylogenetically diverse, specialized, and specifically adapted to their hosts. Among hematophagous dipteran parasites, volatile organic compounds (VOCs) are known to serve as important attractants, leading parasites to compatible sources of blood meals. VOCs have been hypothesized to be mediated by host‐associated bacteria, which may thereby indirectly influence parasitism. Host‐associated bacteria may also influence parasitism directly, as has been observed in interactions between animal gut microbiota and malarial parasites. Hypotheses relating bacterial symbionts and eukaryotic parasitism have rarely been tested among humans and domestic animals, and to our knowledge have not been tested in wild vertebrates. In this study, we used Afrotropical bats, hematophagous ectoparasitic bat flies, and haemosporidian (malarial) parasites vectored by bat flies as a model to test the hypothesis that the vertebrate host microbiome is linked to parasitism in a wild system. We identified significant correlations between bacterial community composition of the skin and dipteran ectoparasite prevalence across four major bat lineages, as well as striking differences in skin microbial network characteristics between ectoparasitized and nonectoparasitized bats. We also identified links between the oral microbiome and presence of malarial parasites among miniopterid bats. Our results support the hypothesis that microbial symbionts may serve as indirect mediators of parasitism among eukaryotic hosts and parasites. see also the Perspective by Kelly A. Speer
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Affiliation(s)
- Holly L Lutz
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.,Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Jack A Gilbert
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Carl W Dick
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA.,Department of Biology, Western Kentucky University, Bowling Green, KY, USA
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40
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Yang K, Hou Y, Zhang Y, Liang H, Sharma A, Zheng W, Wang L, Torres R, Tatebe K, Chmura SJ, Pitroda SP, Gilbert JA, Fu YX, Weichselbaum RR. Suppression of local type I interferon by gut microbiota-derived butyrate impairs antitumor effects of ionizing radiation. J Exp Med 2021; 218:e20201915. [PMID: 33496784 PMCID: PMC7844434 DOI: 10.1084/jem.20201915] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [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: 09/03/2020] [Revised: 11/02/2020] [Accepted: 12/09/2020] [Indexed: 12/27/2022] Open
Abstract
The antitumor effects of ionizing radiation (IR) are mediated in part through activation of innate and adaptive immunity. Here we report that gut microbiota influences tumor control following IR. Vancomycin decreased the abundance of butyrate-producing gut bacteria and enhanced antitumor responses to IR. Oral administration of Lachnospiraceae, a family of vancomycin-sensitive bacteria, was associated with increased systemic and intratumoral butyric acid levels and impaired the efficacy of IR in germ-free (GF) mice. Local butyrate inhibited STING-activated type I IFN expression in dendritic cells (DCs) through blockade of TBK1 and IRF3 phosphorylation, which abrogated IR-induced tumor-specific cytotoxic T cell immune responses without directly protecting tumor cells from radiation. Our findings demonstrate that the selective targeting of butyrate-producing microbiota may provide a novel therapeutic option to enhance tumor radiation sensitivity.
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Affiliation(s)
- Kaiting Yang
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL
- The Ludwig Center for Metastasis Research, University of Chicago, Chicago, IL
| | - Yuzhu Hou
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL
- The Ludwig Center for Metastasis Research, University of Chicago, Chicago, IL
| | - Yuan Zhang
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL
- The Ludwig Center for Metastasis Research, University of Chicago, Chicago, IL
| | - Hua Liang
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL
- The Ludwig Center for Metastasis Research, University of Chicago, Chicago, IL
| | - Anukriti Sharma
- Department of Pediatrics, University of California, San Diego, La Jolla, CA
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA
| | - Wenxin Zheng
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL
- The Ludwig Center for Metastasis Research, University of Chicago, Chicago, IL
| | - Liangliang Wang
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL
- The Ludwig Center for Metastasis Research, University of Chicago, Chicago, IL
| | - Rolando Torres
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL
| | - Ken Tatebe
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL
| | - Steven J. Chmura
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL
| | - Sean P. Pitroda
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL
- The Ludwig Center for Metastasis Research, University of Chicago, Chicago, IL
| | - Jack A. Gilbert
- Department of Pediatrics, University of California, San Diego, La Jolla, CA
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA
| | - Yang-Xin Fu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Ralph R. Weichselbaum
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL
- The Ludwig Center for Metastasis Research, University of Chicago, Chicago, IL
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41
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Xu Y, Tandon R, Ancheta C, Arroyo P, Gilbert JA, Stephens B, Kelley ST. Quantitative profiling of built environment bacterial and fungal communities reveals dynamic material dependent growth patterns and microbial interactions. Indoor Air 2021; 31:188-205. [PMID: 32757488 DOI: 10.1111/ina.12727] [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: 04/26/2020] [Revised: 07/01/2020] [Accepted: 07/29/2020] [Indexed: 06/11/2023]
Abstract
Indoor microbial communities vary in composition and diversity depending on material type, moisture levels, and occupancy. In this study, we integrated bacterial cell counting, fungal biomass estimation, and fluorescence-assisted cell sorting (FACS) with amplicon sequencing of bacterial (16S rRNA) and fungal (ITS) communities to investigate the influence of wetting on medium density fiberboard (MDF) and gypsum wallboard. Surface samples were collected longitudinally from wetted materials maintained at high relative humidity (~95%). Bacterial and fungal growth patterns were strongly time-dependent and material-specific. Fungal growth phenotypes differed between materials: spores dominated MDF surfaces while fungi transitioned from spores to hyphae on gypsum. FACS confirmed that most of the bacterial cells were intact (viable) on both materials over the course of the study. Integrated cell count and biomass data (quantitative profiling) revealed that small changes in relative abundance often resulted from large changes in absolute abundance, while negative correlations in relative abundances were explained by rapid growth of only one group of bacteria or fungi. Comparisons of bacterial-bacterial and fungal-bacterial networks suggested a top-down control of fungi on bacterial growth, possibly via antibiotic production. In conclusion, quantitative profiling provides novel insights into microbial growth dynamics on building materials with potential implications for human health.
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Affiliation(s)
- Ying Xu
- Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA
| | - Ruby Tandon
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Chrislyn Ancheta
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Pablo Arroyo
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Brent Stephens
- Department of Civil, Architectural, and Environmental Engineering, Illinois Institute of Technology, Chicago, IL, USA
| | - Scott T Kelley
- Graduate Program in Bioinformatics and Medical Informatics, San Diego State University, San Diego, CA, USA
- Department of Biology, San Diego State University, San Diego, CA, USA
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42
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Davis BT, Islam MB, Das P, Gilbert JA, Ho KJ, Schwulst SJ. Differential Fecal Microbiome Dysbiosis after Equivalent Traumatic Brain Injury in Aged Versus Young Adult Mice. J Exp Neurol 2021; 2:120-130. [PMID: 34825244 PMCID: PMC8612634 DOI: 10.33696/neurol.2.044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Traumatic brain injury (TBI) has a bimodal age distribution with peak incidence at age 24 and age 65 with worse outcomes developing in aged populations. Few studies have specifically addressed age at the time of injury as an independent biologic variable in TBI-associated secondary pathology. Within the framework of our published work, identifying age related effects of TBI on neuropathology, cognition, memory and motor function we analyzed fecal pellets collected from young and aged TBI animals to assess for age-induced effects in TBI induced dysbiosis. In this follow up, work we hypothesized increased dysbiosis after TBI in aged (80-week-old, N=10) versus young (14-week-old, N=10) mice. C57BL/6 males received a sham incision or TBI via open-head controlled cortical impact. Fresh stool pellets were collected 1-day pre-TBI, then 1, 7, and 28-days post-TBI for 16S rRNA gene sequencing and taxonomic analysis. Data revealed an age induced increase in disease associated microbial species which were exacerbated by injury. Consistent with our hypothesis, aged mice demonstrated a high number of disease associated changes to the gut microbiome pre- and post-injury. Our data suggest divergent microbiome phenotypes in injury between young and aged reflecting a previously unknown interaction between age, TBI, and the gut-brain axis implying the need for different treatment strategies.
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Affiliation(s)
- Booker T Davis
- Department of Surgery, Division of Trauma and Critical Care; Northwestern University, Chicago Il, USA
| | - Mecca B.A.R. Islam
- Department of Surgery, Division of Trauma and Critical Care; Northwestern University, Chicago Il, USA
| | - Promi Das
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Jack A Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Karen J. Ho
- Department of Surgery, Division of Vascular Surgery, Northwestern University, Chicago Il, USA
| | - Steven J. Schwulst
- Department of Surgery, Division of Trauma and Critical Care; Northwestern University, Chicago Il, USA
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43
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Lutz H, Vangelatos A, Gottel N, Osculati A, Visona S, Finley SJ, Gilbert JA, Javan GT. Effects of Extended Postmortem Interval on Microbial Communities in Organs of the Human Cadaver. Front Microbiol 2020; 11:569630. [PMID: 33363519 PMCID: PMC7752770 DOI: 10.3389/fmicb.2020.569630] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [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: 06/04/2020] [Accepted: 11/16/2020] [Indexed: 12/20/2022] Open
Abstract
Human thanatomicrobiota studies have shown that microorganisms inhabit and proliferate externally and internally throughout the body and are the primary mediators of putrefaction after death. Yet little is known about the source and diversity of the thanatomicrobiome or the underlying factors leading to delayed decomposition exhibited by reproductive organs. The use of the V4 hypervariable region of bacterial 16S rRNA gene sequences for taxonomic classification ("barcoding") and phylogenetic analyses of human postmortem microbiota has recently emerged as a possible tool in forensic microbiology. The goal of this study was to apply a 16S rRNA barcoding approach to investigate variation among different organs, as well as the extent to which microbial associations among different body organs in human cadavers can be used to predict forensically important determinations, such as cause and time of death. We assessed microbiota of organ tissues including brain, heart, liver, spleen, prostate, and uterus collected at autopsy from criminal casework of 40 Italian cadavers with times of death ranging from 24 to 432 h. Both the uterus and prostate had a significantly higher alpha diversity compared to other anatomical sites, and exhibited a significantly different microbial community composition from non-reproductive organs, which we found to be dominated by the bacterial orders MLE1-12, Saprospirales, and Burkholderiales. In contrast, reproductive organs were dominated by Clostridiales, Lactobacillales, and showed a marked decrease in relative abundance of MLE1-12. These results provide insight into the observation that the uterus and prostate are the last internal organs to decay during human decomposition. We conclude that distinct community profiles of reproductive versus non-reproductive organs may help guide the application of forensic microbiology tools to investigations of human cadavers.
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Affiliation(s)
- Holly Lutz
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | | | - Neil Gottel
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Antonio Osculati
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Silvia Visona
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Sheree J Finley
- Physical Sciences Department, Forensic Science Programs, Alabama State University, Montgomery, AL, United States
| | - Jack A Gilbert
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Gulnaz T Javan
- Physical Sciences Department, Forensic Science Programs, Alabama State University, Montgomery, AL, United States
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44
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Dodiya HB, Lutz H, Weigle I, Roman‐Santiago C, Patel P, Olszewski M, Zhang C, Zhang X, Schipma MJ, Tanzi RE, Gilbert JA, Sisodia SS. Gut microbiome perturbations influence brain amyloidosis only in the presence of microglia in APPPS1‐21 mice. Alzheimers Dement 2020. [DOI: 10.1002/alz.040609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Holy Lutz
- University of California San Diego San Diego CA USA
| | - Ian Weigle
- The University of Chicago Chicago IL USA
| | | | | | | | - Can Zhang
- Harvard Medical School Boston MA USA
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45
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Li HY, Wang H, Wang HT, Xin PY, Xu XH, Ma Y, Liu WP, Teng CY, Jiang CL, Lou LP, Arnold W, Cralle L, Zhu YG, Chu JF, Gilbert JA, Zhang ZJ. Correction to: The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales. Microbiome 2020; 8:169. [PMID: 33248461 PMCID: PMC7697363 DOI: 10.1186/s40168-020-00945-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
An amendment to this paper has been published and can be accessed via the original article.
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Affiliation(s)
- Hong-Yi Li
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058, China
| | - Hang Wang
- National Plateau Wetlands Research Center, Southwest Forestry University, 300 Bailongsi, Kunming, 650224, China
| | - Hai-Tao Wang
- The Microbiome Center, Biosciences Division, Argonne National Laboratory, Lemont, IL, 60439, USA
- Department of Surgery, University of Chicago, 5640 South Ellis Avenue, Chicago, IL, 60637, USA
| | - Pei-Yong Xin
- National Center of Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Xin-Hua Xu
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058, China
| | - Yun Ma
- College of Biological and Environmental Engineering, Zhejiang University of Technology, 18 Chaowang Ave, Hangzhou, 310014, China
| | - Wei-Ping Liu
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058, China
| | - Chang-Yun Teng
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058, China
- Hangzhou Gusheng Agricultural Technology Company Limited, Chongxian Innovation Industrial Park, Chongxian Ave, Hangzhou, 311108, China
| | - Cheng-Liang Jiang
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058, China
- Hangzhou Gusheng Agricultural Technology Company Limited, Chongxian Innovation Industrial Park, Chongxian Ave, Hangzhou, 311108, China
| | - Li-Ping Lou
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058, China
| | - Wyatt Arnold
- The Microbiome Center, Biosciences Division, Argonne National Laboratory, Lemont, IL, 60439, USA
- Department of Surgery, University of Chicago, 5640 South Ellis Avenue, Chicago, IL, 60637, USA
| | - Lauren Cralle
- The Microbiome Center, Biosciences Division, Argonne National Laboratory, Lemont, IL, 60439, USA
- Department of Surgery, University of Chicago, 5640 South Ellis Avenue, Chicago, IL, 60637, USA
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Ave, Xiamen, 361021, China
| | - Jin-Fang Chu
- National Center of Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Jack A Gilbert
- The Microbiome Center, Biosciences Division, Argonne National Laboratory, Lemont, IL, 60439, USA.
- Department of Surgery, University of Chicago, 5640 South Ellis Avenue, Chicago, IL, 60637, USA.
| | - Zhi-Jian Zhang
- College of Environment and Natural Resource Sciences, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058, China.
- Hangzhou Gusheng Agricultural Technology Company Limited, Chongxian Innovation Industrial Park, Chongxian Ave, Hangzhou, 311108, China.
- China Academy of West Region Development, Zhejiang University, 866 Yuhangtang Ave, Hangzhou, 310058, China.
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46
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Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Garcia MCS, Chiang LY, Salido RA, Shaffer JP, Bryant M, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert JA, Sweeney DA, Allard SM. Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment. medRxiv 2020:2020.11.19.20234229. [PMID: 33236030 PMCID: PMC7685343 DOI: 10.1101/2020.11.19.20234229] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Synergistic effects of bacteria on viral stability and transmission are widely documented but remain unclear in the context of SARS-CoV-2. We collected 972 samples from hospitalized ICU patients with coronavirus disease 2019 (COVID-19), their health care providers, and hospital surfaces before, during, and after admission. We screened for SARS-CoV-2 using RT-qPCR, characterized microbial communities using 16S rRNA gene amplicon sequencing, and contextualized the massive microbial diversity in this dataset in a meta-analysis of over 20,000 samples. Sixteen percent of surfaces from COVID-19 patient rooms were positive, with the highest prevalence in floor samples next to patient beds (39%) and directly outside their rooms (29%). Although bed rail samples increasingly resembled the patient microbiome throughout their stay, SARS-CoV-2 was less frequently detected there (11%). Despite surface contamination in almost all patient rooms, no health care workers providing COVID-19 patient care contracted the disease. SARS-CoV-2 positive samples had higher bacterial phylogenetic diversity across human and surface samples, and higher biomass in floor samples. 16S microbial community profiles allowed for high classifier accuracy for SARS-CoV-2 status in not only nares, but also forehead, stool and floor samples. Across these distinct microbial profiles, a single amplicon sequence variant from the genus Rothia was highly predictive of SARS-CoV-2 across sample types, and had higher prevalence in positive surface and human samples, even when comparing to samples from patients in another intensive care unit prior to the COVID-19 pandemic. These results suggest that bacterial communities contribute to viral prevalence both in the host and hospital environment.
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Affiliation(s)
- Clarisse Marotz
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Farhana Ali
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Promi Das
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Shi Huang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Kalen Cantrell
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Lingjing Jiang
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Division of Biostatistics, University of California, San Diego, La Jolla, California, USA
| | - Cameron Martino
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Rachel E Diner
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Gibraan Rahman
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Daniel McDonald
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - George Armstrong
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Bioinformatics and Systems Biology Program, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Sho Kodera
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Sonya Donato
- Microbiome Core, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Gertrude Ecklu-Mensah
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Neil Gottel
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Mariana C Salas Garcia
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
| | - Leslie Y Chiang
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Rodolfo A Salido
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Justin P Shaffer
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - MacKenzie Bryant
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Karenina Sanders
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Greg Humphrey
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
| | - Niina Haiminen
- IBM, T.J Watson Research Center, Yorktown Heights, New York, USA
| | - Kristen L Beck
- AI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA
| | - Ho-Cheol Kim
- AI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA
| | | | - Laxmi Parida
- AI and Cognitive Software, IBM Research-Almaden, San Jose, California, USA
| | - Yoshiki Vázquez-Baeza
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Francesca J Torriani
- Infection Prevention and Clinical Epidemiology Unit at UC San Diego Health, Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego, San Diego CA, USA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Jack A Gilbert
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Daniel A Sweeney
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California San Diego, La Jolla, California, USA
| | - Sarah M Allard
- Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA
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47
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Zarraonaindia I, Martínez-Goñi XS, Liñero O, Muñoz-Colmenero M, Aguirre M, Abad D, Baroja-Careaga I, de Diego A, Gilbert JA, Estonba A. Response of Horticultural Soil Microbiota to Different Fertilization Practices. Plants (Basel) 2020; 9:plants9111501. [PMID: 33171888 PMCID: PMC7694448 DOI: 10.3390/plants9111501] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 01/11/2023]
Abstract
Environmentally friendly agricultural production necessitates manipulation of microbe-plant interactions, requiring a better understanding of how farming practices influence soil microbiota. We studied the effect of conventional and organic treatment on soil bacterial richness, composition, and predicted functional potential. 16S rRNA sequencing was applied to soils from adjacent plots receiving either a synthetic or organic fertilizer, where two crops were grown within treatment, homogenizing for differences in soil properties, crop, and climate. Conventional fertilizer was associated with a decrease in soil pH, an accumulation of Ag, Mn, As, Fe, Co, Cd, and Ni; and an enrichment of ammonia oxidizers and xenobiotic compound degraders (e.g., Candidatus Nitrososphaera, Nitrospira, Bacillus, Pseudomonas). Soils receiving organic fertilization were enriched in Ti (crop biostimulant), N, and C cycling bacteria (denitrifiers, e.g., Azoarcus, Anaerolinea; methylotrophs, e.g., Methylocaldum, Methanosarcina), and disease-suppression (e.g., Myxococcales). Some predicted functions, such as glutathione metabolism, were slightly, but significantly enriched after a one-time manure application, suggesting the enhancement of sulfur regulation, nitrogen-fixing, and defense of environmental stressors. The study highlights that even a single application of organic fertilization is enough to originate a rapid shift in soil prokaryotes, responding to the differential substrate availability by promoting soil health, similar to recurrent applications.
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Affiliation(s)
- Iratxe Zarraonaindia
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (X.S.M.-G.); (M.M.-C.); (M.A.); (D.A.); (I.B.-C.); (A.E.)
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Bizkaia, Spain
- Correspondence:
| | - Xabier Simón Martínez-Goñi
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (X.S.M.-G.); (M.M.-C.); (M.A.); (D.A.); (I.B.-C.); (A.E.)
| | - Olaia Liñero
- Department of Analytical Chemistry, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (O.L.); (A.d.D.)
| | - Marta Muñoz-Colmenero
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (X.S.M.-G.); (M.M.-C.); (M.A.); (D.A.); (I.B.-C.); (A.E.)
| | - Mikel Aguirre
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (X.S.M.-G.); (M.M.-C.); (M.A.); (D.A.); (I.B.-C.); (A.E.)
| | - David Abad
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (X.S.M.-G.); (M.M.-C.); (M.A.); (D.A.); (I.B.-C.); (A.E.)
| | - Igor Baroja-Careaga
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (X.S.M.-G.); (M.M.-C.); (M.A.); (D.A.); (I.B.-C.); (A.E.)
| | - Alberto de Diego
- Department of Analytical Chemistry, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (O.L.); (A.d.D.)
| | - Jack A. Gilbert
- Department of Pediatrics and Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093, USA;
| | - Andone Estonba
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), 48940 Leioa, Bizkaia, Spain; (X.S.M.-G.); (M.M.-C.); (M.A.); (D.A.); (I.B.-C.); (A.E.)
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48
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Salido RA, Morgan SC, Rojas MI, Magallanes CG, Marotz C, DeHoff P, Belda-Ferre P, Aigner S, Kado DM, Yeo GW, Gilbert JA, Laurent L, Rohwer F, Knight R. Handwashing and Detergent Treatment Greatly Reduce SARS-CoV-2 Viral Load on Halloween Candy Handled by COVID-19 Patients. mSystems 2020; 5:e01074-20. [PMID: 33127739 PMCID: PMC7743156 DOI: 10.1128/msystems.01074-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 10/29/2020] [Indexed: 11/20/2022] Open
Abstract
Due to the COVID-19 pandemic and potential public health implications, we are publishing this peer-reviewed manuscript in its accepted form. The final, copyedited version of the paper will be available at a later date. Although SARS-CoV-2 is primarily transmitted by respiratory droplets and aerosols, transmission by fomites remains plausible. During Halloween, a major event for children in numerous countries, SARS-CoV-2 transmission risk via candy fomites worries many parents. To address this concern, we enrolled 10 recently diagnosed asymptomatic or mildly/moderately symptomatic COVID-19 patients to handle typical Halloween candy (pieces individually wrapped) under three conditions: normal handling with unwashed hands, deliberate coughing and extensive touching, and normal handling following handwashing. We then used a factorial design to subject the candies to two post-handling treatments: no washing (untreated) and household dishwashing detergent. We measured SARS-CoV-2 load by RT-qPCR and LAMP. From the candies not washed post-handling, we detected SARS-CoV-2 on 60% of candies that were deliberately coughed on, 60% of candies normally handled with unwashed hands, but only 10% of candies handled after hand washing. We found that treating candy with dishwashing detergent reduced SARS-CoV-2 load by 62.1% in comparison to untreated candy. Taken together, these results suggest that although the risk of transmission of SARS-CoV-2 by fomites is low even from known COVID-19 patients, viral RNA load can be reduced to near zero by the combination of handwashing by the infected patient and ≥1 minute detergent treatment after collection. We also found that the inexpensive and fast LAMP protocol was more than 80% concordant with RT-qPCR.IMPORTANCE The COVID-19 pandemic is leading to important tradeoffs between risk of SARS-CoV-2 transmission and mental health due to deprivation from normal activities, with these impacts being especially profound in children. Due to the ongoing pandemic, Halloween activities will be curtailed as a result of the concern that candy from strangers might act as fomites. Here we demonstrate that these risks can be mitigated by ensuring that prior to handling candy, the candy giver washes their hands, and by washing collected candy with household dishwashing detergent. Even in the most extreme case, with candy deliberately coughed on by known COVID-19 patients, viral load was reduced dramatically after washing with household detergent. We conclude that with reasonable precautions, even if followed only by either the candy giver or the candy recipient, the risk of viral transmission by this route is very low.
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Affiliation(s)
- Rodolfo A. Salido
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Sydney C. Morgan
- Department of Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, California, USA
| | - Maria I. Rojas
- Department of Biology, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Celestine G. Magallanes
- Department of Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, California, USA
| | - Clarisse Marotz
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Peter DeHoff
- Department of Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, California, USA
| | - Pedro Belda-Ferre
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Stefan Aigner
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
- Stem Cell Program, University of California, San Diego, La Jolla, California, USA
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA
| | - Deborah M. Kado
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, California, USA
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Gene W. Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
- Stem Cell Program, University of California, San Diego, La Jolla, California, USA
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA
| | - Jack A. Gilbert
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Louise Laurent
- Department of Obstetrics, Gynecology, and Reproductive Science, University of California, San Diego, La Jolla, California, USA
| | - Forest Rohwer
- Department of Biology, San Diego State University, San Diego, California, USA
- Viral Information Institute, San Diego State University, San Diego, California, USA
| | - Rob Knight
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
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49
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Hopper CP, De La Cruz LK, Lyles KV, Wareham LK, Gilbert JA, Eichenbaum Z, Magierowski M, Poole RK, Wollborn J, Wang B. Role of Carbon Monoxide in Host-Gut Microbiome Communication. Chem Rev 2020; 120:13273-13311. [PMID: 33089988 DOI: 10.1021/acs.chemrev.0c00586] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nature is full of examples of symbiotic relationships. The critical symbiotic relation between host and mutualistic bacteria is attracting increasing attention to the degree that the gut microbiome is proposed by some as a new organ system. The microbiome exerts its systemic effect through a diverse range of metabolites, which include gaseous molecules such as H2, CO2, NH3, CH4, NO, H2S, and CO. In turn, the human host can influence the microbiome through these gaseous molecules as well in a reciprocal manner. Among these gaseous molecules, NO, H2S, and CO occupy a special place because of their widely known physiological functions in the host and their overlap and similarity in both targets and functions. The roles that NO and H2S play have been extensively examined by others. Herein, the roles of CO in host-gut microbiome communication are examined through a discussion of (1) host production and function of CO, (2) available CO donors as research tools, (3) CO production from diet and bacterial sources, (4) effect of CO on bacteria including CO sensing, and (5) gut microbiome production of CO. There is a large amount of literature suggesting the "messenger" role of CO in host-gut microbiome communication. However, much more work is needed to begin achieving a systematic understanding of this issue.
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Affiliation(s)
- Christopher P Hopper
- Institute for Experimental Biomedicine, University Hospital Wuerzburg, Wuerzburg, Bavaria DE 97080, Germany.,Department of Medicinal Chemistry, College of Pharmacy, The University of Florida, Gainesville, Florida 32611, United States
| | - Ladie Kimberly De La Cruz
- Department of Chemistry & Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
| | - Kristin V Lyles
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
| | - Lauren K Wareham
- The Vanderbilt Eye Institute and Department of Ophthalmology & Visual Sciences, The Vanderbilt University Medical Center and School of Medicine, Nashville, Tennessee 37232, United States
| | - Jack A Gilbert
- Department of Pediatrics, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Zehava Eichenbaum
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
| | - Marcin Magierowski
- Cellular Engineering and Isotope Diagnostics Laboratory, Department of Physiology, Jagiellonian University Medical College, Cracow PL 31-531, Poland
| | - Robert K Poole
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Sheffield S10 2TN, U.K
| | - Jakob Wollborn
- Department of Anesthesiology and Critical Care, Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg DE 79085, Germany.,Department of Anesthesiology, Perioperative and Pain Management, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Binghe Wang
- Department of Chemistry & Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303, United States
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50
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Zhao D, Cardona C, Gottel N, Winton VJ, Thomas PM, Raba DA, Kelley ST, Henry C, Gilbert JA, Stephens B. Chemical composition of material extractives influences microbial growth and dynamics on wetted wood materials. Sci Rep 2020; 10:14500. [PMID: 32879425 PMCID: PMC7467922 DOI: 10.1038/s41598-020-71560-3] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 08/18/2020] [Indexed: 11/12/2022] Open
Abstract
The impact of material chemical composition on microbial growth on building materials remains relatively poorly understood. We investigate the influence of the chemical composition of material extractives on microbial growth and community dynamics on 30 different wood species that were naturally inoculated, wetted, and held at high humidity for several weeks. Microbial growth was assessed by visual assessment and molecular sequencing. Unwetted material powders and microbial swab samples were analyzed using reverse phase liquid chromatography with tandem mass spectrometry. Different wood species demonstrated varying susceptibility to microbial growth after 3 weeks and visible coverage and fungal qPCR concentrations were correlated (R2 = 0.55). Aspergillaceae was most abundant across all samples; Meruliaceae was more prevalent on 8 materials with the highest visible microbial growth. A larger and more diverse set of compounds was detected from the wood shavings compared to the microbial swabs, indicating a complex and heterogeneous chemical composition within wood types. Several individual compounds putatively identified in wood samples showed statistically significant, near-monotonic associations with microbial growth, including C11H16O4, C18H34O4, and C6H15NO. A pilot experiment confirmed the inhibitory effects of dosing a sample of wood materials with varying concentrations of liquid C6H15NO (assuming it presented as Diethylethanolamine).
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Affiliation(s)
- Dan Zhao
- Department of Civil, Architectural, and Environmental Engineering, Illinois Institute of Technology, Alumni Memorial Hall 228E, 3201 South Dearborn Street, Chicago, IL, 60616, USA
| | - Cesar Cardona
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Department of Surgery, The University of Chicago, Chicago, IL, USA
| | - Neil Gottel
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA, USA
| | - Valerie J Winton
- Proteomics Center of Excellence and Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Paul M Thomas
- Proteomics Center of Excellence and Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Daniel A Raba
- Department of Biology, Illinois Institute of Technology, Chicago, IL, USA
| | - Scott T Kelley
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Christopher Henry
- Mathematics and Computer Science, Argonne National Laboratory, Lemont, IL, USA
| | - Jack A Gilbert
- Department of Pediatrics, University of California San Diego School of Medicine, San Diego, CA, USA
| | - Brent Stephens
- Department of Civil, Architectural, and Environmental Engineering, Illinois Institute of Technology, Alumni Memorial Hall 228E, 3201 South Dearborn Street, Chicago, IL, 60616, USA.
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