1
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Yang H, Wang X, Blanco-Gómez A, He L, García-Sancha N, Corchado-Cobos R, Pérez-Baena MJ, Jiménez-Navas A, Wang P, Inman JL, Snijders AM, Threadgill DW, Balmain A, Chang H, Perez-Losada J, Mao JH. A susceptibility gene signature for ERBB2-driven mammary tumour development and metastasis in collaborative cross mice. EBioMedicine 2024; 106:105260. [PMID: 39067134 DOI: 10.1016/j.ebiom.2024.105260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/11/2024] [Accepted: 07/11/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Deeper insights into ERBB2-driven cancers are essential to develop new treatment approaches for ERBB2+ breast cancers (BCs). We employed the Collaborative Cross (CC) mouse model to unearth genetic factors underpinning Erbb2-driven mammary tumour development and metastasis. METHODS 732 F1 hybrid female mice between FVB/N MMTV-Erbb2 and 30 CC strains were monitored for mammary tumour phenotypes. GWAS pinpointed SNPs that influence various tumour phenotypes. Multivariate analyses and models were used to construct the polygenic score and to develop a mouse tumour susceptibility gene signature (mTSGS), where the corresponding human ortholog was identified and designated as hTSGS. The importance and clinical value of hTSGS in human BC was evaluated using public datasets, encompassing TCGA, METABRIC, GSE96058, and I-SPY2 cohorts. The predictive power of mTSGS for response to chemotherapy was validated in vivo using genetically diverse MMTV-Erbb2 mice. FINDINGS Distinct variances in tumour onset, multiplicity, and metastatic patterns were observed in F1-hybrid female mice between FVB/N MMTV-Erbb2 and 30 CC strains. Besides lung metastasis, liver and kidney metastases emerged in specific CC strains. GWAS identified specific SNPs significantly associated with tumour onset, multiplicity, lung metastasis, and liver metastasis. Multivariate analyses flagged SNPs in 20 genes (Stx6, Ramp1, Traf3ip1, Nckap5, Pfkfb2, Trmt1l, Rprd1b, Rer1, Sepsecs, Rhobtb1, Tsen15, Abcc3, Arid5b, Tnr, Dock2, Tti1, Fam81a, Oxr1, Plxna2, and Tbc1d31) independently tied to various tumour characteristics, designated as a mTSGS. hTSGS scores (hTSGSS) based on their transcriptional level showed prognostic values, superseding clinical factors and PAM50 subtype across multiple human BC cohorts, and predicted pathological complete response independent of and superior to MammaPrint score in I-SPY2 study. The power of mTSGS score for predicting chemotherapy response was further validated in an in vivo mouse MMTV-Erbb2 model, showing that, like findings in human patients, mouse tumours with low mTSGS scores were most likely to respond to treatment. INTERPRETATION Our investigation has unveiled many new genes predisposing individuals to ERBB2-driven cancer. Translational findings indicate that hTSGS holds promise as a biomarker for refining treatment strategies for patients with BC. FUNDING The U.S. Department of Defense (DoD) Breast Cancer Research Program (BCRP) (BC190820), United States; MCIN/AEI/10.13039/501100011039 (PID2020-118527RB-I00, PDC2021-121735-I00), the "European Union Next Generation EU/PRTR," the Regional Government of Castile and León (CSI144P20), European Union.
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Affiliation(s)
- Hui Yang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xinzhi Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Adrián Blanco-Gómez
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, 37007, Spain; Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, 37007, Spain
| | - Li He
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430079, China
| | - Natalia García-Sancha
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, 37007, Spain; Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, 37007, Spain
| | - Roberto Corchado-Cobos
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, 37007, Spain; Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, 37007, Spain
| | - Manuel Jesús Pérez-Baena
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, 37007, Spain; Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, 37007, Spain
| | - Alejandro Jiménez-Navas
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, 37007, Spain; Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, 37007, Spain
| | - Pin Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Gastroenterology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, 210008, China
| | - Jamie L Inman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - David W Threadgill
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA; Department of Molecular and Cellular Medicine and Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Allan Balmain
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Jesus Perez-Losada
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC-CIC), Universidad de Salamanca/CSIC, Salamanca, 37007, Spain; Instituto de Investigación Biosanitaria de Salamanca (IBSAL), Salamanca, 37007, Spain.
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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2
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Dubovik T, Lukačišin M, Starosvetsky E, LeRoy B, Normand R, Admon Y, Alpert A, Ofran Y, G'Sell M, Shen-Orr SS. Interactions between immune cell types facilitate the evolution of immune traits. Nature 2024; 632:350-356. [PMID: 38866051 PMCID: PMC11306095 DOI: 10.1038/s41586-024-07661-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 06/04/2024] [Indexed: 06/14/2024]
Abstract
An essential prerequisite for evolution by natural selection is variation among individuals in traits that affect fitness1. The ability of a system to produce selectable variation, known as evolvability2, thus markedly affects the rate of evolution. Although the immune system is among the fastest-evolving components in mammals3, the sources of variation in immune traits remain largely unknown4,5. Here we show that an important determinant of the immune system's evolvability is its organization into interacting modules represented by different immune cell types. By profiling immune cell variation in bone marrow of 54 genetically diverse mouse strains from the Collaborative Cross6, we found that variation in immune cell frequencies is polygenic and that many associated genes are involved in homeostatic balance through cell-intrinsic functions of proliferation, migration and cell death. However, we also found genes associated with the frequency of a particular cell type that are expressed in a different cell type, exerting their effect in what we term cyto-trans. The vertebrate evolutionary record shows that genes associated in cyto-trans have faced weaker negative selection, thus increasing the robustness and hence evolvability2,7,8 of the immune system. This phenomenon is similarly observable in human blood. Our findings suggest that interactions between different components of the immune system provide a phenotypic space in which mutations can produce variation with little detriment, underscoring the role of modularity in the evolution of complex systems9.
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Affiliation(s)
- Tania Dubovik
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- CytoReason, Tel-Aviv, Israel
| | - Martin Lukačišin
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Elina Starosvetsky
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- CytoReason, Tel-Aviv, Israel
| | - Benjamin LeRoy
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
- Nike, Beaverton, OR, USA
| | - Rachelly Normand
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Massachusetts General Hospital, Boston, MA, USA
| | - Yasmin Admon
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- CytoReason, Tel-Aviv, Israel
| | - Ayelet Alpert
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Oncology, Rambam Health Care Campus, Haifa, Israel
| | - Yishai Ofran
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Department of Haematology and Bone Marrow Transplantation, Rambam Health Care Campus, Haifa, Israel
- Haematology and Bone Marrow Transplantation Department and the Eisenberg R&D Authority, Shaare Zedek Medical Centre, Faculty of Medicine, Hebrew University, Jerusalem, Israel
| | - Max G'Sell
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Shai S Shen-Orr
- Department of Immunology, Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.
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3
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Qadri H, Shah AH, Almilaibary A, Mir MA. Microbiota, natural products, and human health: exploring interactions for therapeutic insights. Front Cell Infect Microbiol 2024; 14:1371312. [PMID: 39035357 PMCID: PMC11257994 DOI: 10.3389/fcimb.2024.1371312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 06/03/2024] [Indexed: 07/23/2024] Open
Abstract
The symbiotic relationship between the human digestive system and its intricate microbiota is a captivating field of study that continues to unfold. Comprising predominantly anaerobic bacteria, this complex microbial ecosystem, teeming with trillions of organisms, plays a crucial role in various physiological processes. Beyond its primary function in breaking down indigestible dietary components, this microbial community significantly influences immune system modulation, central nervous system function, and disease prevention. Despite the strides made in microbiome research, the precise mechanisms underlying how bacterial effector functions impact mammalian and microbiome physiology remain elusive. Unlike the traditional DNA-RNA-protein paradigm, bacteria often communicate through small molecules, underscoring the imperative to identify compounds produced by human-associated bacteria. The gut microbiome emerges as a linchpin in the transformation of natural products, generating metabolites with distinct physiological functions. Unraveling these microbial transformations holds the key to understanding the pharmacological activities and metabolic mechanisms of natural products. Notably, the potential to leverage gut microorganisms for large-scale synthesis of bioactive compounds remains an underexplored frontier with promising implications. This review serves as a synthesis of current knowledge, shedding light on the dynamic interplay between natural products, bacteria, and human health. In doing so, it contributes to our evolving comprehension of microbiome dynamics, opening avenues for innovative applications in medicine and therapeutics. As we delve deeper into this intricate web of interactions, the prospect of harnessing the power of the gut microbiome for transformative medical interventions becomes increasingly tantalizing.
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Affiliation(s)
- Hafsa Qadri
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Abdul Haseeb Shah
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Abdullah Almilaibary
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
- Department of Family and Community Medicine, Faculty of Medicine, Al Baha University, Al Bahah, Saudi Arabia
| | - Manzoor Ahmad Mir
- Department of Bioresources, School of Biological Sciences, University of Kashmir, Srinagar, India
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4
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Howard-Varona C, Lindback MM, Fudyma JD, Krongauz A, Solonenko NE, Zayed AA, Andreopoulos WB, Olson HM, Kim YM, Kyle JE, Glavina del Rio T, Adkins JN, Tfaily MM, Paul S, Sullivan MB, Duhaime MB. Environment-specific virocell metabolic reprogramming. THE ISME JOURNAL 2024; 18:wrae055. [PMID: 38552150 PMCID: PMC11170926 DOI: 10.1093/ismejo/wrae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/23/2023] [Accepted: 03/28/2024] [Indexed: 06/14/2024]
Abstract
Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.
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Affiliation(s)
- Cristina Howard-Varona
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Morgan M Lindback
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, United States
| | - Jane D Fudyma
- Department of Environmental Science, University of Arizona, 1177 E 4th St, Tucson, AZ 85719, United States
- Present address: Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, United States
| | - Azriel Krongauz
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH 43210, United States
| | - Natalie E Solonenko
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - Ahmed A Zayed
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
| | - William B Andreopoulos
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, United States
- Present address: Department of Computer Science, San Jose State University, One Washington Square, San Jose CA 95192, United States
| | - Heather M Olson
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Jennifer E Kyle
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
| | - Tijana Glavina del Rio
- US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, United States
| | - Joshua N Adkins
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99354, United States
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, United States
| | - Malak M Tfaily
- Department of Environmental Science, University of Arizona, 1177 E 4th St, Tucson, AZ 85719, United States
| | - Subhadeep Paul
- Department of Statistics, The Ohio State University, 1958 Neil Ave, Columbus, OH 43210, United States
| | - Matthew B Sullivan
- Department of Microbiology, The Ohio State University, 484 W 12th Ave, Columbus, OH 43210, United States
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, 2070 Neil Ave, Columbus, OH 43210, United States
- Center for RNA Biology and Center of Microbiome Science, The Ohio State University, 484 W. 12th Ave, Columbus, OH 43210, United States
| | - Melissa B Duhaime
- Department of Ecology and Evolutionary Biology, University of Michigan, 1105 North University Ave, Ann Arbor, MI 48109, United States
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5
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Duffy EP, Bachtell RK, Ehringer MA. Opioid trail: Tracking contributions to opioid use disorder from host genetics to the gut microbiome. Neurosci Biobehav Rev 2024; 156:105487. [PMID: 38040073 PMCID: PMC10836641 DOI: 10.1016/j.neubiorev.2023.105487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023]
Abstract
Opioid use disorder (OUD) is a worldwide public health crisis with few effective treatment options. Traditional genetics and neuroscience approaches have provided knowledge about biological mechanisms that contribute to OUD-related phenotypes, but the complexity and magnitude of effects in the brain and body remain poorly understood. The gut-brain axis has emerged as a promising target for future therapeutics for several psychiatric conditions, so characterizing the relationship between host genetics and the gut microbiome in the context of OUD will be essential for development of novel treatments. In this review, we describe evidence that interactions between host genetics, the gut microbiome, and immune signaling likely play a key role in mediating opioid-related phenotypes. Studies in humans and model organisms consistently demonstrated that genetic background is a major determinant of gut microbiome composition. Furthermore, the gut microbiome is susceptible to environmental influences such as opioid exposure. Additional work focused on gene by microbiome interactions will be necessary to gain improved understanding of their effects on OUD-related behaviors.
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Affiliation(s)
- Eamonn P Duffy
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA; Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA.
| | - Ryan K Bachtell
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA; Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Marissa A Ehringer
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA; Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
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6
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Li D, Zhong C, Yang M, He L, Chang H, Zhu N, Celniker SE, Threadgill DW, Snijders AM, Mao JH, Yuan Y. Genetic and microbial determinants of azoxymethane-induced colorectal tumor susceptibility in Collaborative Cross mice and their implication in human cancer. Gut Microbes 2024; 16:2341647. [PMID: 38659246 PMCID: PMC11057575 DOI: 10.1080/19490976.2024.2341647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
The insights into interactions between host genetics and gut microbiome (GM) in colorectal tumor susceptibility (CTS) remains lacking. We used Collaborative Cross mouse population model to identify genetic and microbial determinants of Azoxymethane-induced CTS. We identified 4417 CTS-associated single nucleotide polymorphisms (SNPs) containing 334 genes that were transcriptionally altered in human colorectal cancers (CRCs) and consistently clustered independent human CRC cohorts into two subgroups with different prognosis. We discovered a set of genera in early-life associated with CTS and defined a 16-genus signature that accurately predicted CTS, the majority of which were correlated with human CRCs. We identified 547 SNPs associated with abundances of these genera. Mediation analysis revealed GM as mediators partially exerting the effect of SNP UNC3869242 within Duox2 on CTS. Intestine cell-specific depletion of Duox2 altered GM composition and contribution of Duox2 depletion to CTS was significantly influenced by GM. Our findings provide potential novel targets for personalized CRC prevention and treatment.
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Affiliation(s)
- Dan Li
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, ZJ, China
| | - Chenhan Zhong
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mengyuan Yang
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
| | - Li He
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ning Zhu
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
| | - Susan E Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David W Threadgill
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX, USA
- Department of Molecular and Cellular Medicine and Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ying Yuan
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
- Zhejiang Provincial Clinical Research Center for CANCER, Hangzhou, ZJ, China
- Cancer Center, Zhejiang University, Hangzhou, ZJ, China
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7
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He L, Zhong C, Chang H, Inman JL, Celniker SE, Ioakeim-Ioannidou M, Liu KX, Haas-Kogan D, MacDonald SM, Threadgill DW, Kogan SC, Mao JH, Snijders AM. Genetic architecture of the acute and persistent immune cell response after radiation exposure. CELL GENOMICS 2023; 3:100422. [PMID: 38020972 PMCID: PMC10667298 DOI: 10.1016/j.xgen.2023.100422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/19/2023] [Accepted: 09/12/2023] [Indexed: 12/01/2023]
Abstract
Hematologic toxicity is a common side effect of multimodal cancer therapy. Nearly all animal studies investigating the causes of radiotherapy-induced hematologic toxicity use inbred strains with limited genetic diversity and do not reflect the diverse responses observed in humans. We used the population-based Collaborative Cross (CC) mouse resource to investigate the genetic architecture of the acute and persistent immune response after radiation exposure by measuring 22 immune parameters in 1,720 CC mice representing 35 strains. We determined relative acute and persistent radiation resistance scores at the individual strain level considering contributions from all immune parameters. Genome-wide association analysis identified quantitative trait loci associated with baseline and radiation responses. A cross-species radiation resistance score predicted recurrence-free survival in medulloblastoma patients. We present a community resource of immune parameters and genome-wide association analyses before and after radiation exposure for future investigations of the contributions of host genetics on radiosensitivity.
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Affiliation(s)
- Li He
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430079, China
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chenhan Zhong
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Medical Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jamie L. Inman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Susan E. Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California Berkeley, Berkeley, CA 94720, USA
| | | | - Kevin X. Liu
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daphne Haas-Kogan
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shannon M. MacDonald
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David W. Threadgill
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX 77843, USA
- Departments of Nutrition and Cell Biology and Genetics, Texas A&M University, College Station, TX 77843, USA
| | - Scott C. Kogan
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California Berkeley, Berkeley, CA 94720, USA
| | - Antoine M. Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Comparative Biochemistry Program, University of California Berkeley, Berkeley, CA 94720, USA
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8
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Ahmad J, Khan I, Zengin G, Mahomoodally MF. The gut microbiome in the fight against obesity: The potential of dietary factors. FASEB J 2023; 37:e23258. [PMID: 37843880 DOI: 10.1096/fj.202300864rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023]
Abstract
Obesity as a global public health burden has experienced a drastic growing trend recently. The management of obesity is challenging because of its complex etiology, and various factors are involved in its development, such as genetic and environmental factors. Different approaches are available to treat and/or manage obesity, including diet, physical activity, lifestyle changes, medications, and surgery. However, some of these approaches have inherent limitations and are closely associated with adverse effects. Therefore, probing into a novel/safe approach to treat and/or manage obesity is of fundamental importance. One such approach gaining renewed interest is the potential role of gut microbiota in obesity and its effectiveness in treating this condition. However, there is a dearth of comprehensive compilation of data on the potential role of the gut microbiome in obesity, particularly regarding dietary factors as a therapeutic approach. Therefore, this review aims to provide an updated overview of the role of gut microbiota in obesity, further highlighting the importance of dietary factors, particularly diet, prebiotics, and probiotics, as potential complementary and/or alternative therapeutic options. Moreover, the association of gut microbiota with obese or lean individuals has also been discussed.
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Affiliation(s)
- Jamil Ahmad
- Department of Human Nutrition, The University of Agriculture Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Imran Khan
- Department of Human Nutrition, The University of Agriculture Peshawar, Khyber Pakhtunkhwa, Pakistan
| | - Gokhan Zengin
- Department of Biology, Science Faculty, Selcuk University, Konya, Turkey
| | - Mohamad Fawzi Mahomoodally
- Institute of Research and Development, Duy Tan University, Da Nang, Vietnam
- School of Engineering & Technology, Duy Tan University, Da Nang, Vietnam
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9
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Shen Y, An Z, Huyan Z, Shu X, Wu D, Zhang N, Pellegrini N, Rubert J. Lipid complexation reduces rice starch digestibility and boosts short-chain fatty acid production via gut microbiota. NPJ Sci Food 2023; 7:56. [PMID: 37853069 PMCID: PMC10584848 DOI: 10.1038/s41538-023-00230-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/02/2023] [Indexed: 10/20/2023] Open
Abstract
In this study, two rice varieties (RS4 and GZ93) with different amylose and lipid contents were studied, and their starch was used to prepare starch-palmitic acid complexes. The RS4 samples showed a significantly higher lipid content in their flour, starch, and complex samples compared to GZ93. The static in vitro digestion highlighted that RS4 samples had significantly lower digestibility than the GZ93 samples. The C∞ of the starch-lipid complex samples was found to be 17.7% and 18.5% lower than that of the starch samples in GZ93 and RS4, respectively. The INFOGEST undigested fractions were subsequently used for in vitro colonic fermentation. Short-chain fatty acids (SCFAs) concentrations, mainly acetate, and propionate were significantly higher in starch-lipid complexes compared to native flour or starch samples. Starch-lipid complexes produced a distinctive microbial composition, which resulted in different gene functions, mainly related to pyruvate, fructose, and mannose metabolism. Using Model-based Integration of Metabolite Observations and Species Abundances 2 (MIMOSA2), SCFA production was predicted and associated with the gut microbiota. These results indicated that incorporating lipids into rice starch promotes SCFA production by modulating the gut microbiota selectively.
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Affiliation(s)
- Yi Shen
- State Key Laboratory of Rice Biology, Key Laboratory of the Ministry of Agriculture for Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310058, PR China
- Food Quality and Design Group, Wageningen University & Research, P. O. Box 17, 6700 AA, Wageningen, The Netherlands
| | - Zengxu An
- State Key Laboratory of Rice Biology, Key Laboratory of the Ministry of Agriculture for Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Zongyao Huyan
- Food Quality and Design Group, Wageningen University & Research, P. O. Box 17, 6700 AA, Wageningen, The Netherlands
| | - Xiaoli Shu
- State Key Laboratory of Rice Biology, Key Laboratory of the Ministry of Agriculture for Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310058, PR China
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, PR China
| | - Dianxing Wu
- State Key Laboratory of Rice Biology, Key Laboratory of the Ministry of Agriculture for Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310058, PR China
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, PR China
| | - Ning Zhang
- State Key Laboratory of Rice Biology, Key Laboratory of the Ministry of Agriculture for Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Nicoletta Pellegrini
- Food Quality and Design Group, Wageningen University & Research, P. O. Box 17, 6700 AA, Wageningen, The Netherlands
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, via Sondrio 2/A, Udine, 33100, Italy
| | - Josep Rubert
- Food Quality and Design Group, Wageningen University & Research, P. O. Box 17, 6700 AA, Wageningen, The Netherlands.
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10
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Salvador AC, Huda MN, Arends D, Elsaadi AM, Gacasan CA, Brockmann GA, Valdar W, Bennett BJ, Threadgill DW. Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets. MICROBIOME 2023; 11:220. [PMID: 37784178 PMCID: PMC10546677 DOI: 10.1186/s40168-023-01588-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/01/2023] [Indexed: 10/04/2023]
Abstract
BACKGROUND The gut microbiota is modulated by a combination of diet, host genetics, and sex effects. The magnitude of these effects and interactions among them is important to understanding inter-individual variability in gut microbiota. In a previous study, mouse strain-specific responses to American and ketogenic diets were observed along with several QTLs for metabolic traits. In the current study, we searched for genetic variants underlying differences in the gut microbiota in response to American and ketogenic diets, which are high in fat and vary in carbohydrate composition, between C57BL/6 J (B6) and FVB/NJ (FVB) mouse strains. RESULTS Genetic mapping of microbial features revealed 18 loci under the QTL model (i.e., marginal effects that are not specific to diet or sex), 12 loci under the QTL by diet model, and 1 locus under the QTL by sex model. Multiple metabolic and microbial features map to the distal part of Chr 1 and Chr 16 along with eigenvectors extracted from principal coordinate analysis of measures of β-diversity. Bilophila, Ruminiclostridium 9, and Rikenella (Chr 1) were identified as sex- and diet-independent QTL candidate keystone organisms, and Parabacteroides (Chr 16) was identified as a diet-specific, candidate keystone organism in confirmatory factor analyses of traits mapping to these regions. For many microbial features, irrespective of which QTL model was used, diet or the interaction between diet and a genotype were the strongest predictors of the abundance of each microbial trait. Sex, while important to the analyses, was not as strong of a predictor for microbial abundances. CONCLUSIONS These results demonstrate that sex, diet, and genetic background have different magnitudes of effects on inter-individual differences in gut microbiota. Therefore, Precision Nutrition through the integration of genetic variation, microbiota, and sex affecting microbiota variation will be important to predict response to diets varying in carbohydrate composition. Video Abstract.
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Affiliation(s)
- Anna C Salvador
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
| | - M Nazmul Huda
- Department of Nutrition, University of California Davis, Sacramento, CA, 95616, USA
- Obesity and Metabolism Unit, Western Human Nutrition Research Center, USDA-ARS, Davis, CA, 95616, USA
| | - Danny Arends
- Albrecht Daniel Thaer-Institut, 10115, Berlin, Germany
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, UK
| | - Ahmed M Elsaadi
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX, 77843, USA
| | - C Anthony Gacasan
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX, 77843, USA
| | | | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brian J Bennett
- Department of Nutrition, University of California Davis, Sacramento, CA, 95616, USA
- Obesity and Metabolism Unit, Western Human Nutrition Research Center, USDA-ARS, Davis, CA, 95616, USA
| | - David W Threadgill
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX, 77843, USA.
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA.
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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11
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Mayali X, Samo TJ, Kimbrel JA, Morris MM, Rolison K, Swink C, Ramon C, Kim YM, Munoz-Munoz N, Nicora C, Purvine S, Lipton M, Stuart RK, Weber PK. Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum. Nat Commun 2023; 14:5642. [PMID: 37704622 PMCID: PMC10499878 DOI: 10.1038/s41467-023-41179-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/24/2023] [Indexed: 09/15/2023] Open
Abstract
Bacterial remineralization of algal organic matter fuels algal growth but is rarely quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others. Here, we quantified bacterial incorporation of algal-derived complex dissolved organic carbon and nitrogen and algal incorporation of remineralized carbon and nitrogen in fifteen bacterial co-cultures growing with the diatom Phaeodactylum tricornutum at the single-cell level using isotope tracing and nanoSIMS. We found unexpected strain-to-strain and cell-to-cell variability in net carbon and nitrogen incorporation, including non-ubiquitous complex organic nitrogen utilization and remineralization. We used these data to identify three distinct functional guilds of metabolic interactions, which we termed macromolecule remineralizers, macromolecule users, and small-molecule users, the latter exhibiting efficient growth under low carbon availability. The functional guilds were not linked to phylogeny and could not be elucidated strictly from metabolic capacity as predicted by comparative genomics, highlighting the need for direct activity-based measurements in ecological studies of microbial metabolic interactions.
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Affiliation(s)
- Xavier Mayali
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Ty J Samo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jeff A Kimbrel
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Megan M Morris
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Kristina Rolison
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Courtney Swink
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Christina Ramon
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Nathalie Munoz-Munoz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Carrie Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Sam Purvine
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Mary Lipton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Rhona K Stuart
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
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12
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Liu H, Bai Y, Yu Y, Qi Z, Zhang G, Li G, Yu Y, An T. Maternal transfer of resorcinol-bis(diphenyl)-phosphate perturbs gut microbiota development and gut metabolism of offspring in rats. ENVIRONMENT INTERNATIONAL 2023; 178:108039. [PMID: 37336026 DOI: 10.1016/j.envint.2023.108039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/21/2023]
Abstract
Resorcinol-bis(diphenyl)-phosphate (RDP), an emerging organophosphate flame retardant, is increasingly used as a primary alternative for decabromodiphenyl ether and is frequently detected in global environmental matrices. However, the long-term effects of its exposure to humans remain largely unknown. To investigate its intergenerational transfer capacity and health risks, female Sprague Dawley rats were orally exposed to RDP from the beginning of pregnancy to the end of the lactation period. The RDP content, gut microbiota homeostasis, and metabolic levels were determined. RDP accumulation occurred in the livers of maternal rats and offspring and increased with exposure time. 16S rRNA gene sequencing showed that exposure to RDP during pregnancy and/or lactation significantly disrupted gut microbiota homeostasis, as evidenced by decreased abundance and diversity. In particular, the abundance of Turicibacter, Adlercreutzia, and YRC22 decreased, correlating significantly with glycollipic metabolism. This finding was consistent with the reduced levels of short-chain fatty acids, the crucial gut microbial metabolites. Meanwhile, RDP exposure resulted in changes in gut microbiome-related metabolism. Nine critical overlapping KEGG metabolic pathways were identified, and the levels of related differential metabolites decreased. Our results suggest that the significant adverse impacts of RDP on gut microbiota homeostasis and metabolic function may increase the long-term risks related to inflammation, obesity, and metabolic diseases.
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Affiliation(s)
- Hongli Liu
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangdong Engineering Technology Research Center for Photocatalytic Technology Integration and Equipment, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Yixiu Bai
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangdong Engineering Technology Research Center for Photocatalytic Technology Integration and Equipment, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Yingying Yu
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangdong Engineering Technology Research Center for Photocatalytic Technology Integration and Equipment, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Zenghua Qi
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangdong Engineering Technology Research Center for Photocatalytic Technology Integration and Equipment, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Guoxia Zhang
- Department of Environmental Health, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Guiying Li
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangdong Engineering Technology Research Center for Photocatalytic Technology Integration and Equipment, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Yingxin Yu
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangdong Engineering Technology Research Center for Photocatalytic Technology Integration and Equipment, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China.
| | - Taicheng An
- Guangdong Key Laboratory of Environmental Catalysis and Health Risk Control, Guangdong-Hong Kong-Macao Joint Laboratory for Contaminants Exposure and Health, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China; Guangdong Engineering Technology Research Center for Photocatalytic Technology Integration and Equipment, Guangzhou Key Laboratory of Environmental Catalysis and Pollution Control, School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, China
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13
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Nagarajan A, Scoggin K, Gupta J, Threadgill DW, Andrews-Polymenis HL. Using the collaborative cross to identify the role of host genetics in defining the murine gut microbiome. MICROBIOME 2023; 11:149. [PMID: 37420306 PMCID: PMC10329326 DOI: 10.1186/s40168-023-01552-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/18/2023] [Indexed: 07/09/2023]
Abstract
BACKGROUND The human gut microbiota is a complex community comprised of trillions of bacteria and is critical for the digestion and absorption of nutrients. Bacterial communities of the intestinal microbiota influence the development of several conditions and diseases. We studied the effect of host genetics on gut microbial composition using Collaborative Cross (CC) mice. CC mice are a panel of mice that are genetically diverse across strains, but genetically identical within a given strain allowing repetition and deeper analysis than is possible with other collections of genetically diverse mice. RESULTS 16S rRNA from the feces of 167 mice from 28 different CC strains was sequenced and analyzed using the Qiime2 pipeline. We observed a large variance in the bacterial composition across CC strains starting at the phylum level. Using bacterial composition data, we identified 17 significant Quantitative Trait Loci (QTL) linked to 14 genera on 9 different mouse chromosomes. Genes within these intervals were analyzed for significant association with pathways and the previously known human GWAS database using Enrichr analysis and Genecards database. Multiple host genes involved in obesity, glucose homeostasis, immunity, neurological diseases, and many other protein-coding genes located in these regions may play roles in determining the composition of the gut microbiota. A subset of these CC mice was infected with Salmonella Typhimurium. Using infection outcome data, an increase in abundance of genus Lachnospiraceae and decrease in genus Parasutterella correlated with positive health outcomes after infection. Machine learning classifiers accurately predicted the CC strain and the infection outcome using pre-infection bacterial composition data from the feces. CONCLUSION Our study supports the hypothesis that multiple host genes influence the gut microbiome composition and homeostasis, and that certain organisms may influence health outcomes after S. Typhimurium infection. Video Abstract.
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Affiliation(s)
- Aravindh Nagarajan
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
| | - Kristin Scoggin
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX USA
| | - Jyotsana Gupta
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
| | - David W. Threadgill
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX USA
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX USA
- Department of Biochemistry & Biophysics and Department of Nutrition, Texas A&M University, College Station, TX USA
| | - Helene L. Andrews-Polymenis
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX USA
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, TX USA
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14
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Ziab M, Chaganti SR, Heath DD. The effects of host quantitative genetic architecture on the gut microbiota composition of Chinook salmon (Oncorhynchus tshawytscha). Heredity (Edinb) 2023; 131:43-55. [PMID: 37179383 PMCID: PMC10313681 DOI: 10.1038/s41437-023-00620-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
The microbiota consists of microbes living in or on an organism and has been implicated in host health and function. Environmental and host-related factors were shown to shape host microbiota composition and diversity in many fish species, but the role of host quantitative architecture across populations and among families within a population is not fully characterized. Here, Chinook salmon were used to determine if inter-population differences and additive genetic variation within populations influenced the gut microbiota diversity and composition. Specifically, hybrid stocks of Chinook salmon were created by crossing males from eight populations with eggs from an inbred line created from self-fertilized hermaphrodite salmon. Based on high-throughput sequencing of the 16S rRNA gene, significant gut microbial community diversity and composition differences were found among the hybrid stocks. Furthermore, additive genetic variance components varied among hybrid stocks, indicative of population-specific heritability patterns, suggesting the potential to select for specific gut microbiota composition for aquaculture purposes. Determining the role of host genetics in shaping their gut microbiota has important implications for predicting population responses to environmental changes and will thus impact conservation efforts for declining populations of Chinook salmon.
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Affiliation(s)
- Mubarak Ziab
- Great Lakes Institute for Environmental Research (GLIER), University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada
| | - Subba Rao Chaganti
- Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Daniel D Heath
- Great Lakes Institute for Environmental Research (GLIER), University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada.
- Department of Integrative Biology, University of Windsor, 401 Sunset Avenue, Windsor, Ontario, N9B 3P4, Canada.
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15
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Henry LP, Bergelson J. Evolutionary implications of host genetic control for engineering beneficial microbiomes. CURRENT OPINION IN SYSTEMS BIOLOGY 2023; 34:None. [PMID: 37287906 PMCID: PMC10242548 DOI: 10.1016/j.coisb.2023.100455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Engineering new functions in the microbiome requires understanding how host genetic control and microbe-microbe interactions shape the microbiome. One key genetic mechanism underlying host control is the immune system. The immune system can promote stability in the composition of the microbiome by reshaping the ecological dynamics of its members, but the degree of stability will depend on the interplay between ecological context, immune system development, and higher-order microbe-microbe interactions. The eco-evolutionary interplay affecting composition and stability should inform the strategies used to engineer new functions in the microbiome. We conclude with recent methodological developments that provide an important path forward for both engineering new functionality in the microbiome and broadly understanding how ecological interactions shape evolutionary processes in complex biological systems.
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16
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Pandey U, Tambat S, Aich P. Postnatal 14D is the Key Window for Mice Intestinal Development- An Insight from Age-Dependent Antibiotic-Mediated Gut Microbial Dysbiosis Study. Adv Biol (Weinh) 2023:e2300089. [PMID: 37178322 DOI: 10.1002/adbi.202300089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/13/2023] [Indexed: 05/15/2023]
Abstract
The postnatal period is one of the critical windows for the structure-function development of the gastrointestinal tract and associated mucosal immunity. Along with other constituent members, recent studies suggest the contribution of gut microbiota in maintaining host health, immunity, and development. Although the gut microbiota's role in maintaining barrier integrity is known, its function in early life development still needs to be better understood. To understand the details of gut microbiota's effects on intestinal integrity, epithelium development, and immune profile, the route of antibiotic-mediated perturbation is taken. Mice on days 7(P7D), 14(P14D), 21(P21D) and 28(P28D) are sacrificed and 16S rRNA metagenomic analysis is performed. The barrier integrity, tight junction proteins (TJPs) expression, intestinal epithelial cell (IEC) markers, and inflammatory cytokines are analyzed. Results reveal a postnatal age-related impact of gut microbiota perturbation, with a gradual increase in the relative abundance of Proteobacteria and a reduction in Bacteroidetes and Firmicutes. Significant barrier integrity disruption, reduced TJPs and IECs marker expression, and increased systemic inflammation at P14D of AVNM-treated mice are found. Moreover, the microbiota transplantation shows recolonization of Verrucomicrobia, proving a causal role in barrier functions. The investigation reveals P14D as a critical period for neonatal intestinal development, regulated by specific microbiota composition.
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Affiliation(s)
- Uday Pandey
- School of Biological Sciences, National Institute of Science Education and Research (NISER), P.O. Jatni, Khurda, Odisha, 752050, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Subodh Tambat
- Department of Life Sciences and Healthcare, Persistent Systems Limited, Pune, Maharashtra, 411004, India
| | - Palok Aich
- School of Biological Sciences, National Institute of Science Education and Research (NISER), P.O. Jatni, Khurda, Odisha, 752050, India
- Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai, 400094, India
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17
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Yang H, Wang X, Wang P, He L, Schick SF, Jacob P, Benowitz N, Gundel LA, Zhu C, Xia Y, Inman JL, Chang H, Snijders AM, Mao JH, Hang B. Thirdhand tobacco smoke exposure increases the genetic background-dependent risk of pan-tumor development in Collaborative Cross mice. ENVIRONMENT INTERNATIONAL 2023; 174:107876. [PMID: 36940581 DOI: 10.1016/j.envint.2023.107876] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 02/15/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Increasing evidence has shown that thirdhand smoke (THS) exposure is likely to induce adverse health effects. An important knowledge gap remains in our understanding of THS exposure related to cancer risk in the human population. Population-based animal models are useful and powerful in investigating the interplay between host genetics and THS exposure on cancer risk. Here, we used the Collaborative Cross (CC) mouse population-based model system, which recapitulates the genetic and phenotypic diversity observed in the human population, to assess cancer risk after a short period of exposure, between 4 and 9 weeks of age. Eight CC strains (CC001, CC019, CC026, CC036, CC037, CC041, CC042 and CC051) were included in our study. We quantified pan-tumor incidence, tumor burden per mouse, organ tumor spectrum and tumor-free survival until 18 months of age. At the population level, we observed a significantly increased pan-tumor incidence and tumor burden per mouse in THS-treated mice as compared to the control (p = 3.04E-06). Lung and liver tissues exhibited the largest risk of undergoing tumorigenesis after THS exposure. Tumor-free survival was significantly reduced in THS-treated mice compared to control (p = 0.044). At the individual strain level, we observed a large variation in tumor incidence across the 8 CC strains. CC036 and CC041 exhibited a significant increase in pan-tumor incidence (p = 0.0084 and p = 0.000066, respectively) after THS exposure compared to control. We conclude that early-life THS exposure increases tumor development in CC mice and that host genetic background plays an important role in individual susceptibility to THS-induced tumorigenesis. Genetic background is an important factor that should be taken into account when determining human cancer risk of THS exposure.
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Affiliation(s)
- Hui Yang
- Department of Radiation and Medical Oncology, Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Xinzhi Wang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210046, China
| | - Pin Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Li He
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Suzyann F Schick
- Department of Medicine, Division of Occupational and Environmental Medicine, University of California, San Francisco, CA 94143, USA
| | - Peyton Jacob
- Department of Medicine, Division of Cardiology, Clinical Pharmacology Program, University of California, San Francisco, CA 94143, USA
| | - Neal Benowitz
- Department of Medicine, Division of Cardiology, Clinical Pharmacology Program, University of California, San Francisco, CA 94143, USA
| | - Lara A Gundel
- Indoor Environment Group, Energy Technologies Area, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chi Zhu
- Hanszen College, Rice University, Houston, TX 77005, USA
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jamie L Inman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Impact of diet and host genetics on the murine intestinal mycobiome. Nat Commun 2023; 14:834. [PMID: 36788222 PMCID: PMC9929102 DOI: 10.1038/s41467-023-36479-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/01/2023] [Indexed: 02/16/2023] Open
Abstract
The mammalian gut is home to a diverse microbial ecosystem, whose composition affects various physiological traits of the host. Next-generation sequencing-based metagenomic approaches demonstrated how the interplay of host genetics, bacteria, and environmental factors shape complex traits and clinical outcomes. However, the role of fungi in these complex interactions remains understudied. Here, using 228 males and 363 females from an advanced-intercross mouse line, we provide evidence that fungi are regulated by host genetics. In addition, we map quantitative trait loci associated with various fungal species to single genes in mice using whole genome sequencing and genotyping. Moreover, we show that diet and its' interaction with host genetics alter the composition of fungi in outbred mice, and identify fungal indicator species associated with different dietary regimes. Collectively, in this work, we uncover an association of the intestinal fungal community with host genetics and a regulatory role of diet in this ecological niche.
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19
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Salvador AC, Huda MN, Arends D, Elsaadi AM, Gacasan AC, Brockmann GA, Valdar W, Bennett BJ, Threadgill DW. Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets. RESEARCH SQUARE 2023:rs.3.rs-2540322. [PMID: 36778219 PMCID: PMC9915790 DOI: 10.21203/rs.3.rs-2540322/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background The gut microbiota is modulated by a combination of diet, host genetics, and sex effects. The magnitude of these effects and interactions among them is important to understanding inter-individual variability in gut microbiota. In a previous study, mouse strain-specific responses to American and ketogenic diets were observed along with several QTL for metabolic traits. In the current study, we searched for genetic variants underlying differences in the gut microbiota in response to American and ketogenic diets, which are high in fat and vary in carbohydrate composition, between C57BL/6J (B6) and FVB/NJ (FVB) mouse strains. Results Genetic mapping of microbial features revealed 18 loci under the QTL model (i.e., marginal effects that are not specific to diet or sex), 12 loci under the QTL by diet model, and 1 locus under the QTL by sex model. Multiple metabolic and microbial features map to the distal part of Chr 1 and Chr 16 along with eigenvectors extracted from principal coordinate analysis of measures of β-diversity. Bilophila , Ruminiclostridium 9 , and Rikenella (Chr 1) were identified as sex and diet independent QTL candidate keystone organisms and Rikenelleceae RC9 Gut Group (Chr 16) was identified as a diet-specific, candidate keystone organism in confirmatory factor analyses of traits mapping to these regions. For many microbial features, irrespective of which QTL model was used, diet or the interaction between diet and a genotype were the strongest predictors of the abundance of each microbial trait. Sex, while important to the analyses, was not as strong of a predictor for microbial abundances. Conclusions These results demonstrate that sex, diet, and genetic background have different magnitudes of effects on inter-individual differences in gut microbiota. Therefore, Precision Nutrition through the integration of genetic variation, microbiota, and sex affecting microbiota variation will be important to predict response to diets varying in carbohydrate composition.
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20
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Cekanaviciute E, Tran D, Nguyen H, Lopez Macha A, Pariset E, Langley S, Babbi G, Malkani S, Penninckx S, Schisler JC, Nguyen T, Karpen GH, Costes SV. Mouse genomic associations with in vitro sensitivity to simulated space radiation. LIFE SCIENCES IN SPACE RESEARCH 2023; 36:47-58. [PMID: 36682829 DOI: 10.1016/j.lssr.2022.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/23/2022] [Accepted: 07/26/2022] [Indexed: 06/17/2023]
Abstract
Exposure to ionizing radiation is considered by NASA to be a major health hazard for deep space exploration missions. Ionizing radiation sensitivity is modulated by both genomic and environmental factors. Understanding their contributions is crucial for designing experiments in model organisms, evaluating the risk of deep space (i.e. high-linear energy transfer, or LET, particle) radiation exposure in astronauts, and also selecting therapeutic irradiation regimes for cancer patients. We identified single nucleotide polymorphisms in 15 strains of mice, including 10 collaborative cross model strains and 5 founder strains, associated with spontaneous and ionizing radiation-induced in vitro DNA damage quantified based on immunofluorescent tumor protein p53 binding protein (53BP1) positive nuclear foci. Statistical analysis suggested an association with pathways primarily related to cellular signaling, metabolism, tumorigenesis and nervous system damage. We observed different genomic associations in early (4 and 8 h) responses to different LET radiation, while later (24 hour) DNA damage responses showed a stronger overlap across all LETs. Furthermore, a subset of pathways was associated with spontaneous DNA damage, suggesting 53BP1 positive foci as a potential biomarker for DNA integrity in mouse models. Our results suggest several mouse strains as new models to further study the impact of ionizing radiation and validate the identified genetic loci. We also highlight the importance of future human in vitro studies to refine the association of genes and pathways with the DNA damage response to ionizing radiation and identify targets for space travel countermeasures.
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Affiliation(s)
- Egle Cekanaviciute
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Duc Tran
- Department of Computer Science and Engineering, University of Nevada, Reno, NV 89557, USA
| | - Hung Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, NV 89557, USA
| | - Alejandra Lopez Macha
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Blue Marble Space Institute of Science, 600 1st Avenue, 1st Floor, Seattle, WA 98104, USA
| | - Eloise Pariset
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Universities Space Research Association, 615 National Avenue, Mountain View, CA 94043, USA
| | - Sasha Langley
- Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA, and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Giulia Babbi
- Bologna Biocomputing Group, FABIT, University of Bologna, Via Belmeloro 6, Bologna, Italy
| | - Sherina Malkani
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Blue Marble Space Institute of Science, 600 1st Avenue, 1st Floor, Seattle, WA 98104, USA
| | - Sébastien Penninckx
- Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA, and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA; Medical Physics Department, Jules Bordet Institute, Université Libre de Bruxelles, 90 Rue Meylemeersch, 1070 Brussels, Belgium
| | - Jonathan C Schisler
- McAllister Heart Institute and Department of Pharmacology, The University of North Carolina at Chapel Hill, NC 27599, USA
| | - Tin Nguyen
- Department of Computer Science and Engineering, University of Nevada, Reno, NV 89557, USA
| | - Gary H Karpen
- Molecular and Cell Biology, UC Berkeley, Berkeley, CA 94720, USA, and Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.
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21
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Roman LJ, Snijders AM, Chang H, Mao JH, Jones KJA, Lawson GW. Effect of Husbandry Practices on the Fecal Microbiota of C57BL/6J Breeding Colonies Housed in 2 Different Barrier Facilities in the Same Institution. JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE : JAALAS 2023; 62:26-37. [PMID: 36755206 PMCID: PMC9936858 DOI: 10.30802/aalas-jaalas-22-000068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Evidence showing a relationship between the mouse gut microbiome and properties such as phenotype and reaction to therapeutic agents and other treatments has increased significantly over the past 20 to 30 y. Recent concerns regarding the reproducibility of animal experiments have underscored the importance of understanding this relationship and how differences in husbandry practices can affect the gut microbiome. The current study focuses on effects of different barrier practices in 2 barrier facilities at the same institution on the fecal microbiome of breeding C57Bl/6J mice. Ten female and 10 male C57Bl/6J mice were obtained in one shipment from Jackson Laboratories and were housed under different barrier conditions upon arrival. Fecal samples were collected on arrival and periodically thereafter and were sent to TransnetYX for microbiome analysis. Mice used for collection of feces were housed as breeding pairs, with a total of 5 breeding pairs per barrier. An additional fecal sample was collected from these mice at 8 wk after arrival. One F1 female and one F1 male from each breeding cage were housed as brother-sister breeding pairs and a fecal sample was collected from them at 8 wk of age. Brother-sister breeding colonies were continued through F3, with fecal samples for microbiome analysis were collected from each generation at 8 wk of age. Breeding colonies in the 2 barriers showed differences in relative abundance, α -diversity, and β -diversity. Our data indicate that differences in barrier husbandry practices, including the use of autoclaved cages, the degree of restricted access, feed treatment practices, and water provision practices, can affect fecal microbiome divergence in both the parental and filial generations of different breeding colonies. To our knowledge, this is the first study to examine the effect of barrier husbandry practices on the microbiome of breeding colonies through the F3 generation.
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Affiliation(s)
- Libette J Roman
- Office of Laboratory Animal Care, University of California Berkeley, Berkeley, California,,Corresponding author.
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Kristina JA Jones
- Office of Laboratory Animal Care, University of California Berkeley, Berkeley, California
| | - Gregory W Lawson
- Office of Laboratory Animal Care, University of California Berkeley, Berkeley, California
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22
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Hanhimäki E, Watts PC, Koskela E, Koteja P, Mappes T, Hämäläinen AM. Evolved high aerobic capacity has context-specific effects on gut microbiota. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.934164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Gut microbiota is expected to coevolve with the host's physiology and may play a role in adjusting the host's energy metabolism to suit the host's environment. To evaluate the effects of both evolved host metabolism and the environmental context in shaping the gut microbiota, we used a unique combination of (1) experimental evolution to create selection lines for a fast metabolism and (2) a laboratory-to-field translocation study. Mature bank voles Myodes glareolus from lines selected for high aerobic capacity (A lines) and from unselected control (C lines) were released into large (0.2 ha) outdoor enclosures for longitudinal monitoring. To examine whether the natural environment elicited a similar or more pronounced impact on the gut microbiota of the next generation, we also sampled the field-reared offspring. The gut microbiota were characterized using 16S rRNA amplicon sequencing of fecal samples. The artificial selection for fast metabolism had minimal impact on the gut microbiota in laboratory conditions but in field conditions, there were differences between the selection lines (A lines vs. C lines) in the diversity, community, and resilience of the gut microbiota. Notably, the selection lines differed in the less abundant bacteria throughout the experiment. The lab-to-field transition resulted in an increase in alpha diversity and an altered community composition in the gut microbiota, characterized by a significant increase in the relative abundance of Actinobacteria and a decrease of Patescibacteria. Also, the selection lines showed different temporal patterns in changes in microbiota composition, as the average gut microbiota alpha diversity of the C lines, but not A lines, was temporarily reduced during the initial transition to the field. In surviving young voles, the alpha diversity of gut microbiota was significantly higher in A-line than C-line voles. These results indicate that the association of host metabolism and gut microbiota is context-specific, likely mediated by behavioral or physiological modifications in response to the environment.
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23
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Strilbytska OM, Semaniuk UV, Strutynska TR, Burdyliuk NI, Tsiumpala S, Bubalo V, Lushchak O. Herbicide Roundup shows toxic effects in nontarget organism Drosophila. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 110:e21893. [PMID: 35388481 DOI: 10.1002/arch.21893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/10/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
Glyphosate-based herbicide Roundup, as the most employed herbicide used for multiple purposes in agriculture, adversely affects nontarget organisms. We tested the effects of Roundup applied at larval and adult stages. Roundup caused developmental delay and increased larvae mortality. Roundup treatment reduced hemolymph glucose and glycogen levels in adult flies of both sexes at the highest concentration tested. Sex-dependent diverse effects were found in catalase and Cu,Zn superoxide dismutase (Cu,Zn-SOD) activities. Decreased aconitase activity, contents of thiols, and lipid peroxides were found after larval Roundup exposure. Furthermore, chronic exposure to adult flies decreased appetite, body weight, and shortened lifespan. Thus, our results suggest that high concentrations of Roundup are deleterious to both larvae and adults, resulting in a shift of the metabolism and antioxidant defense system in Drosophila melanogaster.
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Affiliation(s)
- Olha M Strilbytska
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
| | - Uliana V Semaniuk
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
| | - Tetiana R Strutynska
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
| | - Nadia I Burdyliuk
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
| | - Sviatoslav Tsiumpala
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
| | - Volodymyr Bubalo
- Laboratory of Experimental Toxicology and Mutagenesis, L.I. Medved's Research Center of Preventive Toxicology, Food and Chemical Safety, MHU, Kyiv, Ukraine
| | - Oleh Lushchak
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
- Research and Development University, Ivano-Frankivsk, Ukraine
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24
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Killinger BJ, Whidbey C, Sadler NC, DeLeon AJ, Munoz N, Kim YM, Wright AT. Activity-based protein profiling identifies alternating activation of enzymes involved in the bifidobacterium shunt pathway or mucin degradation in the gut microbiome response to soluble dietary fiber. NPJ Biofilms Microbiomes 2022; 8:60. [PMID: 35858888 PMCID: PMC9300575 DOI: 10.1038/s41522-022-00313-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/14/2022] [Indexed: 02/07/2023] Open
Abstract
While deprivation of dietary fiber has been associated with adverse health outcomes, investigations concerning the effect of dietary fiber on the gut microbiome have been largely limited to compositional sequence-based analyses or utilize a defined microbiota not native to the host. To extend understanding of the microbiome's functional response to dietary fiber deprivation beyond correlative evidence from sequence-based analyses, approaches capable of measuring functional enzymatic activity are needed. In this study, we use an activity-based protein profiling (ABPP) approach to identify sugar metabolizing and transport proteins in native mouse gut microbiomes that respond with differential activity to the deprivation or supplementation of the soluble dietary fibers inulin and pectin. We found that the microbiome of mice subjected to a high fiber diet high in soluble fiber had increased functional activity of multiple proteins, including glycoside hydrolases, polysaccharide lyases, and sugar transport proteins from diverse taxa. The results point to an increase in activity of the Bifidobacterium shunt metabolic pathway in the microbiome of mice fed high fiber diets. In those subjected to a low fiber diet, we identified a shift from the degradation of dietary fibers to that of gut mucins, in particular by the recently isolated taxon "Musculibacterium intestinale", which experienced dramatic growth in response to fiber deprivation. When combined with metabolomics and shotgun metagenomics analyses, our findings provide a functional investigation of dietary fiber metabolism in the gut microbiome and demonstrates the power of a combined ABPP-multiomics approach for characterizing the response of the gut microbiome to perturbations.
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Affiliation(s)
- Bryan J Killinger
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, 99163, USA
| | - Christopher Whidbey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
- Chemistry Department, Seattle University, Seattle, WA, 98122, USA
| | - Natalie C Sadler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Adrian J DeLeon
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Nathalie Munoz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Aaron T Wright
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
- The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, WA, 99163, USA.
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25
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Doms S, Fokt H, Rühlemann MC, Chung CJ, Kuenstner A, Ibrahim SM, Franke A, Turner LM, Baines JF. Key features of the genetic architecture and evolution of host-microbe interactions revealed by high-resolution genetic mapping of the mucosa-associated gut microbiome in hybrid mice. eLife 2022; 11:75419. [PMID: 35866635 PMCID: PMC9307277 DOI: 10.7554/elife.75419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 06/14/2022] [Indexed: 12/13/2022] Open
Abstract
Determining the forces that shape diversity in host-associated bacterial communities is critical to understanding the evolution and maintenance of metaorganisms. To gain deeper understanding of the role of host genetics in shaping gut microbial traits, we employed a powerful genetic mapping approach using inbred lines derived from the hybrid zone of two incipient house mouse species. Furthermore, we uniquely performed our analysis on microbial traits measured at the gut mucosal interface, which is in more direct contact with host cells and the immune system. Several mucosa-associated bacterial taxa have high heritability estimates, and interestingly, 16S rRNA transcript-based heritability estimates are positively correlated with cospeciation rate estimates. Genome-wide association mapping identifies 428 loci influencing 120 taxa, with narrow genomic intervals pinpointing promising candidate genes and pathways. Importantly, we identified an enrichment of candidate genes associated with several human diseases, including inflammatory bowel disease, and functional categories including innate immunity and G-protein-coupled receptors. These results highlight key features of the genetic architecture of mammalian host-microbe interactions and how they diverge as new species form. The digestive system, particularly the large intestine, hosts many types of bacteria which together form the gut microbiome. The exact makeup of different bacterial species is specific to an individual, but microbiomes are often more similar between related individuals, and more generally, across related species. Whether this is because individuals share similar environments or similar genetic backgrounds remains unclear. These two factors can be disentangled by breeding different animal lineages – which have different genetic backgrounds while belonging to the same species – and then raising the progeny in the same environment. To investigate this question, Doms et al. studied the genes and microbiomes of mice resulting from breeding strains from multiple locations in a natural hybrid zone between different subspecies. The experiments showed that 428 genetic regions affected the makeup of the microbiome, many of which were known to be associated with human diseases. Further analysis revealed 79 genes that were particularly interesting, as they were involved in recognition and communication with bacteria. These results show how the influence of the host genome on microbiome composition becomes more specialized as animals evolve. Overall, the work by Doms et al. helps to pinpoint the genes that impact the microbiome; this knowledge could be helpful to examine how these interactions contribute to the emergence of conditions such as diabetes or inflammatory bowel disease, which are linked to perturbations in gut bacteria.
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Affiliation(s)
- Shauni Doms
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Hanna Fokt
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Malte Christoph Rühlemann
- Institute for Clinical Molecular Biology (IKMB), Kiel University, Kiel, Germany.,Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Cecilia J Chung
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Axel Kuenstner
- Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Saleh M Ibrahim
- Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany.,Sharjah Institute of Medical Research, Sharjah, United Arab Emirates
| | - Andre Franke
- Institute for Clinical Molecular Biology (IKMB), Kiel University, Kiel, Germany
| | - Leslie M Turner
- Milner Centre for Evolution, Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, Plön, Germany.,Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
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26
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Özçam M, Oh JH, Tocmo R, Acharya D, Zhang S, Astmann TJ, Heggen M, Ruiz-Ramírez S, Li F, Cheng CC, Vivas E, Rey FE, Claesen J, Bugni TS, Walter J, van Pijkeren JP. A secondary metabolite drives intraspecies antagonism in a gut symbiont that is inhibited by cell-wall acetylation. Cell Host Microbe 2022; 30:824-835.e6. [PMID: 35443156 DOI: 10.1016/j.chom.2022.03.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/16/2021] [Accepted: 03/25/2022] [Indexed: 11/03/2022]
Abstract
The mammalian microbiome encodes numerous secondary metabolite biosynthetic gene clusters; yet, their role in microbe-microbe interactions is unclear. Here, we characterized two polyketide synthase gene clusters (fun and pks) in the gut symbiont Limosilactobacillus reuteri. The pks, but not the fun, cluster encodes antimicrobial activity. Forty-one of 51 L. reuteri strains tested are sensitive to Pks products; this finding was independent of strains' host origin. Sensitivity to Pks was also established in intraspecies competition experiments in gnotobiotic mice. Comparative genome analyses between Pks-resistant and -sensitive strains identified an acyltransferase gene (act) unique to Pks-resistant strains. Subsequent cell-wall analysis of wild-type and act mutant strains showed that Act acetylates cell-wall components, providing resistance to Pks-mediated killing. Additionally, pks mutants lost their competitive advantage, while act mutants lost their Pks resistance in in vivo competition assays. These findings provide insight into how closely related gut symbionts can compete and co-exist in the gastrointestinal tract.
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Affiliation(s)
- Mustafa Özçam
- Department of Food Science, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jee-Hwan Oh
- Department of Food Science, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Restituto Tocmo
- Department of Food Science, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Deepa Acharya
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Shenwei Zhang
- Department of Food Science, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Theresa J Astmann
- Department of Food Science, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Mark Heggen
- Department of Food Science, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Fuyong Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Christopher C Cheng
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Eugenio Vivas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Federico E Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jan Claesen
- Department of Cardiovascular and Metabolic Sciences and Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Tim S Bugni
- Pharmaceutical Sciences Division, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jens Walter
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2P5, Canada; Department of Medicine and APC Microbiome Ireland, University College Cork, Cork T12 K8AF, Ireland; School of Microbiology, University College Cork, Cork T12 YT20, Ireland
| | - Jan-Peter van Pijkeren
- Department of Food Science, University of Wisconsin-Madison, Madison, WI 53706, USA; Food Research Institute, University of Wisconsin-Madison, Madison, WI 53706, USA.
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27
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Carranco AS, Romo D, de Lourdes Torres M, Wilhelm K, Sommer S, Gillingham MAF. Egg microbiota is the starting point of hatchling gut microbiota in the endangered yellow-spotted Amazon river turtle. Mol Ecol 2022; 31:3917-3933. [PMID: 35621392 DOI: 10.1111/mec.16548] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/30/2022] [Accepted: 05/17/2022] [Indexed: 11/29/2022]
Abstract
Establishment and development of gut microbiota during vertebrates' early life are likely to be important predictors of health and fitness. Host-parental and host-environment interactions are essential to these processes. In oviparous reptiles whose nests represent a source of the parent's microbial inocula, the relative role of host-selection and stochastic environmental factors during gut microbial assemblage remains unknown. We sampled eggs incubated in artificial nests as well as hatchlings and juveniles (up to 30 days old) of the yellow-spotted Amazon river turtle (Podocnemis unifilis) developing in tubs filled with river water. We examined the relative role of the internal egg microbiota and the abiotic environment on hatchling and juvenile turtle's cloacal microbiota assemblages during the first 30 days of development. A mean of 71% of ASVs in hatched eggs could be traced to the nest environmental microbiota and in turn a mean of 77% of hatchlings' cloacal ASVs were traced to hatched eggs. Between day 5 and 20 of juvenile turtle's development, the river water environment plays a key role in the establishment of the gut microbiota (accounting for a mean of 13%-34.6% of cloacal ASVs) and strongly influences shifts in microbial diversity and abundance. After day 20, shifts in gut microbiota composition were mainly driven by host-selection processes. Therefore, colonization by environmental microbiota is key in the initial stages of establishing the host's gut microbiota which is subsequently shaped by host-selection processes. Our study provides a novel quantitative understanding of the host-environment interactions during gut microbial assemblage of oviparous reptiles.
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Affiliation(s)
- Ana Sofia Carranco
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - David Romo
- Tiputini Biodiversity Station, Universidad San Francisco de Quito, Cumbaya-, Quito, Ecuador
| | - Maria de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito, Cumbaya-, Quito, Ecuador
| | - Kerstin Wilhelm
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Mark A F Gillingham
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany.,Biodiversity Research Institute (CSIC, Oviedo University, Principality of Asturias), Campus of Mieres, University of Oviedo, 33600, Mieres, Spain
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28
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Juhász Á, Molnár-Nagy V, Bata Z, Tso KH, Mayer Z, Posta K. Alternative to ZnO to establish balanced intestinal microbiota for weaning piglets. PLoS One 2022; 17:e0265573. [PMID: 35298549 PMCID: PMC8929640 DOI: 10.1371/journal.pone.0265573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/02/2022] [Indexed: 11/28/2022] Open
Abstract
A wide range of phytobiotic feed additives are available on the market claiming to have beneficial effects on the growth of the host animal and to promote the development of a balanced microflora. The present study investigated the effects of the phytobiotic-prebiotic mixture of curcumin, wheat germ, and chicory on the growth performance and on the intestinal microflora composition of weaning piglets. Post weaning diarrhea causes significant losses for the producers, most commonly it is prevented by feeding high doses of zinc oxide (ZnO). The effect of a phytobiotic-prebiotic feed additive (1 kg T-1) was compared to a positive control (3.1 kg T-1 ZnO) and to a negative control (no feed supplement) in an in vivo animal trial. There was no significant difference in the final body weight and average daily gain of the trial and positive control groups, and both groups showed significantly (P<0.05) better results than the negative control. The feed conversion ratio of the phytobiotic-prebiotic supplemented group was significantly improved (P<0.05) compared to both controls. Both phytobiotic-prebiotic mixture and ZnO were able to significantly reduce (P<0.05) the amount of coliforms after weaning, even though ZnO reduced the amount of coliforms more efficiently than the trial feed additive, it also reduced the amount of potentially beneficial bacteria. Metagenomic data also corroborated the above conclusion. In the trial and positive control groups, the relative abundance of Enterobacteriaceae decreased by 85 and 88% between 3 weeks and 6 weeks of age, while in the negative control group a slight increase occurred. Lactobacillaceae were more abundant in the trial group (29.98%) than in the positive (8.67%) or in the negative (22.45%) control groups at 6 weeks of age. In summary, this study demonstrated that a phytobiotic-prebiotic feed additive may be a real alternative to ZnO for the prevention of post weaning diarrhea and promote the development of a balanced gut system.
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Affiliation(s)
- Ákos Juhász
- Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
- * E-mail:
| | | | | | - Ko-Hua Tso
- Dr. Bata Ltd, Ócsa, Hungary
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
| | - Zoltán Mayer
- Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Katalin Posta
- Department of Microbiology and Applied Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
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Davies CS, Worsley SF, Maher KH, Komdeur J, Burke T, Dugdale HL, Richardson DS. Immunogenetic variation shapes the gut microbiome in a natural vertebrate population. MICROBIOME 2022; 10:41. [PMID: 35256003 PMCID: PMC8903650 DOI: 10.1186/s40168-022-01233-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The gut microbiome (GM) can influence many biological processes in the host, impacting its health and survival, but the GM can also be influenced by the host's traits. In vertebrates, Major Histocompatibility Complex (MHC) genes play a pivotal role in combatting pathogens and are thought to shape the host's GM. Despite this-and the documented importance of both GM and MHC variation to individual fitness-few studies have investigated the association between the GM and MHC in the wild. RESULTS We characterised MHC class I (MHC-I), MHC class II (MHC-II) and GM variation in individuals within a natural population of the Seychelles warbler (Acrocephalus sechellensis). We determined how the diversity and composition of the GM varied with MHC characteristics, in addition to environmental factors and other host traits. Our results show that the presence of specific MHC alleles, but not MHC diversity, influences both the diversity and composition of the GM in this population. MHC-I alleles, rather than MHC-II alleles, had the greatest impact on the GM. GM diversity was negatively associated with the presence of three MHC-I alleles (Ase-ua3, Ase-ua4, Ase-ua5), and one MHC-II allele (Ase-dab4), while changes in GM composition were associated with the presence of four different MHC-I alleles (Ase-ua1, Ase-ua7, Ase-ua10, Ase-ua11). There were no associations between GM diversity and TLR3 genotype, but GM diversity was positively correlated with genome-wide heterozygosity and varied with host age and field period. CONCLUSIONS These results suggest that components of the host's immune system play a role in shaping the GM of wild animals. Host genotype-specifically MHC-I and to a lesser degree MHC-II variation-can modulate the GM, although whether this occurs directly, or indirectly through effects on host health, is unclear. Importantly, if immune genes can regulate host health through modulation of the microbiome, then it is plausible that the microbiome could also influence selection on immune genes. As such, host-microbiome coevolution may play a role in maintaining functional immunogenetic variation within natural vertebrate populations. Video abstract.
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Affiliation(s)
- Charli S Davies
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK.
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
| | - Kathryn H Maher
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jan Komdeur
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Terry Burke
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Hannah L Dugdale
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
- Faculty of Biological Sciences, School of Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norfolk, NR4 7TJ, UK
- Nature Seychelles, Roche Caiman, Mahé, Republic of Seychelles
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Noecker C, Eng A, Muller E, Borenstein E. MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data. Bioinformatics 2022; 38:1615-1623. [PMID: 34999748 PMCID: PMC8896604 DOI: 10.1093/bioinformatics/btac003] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/22/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
MOTIVATION Recent technological developments have facilitated an expansion of microbiome-metabolome studies, in which samples are assayed using both genomic and metabolomic technologies to characterize the abundances of microbial taxa and metabolites. A common goal of these studies is to identify microbial species or genes that contribute to differences in metabolite levels across samples. Previous work indicated that integrating these datasets with reference knowledge on microbial metabolic capacities may enable more precise and confident inference of microbe-metabolite links. RESULTS We present MIMOSA2, an R package and web application for model-based integrative analysis of microbiome-metabolome datasets. MIMOSA2 uses genomic and metabolic reference databases to construct a community metabolic model based on microbiome data and uses this model to predict differences in metabolite levels across samples. These predictions are compared with metabolomics data to identify putative microbiome-governed metabolites and taxonomic contributors to metabolite variation. MIMOSA2 supports various input data types and customization with user-defined metabolic pathways. We establish MIMOSA2's ability to identify ground truth microbial mechanisms in simulation datasets, compare its results with experimentally inferred mechanisms in honeybee microbiota, and demonstrate its application in two human studies of inflammatory bowel disease. Overall, MIMOSA2 combines reference databases, a validated statistical framework, and a user-friendly interface to facilitate modeling and evaluating relationships between members of the microbiota and their metabolic products. AVAILABILITY AND IMPLEMENTATION MIMOSA2 is implemented in R under the GNU General Public License v3.0 and is freely available as a web server at http://elbo-spice.cs.tau.ac.il/shiny/MIMOSA2shiny/ and as an R package from http://www.borensteinlab.com/software_MIMOSA2.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Cecilia Noecker
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Alexander Eng
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Efrat Muller
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Elhanan Borenstein
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 6997801, Israel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Santa Fe Institute, Santa Fe, NM 87501, USA
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Ryu EP, Davenport ER. Host Genetic Determinants of the Microbiome Across Animals: From Caenorhabditis elegans to Cattle. Annu Rev Anim Biosci 2022; 10:203-226. [PMID: 35167316 PMCID: PMC11000414 DOI: 10.1146/annurev-animal-020420-032054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Animals harbor diverse communities of microbes within their gastrointestinal tracts. Phylogenetic relationship, diet, gut morphology, host physiology, and ecology all influence microbiome composition within and between animal clades. Emerging evidence points to host genetics as also playing a role in determining gut microbial composition within species. Here, we discuss recent advances in the study of microbiome heritability across a variety of animal species. Candidate gene and discovery-based studies in humans, mice, Drosophila, Caenorhabditis elegans, cattle, swine, poultry, and baboons reveal trends in the types of microbes that are heritable and the host genes and pathways involved in shaping the microbiome. Heritable gut microbes within a host species tend to be phylogenetically restricted. Host genetic variation in immune- and growth-related genes drives the abundances of these heritable bacteria within the gut. With only a small slice of the metazoan branch of the tree of life explored to date, this is an area rife with opportunities to shed light into the mechanisms governing host-microbe relationships.
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Affiliation(s)
- Erica P Ryu
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA; ,
| | - Emily R Davenport
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, USA; ,
- Huck Institutes of the Life Sciences and Institute for Computational and Data Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
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Irons EE, Cortes Gomez E, Andersen VL, Lau JTY. Bacterial colonization and TH17 immunity are shaped by intestinal sialylation in neonatal mice. Glycobiology 2022; 32:414-428. [PMID: 35157771 PMCID: PMC9022908 DOI: 10.1093/glycob/cwac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/10/2022] [Accepted: 01/30/2022] [Indexed: 11/14/2022] Open
Abstract
Interactions between the neonate host and its gut microbiome are central to the development of a healthy immune system. However, the mechanisms by which animals alter early colonization of microbiota for their benefit remain unclear. Here, we investigated the role of early-life expression of the α2,6-sialyltransferase ST6GAL1 in microbiome phylogeny and mucosal immunity. Fecal, upper respiratory, and oral microbiomes of pups expressing or lacking St6gal1 were analyzed by 16S rRNA sequencing. At weaning, the fecal microbiome of St6gal1-KO mice had reduced Clostridiodes, Coprobacillus, and Adlercreutzia, but increased Helicobacter and Bilophila. Pooled fecal microbiomes from syngeneic donors were transferred to antibiotic-treated wild-type mice, before analysis of recipient mucosal immune responses by flow cytometry, RT-qPCR, microscopy, and ELISA. Transfer of St6gal1-KO microbiome induced a mucosal Th17 response, with expression of T-bet and IL-17, and IL-22-dependent gut lengthening. Early life intestinal sialylation was characterized by RT-qPCR, immunoblot, microscopy, and sialyltransferase enzyme assays in genetic mouse models at rest or with glucocorticoid receptor modulators. St6gal1 expression was greatest in the duodenum, where it was mediated by the P1 promoter and efficiently inhibited by dexamethasone. Our data show that the inability to produce α2,6-sialyl ligands contributes to microbiome-dependent Th17 inflammation, highlighting a pathway by which the intestinal glycosylation regulates mucosal immunity.
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Affiliation(s)
- Eric E Irons
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY 14263, United States
| | - Eduardo Cortes Gomez
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY 14263, United States
| | - Valerie L Andersen
- Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY 14263, United States
| | - Joseph T Y Lau
- Corresponding author: Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, NY 14263, USA.
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Di DS, Li C, Dai Y, Wei MH, Wang SS, Song WJ, Zhou HL, Cui Y, Zhang RY, Huang Q, Wang Q. Integrative Analysis of LGR5/6 Gene Variants, Gut Microbiota Composition and Osteoporosis Risk in Elderly Population. Front Microbiol 2021; 12:765008. [PMID: 34795657 PMCID: PMC8593465 DOI: 10.3389/fmicb.2021.765008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022] Open
Abstract
Objective: This study aimed to explore the relationships between the common variants of R-spondin/Wnt signaling genes, gut microbiota composition, and osteoporosis (OP) risk in elderly Chinese Han population. Design: Dual-energy X-ray absorptiometry was used to obtain the OP-associated measurements at multiple skeleton sites among all 1,168 participants. Genotyping data was obtained by using the next-generation sequencing in the discovery stage (n = 400, 228 OP patients) and SNPscan technology in the replication stage (n = 768, 356 OP patients). Bioinformatic analysis was performed to provide more evidence for the genotype-OP associations. The 16S ribosomal RNA gene high-throughput sequencing technology was adopted to explore OP-associated gut microbiota variations. Results: The genetic variants of rs10920362 in the LGR6 gene (P-FDR = 1.19 × 10–6) and rs11178860 in the LGR5 gene (P-FDR = 1.51 × 10–4) were found to associate with OP risk significantly. Several microbial taxa were associated with the BMDs and T-scores at multiple skeleton sites. The associations between rs10920362 and BMD-associated microbiota maintained significance after adjusting confounders. The rs10920362 CT/TT genotype associated with a decreased relative abundance of Actinobacteria (β = −1.32, P < 0.001), Bifidobacteriaceae (β = −1.70, P < 0.001), and Bifidobacterium (β = −1.70, P < 0.001) compared to the CC genotype. Conclusion: Our findings suggested that the variants loci of LGR6 may be associate with OP pathogenesis via gut microbiota modifications. The relationship between host genetics and gut microbiome provides new perspectives about OP prevention and treatment.
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Affiliation(s)
- Dong-Sheng Di
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Can Li
- Department of Cancer Prevention and Control, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Yu Dai
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mu-Hong Wei
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shan-Shan Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wen-Jing Song
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hao-Long Zhou
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Cui
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ru-Yi Zhang
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qin Huang
- Department of Rehabilitation Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qi Wang
- MOE Key Lab of Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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De Spiegeleer M, De Paepe E, Van Meulebroek L, Gies I, De Schepper J, Vanhaecke L. Paediatric obesity: a systematic review and pathway mapping of metabolic alterations underlying early disease processes. Mol Med 2021; 27:145. [PMID: 34742239 PMCID: PMC8571978 DOI: 10.1186/s10020-021-00394-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/02/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The alarming trend of paediatric obesity deserves our greatest awareness to hinder the early onset of metabolic complications impacting growth and functionality. Presently, insight into molecular mechanisms of childhood obesity and associated metabolic comorbidities is limited. This systematic review aimed at scrutinising what has been reported on putative metabolites distinctive for metabolic abnormalities manifesting at young age by searching three literature databases (Web of Science, Pubmed and EMBASE) during the last 6 years (January 2015-January 2021). Global metabolomic profiling of paediatric obesity was performed (multiple biological matrices: blood, urine, saliva and adipose tissue) to enable overarching pathway analysis and network mapping. Among 2792 screened Q1 articles, 40 met the eligibility criteria and were included to build a database on metabolite markers involved in the spectrum of childhood obesity. Differential alterations in multiple pathways linked to lipid, carbohydrate and amino acid metabolisms were observed. High levels of lactate, pyruvate, alanine and acetate marked a pronounced shift towards hypoxic conditions in children with obesity, and, together with distinct alterations in lipid metabolism, pointed towards dysbiosis and immunometabolism occurring early in life. Additionally, aberrant levels of several amino acids, most notably belonging to tryptophan metabolism including the kynurenine pathway and its relation to histidine, phenylalanine and purine metabolism were displayed. Moreover, branched-chain amino acids were linked to lipid, carbohydrate, amino acid and microbial metabolism, inferring a key role in obesity-associated insulin resistance. CONCLUSIONS This systematic review revealed that the main metabolites at the crossroad of dysregulated metabolic pathways underlying childhood obesity could be tracked down to one central disturbance, i.e. impending insulin resistance for which reference values and standardised measures still are lacking. In essence, glycolytic metabolism was evinced as driving energy source, coupled to impaired Krebs cycle flux and ß-oxidation. Applying metabolomics enabled to retrieve distinct metabolite alterations in childhood obesity(-related insulin resistance) and associated pathways at early age and thus could provide a timely indication of risk by elucidating early-stage biomarkers as hallmarks of future metabolically unhealthy phenotypes.
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Affiliation(s)
- Margot De Spiegeleer
- Laboratory of Chemical Analysis, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Ellen De Paepe
- Laboratory of Chemical Analysis, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Lieven Van Meulebroek
- Laboratory of Chemical Analysis, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Inge Gies
- KidZ Health Castle, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101, 1090, Brussel, Belgium
| | - Jean De Schepper
- KidZ Health Castle, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Laarbeeklaan 101, 1090, Brussel, Belgium.,Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Lynn Vanhaecke
- Laboratory of Chemical Analysis, Department of Translational Physiology, Infectiology and Public Health, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium. .,Institute for Global Food Security, School of Biological Sciences, Queen's University, University Road, Belfast, BT7 1NN, UK.
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Xu J, Zhang JN, Sun BH, Liu Q, Ma J, Zhang Q, Liu YX, Chen N, Chen F. The role of genotype and diet in shaping gut microbiome in a genetic vitamin A deficient mouse model. J Genet Genomics 2021; 49:155-164. [PMID: 34537414 DOI: 10.1016/j.jgg.2021.08.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/26/2022]
Abstract
Multifactors have been reported to affect the gut microbiome, including genotype, age, diet, and nutrition. However, few reports have investigated the relative capacity of different factors to shape the gut microbiome in a single study. Our design used a genetic vitamin A-deficient mouse model, the Rbp4-/- mouse, feeding with the low vitamin A diets at different ages of initiation (4 or 7 weeks) for 28 days. Fecal samples were collected for bacterial profiling at seven time points after diet controlling. With RBP4 depletion, Akkermansia decreased and Bacteroides increased, whereas Desulfovibrio, Barnesiella, Clostridium_XlVa, and Lactobacillus fluctuated. The bacterial community swiftly adjusted with the vitamin A-deficient diet administration and gradually changed (e.g., decrease of Barnesiella and increase of Desulfovibrio). Age exerted a relatively weaker but long-last influence. At an earlier age to feed a vitamin A-deficient diet, a higher microbial dysbiosis index will be valued. Of note, the shaping effects of diet and age on the bacterial community varied with the difference of genotype, which might indicate a greater role of genotype than diet and age in shaping the gut microbiome.
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Affiliation(s)
- Jun Xu
- Department of Gastroenterology, Peking University People's Hospital, Beijing 100044, China; Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing 100044, China; Institute of Clinical Molecular Biology & Central Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Jie-Ni Zhang
- Department of Orthodontics, Peking University School of Stomatology, Beijing 100081, China
| | - Bo-Hui Sun
- Department of Orthodontics, Peking University School of Stomatology, Beijing 100081, China
| | - Qing Liu
- Department of Gastroenterology, Peking University People's Hospital, Beijing 100044, China; Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing 100044, China
| | - Juan Ma
- Department of Gastroenterology, Peking University People's Hospital, Beijing 100044, China; Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing 100044, China
| | - Qian Zhang
- Central Laboratory, Peking University School of Stomatology, Beijing 100081, China
| | - Yong-Xin Liu
- CAS Center for Excellence in Biotic Interactions, Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Chen
- Department of Gastroenterology, Peking University People's Hospital, Beijing 100044, China; Clinical Center of Immune-Mediated Digestive Diseases, Peking University People's Hospital, Beijing 100044, China.
| | - Feng Chen
- Department of Orthodontics, Peking University School of Stomatology, Beijing 100081, China; Central Laboratory, Peking University School of Stomatology, Beijing 100081, China.
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Bredeck G, Kämpfer AAM, Sofranko A, Wahle T, Lison D, Ambroise J, Stahlmecke B, Albrecht C, Schins RPF. Effects of dietary exposure to the engineered nanomaterials CeO 2, SiO 2, Ag, and TiO 2 on the murine gut microbiome. Nanotoxicology 2021; 15:934-950. [PMID: 34380002 DOI: 10.1080/17435390.2021.1940339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Rodent studies on the effects of engineered nanomaterials (ENM) on the gut microbiome have revealed contradictory results. Our aim was to assess the effects of four well-investigated model ENM using a realistic exposure scenario. Two independent ad libitum feeding studies were performed. In study 1, female mice from the local breeding facility received feed pellets containing 1% CeO2 or 1% SiO2 for three weeks. In study 2, both female and male mice were purchased and exposed to 0.2% Ag-PVP or 1% TiO2 for four weeks. A next generation 16S rDNA sequencing-based approach was applied to assess impacts on the gut microbiome. None of the ENM had an effect on the α- or β-diversity. A decreased relative abundance of the phylum Actinobacteria was observed in SiO2 exposed mice. In female mice, the relative abundance of the genus Roseburia was increased with Ag exposure. Furthermore, in study 2, a sex-related difference in the β-diversity was observed. A difference in the β-diversity was also shown between the female control mice of the two studies. We did not find major effects on the gut microbiome. This contrast to other studies may be due to variations in the study design. Our investigation underlined the important role of the sex of test animals and their microbiome composition prior to ENM exposure initiation. Hence, standardization of microbiome studies is strongly required to increase comparability. The ENM-specific effects on Actinobacteria and Roseburia, two taxa pivotal for the human gut homeostasis, warrant further research on their relevance for health.
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Affiliation(s)
- Gerrit Bredeck
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Angela A M Kämpfer
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Adriana Sofranko
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Tina Wahle
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Dominique Lison
- Louvain Centre for Toxicology and Applied Pharmacology, Université Catholique de Louvain, Brussels, Belgium
| | - Jérôme Ambroise
- Centre de Technologies Moléculaires Appliquées, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium
| | - Burkhard Stahlmecke
- Institute for Energy and Environmental Technology e.V. (IUTA), Duisburg, Germany
| | - Catrin Albrecht
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
| | - Roel P F Schins
- IUF - Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
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Bubier JA, Chesler EJ, Weinstock GM. Host genetic control of gut microbiome composition. Mamm Genome 2021; 32:263-281. [PMID: 34159422 PMCID: PMC8295090 DOI: 10.1007/s00335-021-09884-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/07/2021] [Indexed: 02/07/2023]
Abstract
The gut microbiome plays a significant role in health and disease, and there is mounting evidence indicating that the microbial composition is regulated in part by host genetics. Heritability estimates for microbial abundance in mice and humans range from (0.05-0.45), indicating that 5-45% of inter-individual variation can be explained by genetics. Through twin studies, genetic association studies, systems genetics, and genome-wide association studies (GWAS), hundreds of specific host genetic loci have been shown to associate with the abundance of discrete gut microbes. Using genetically engineered knock-out mice, at least 30 specific genes have now been validated as having specific effects on the microbiome. The relationships among of host genetics, microbiome composition, and abundance, and disease is now beginning to be unraveled through experiments designed to test causality. The genetic control of disease and its relationship to the microbiome can manifest in multiple ways. First, a genetic variant may directly cause the disease phenotype, resulting in an altered microbiome as a consequence of the disease phenotype. Second, a genetic variant may alter gene expression in the host, which in turn alters the microbiome, producing the disease phenotype. Finally, the genetic variant may alter the microbiome directly, which can result in the disease phenotype. In order to understand the processes that underlie the onset and progression of certain diseases, future research must take into account the relationship among host genetics, microbiome, and disease phenotype, and the resources needed to study these relationships.
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Affiliation(s)
- Jason A Bubier
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME, 04609, USA.
| | - Elissa J Chesler
- The Jackson Laboratory for Mammalian Genetics, 600 Main Street, Bar Harbor, ME, 04609, USA
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Li H, Zhao C, Yang Y, Zhou Z, Qi J, Li C. The Influence of Gut Microbiota on the Fecundity of Henosepilachna vigintioctopunctata (Coleoptera: Coccinellidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:15. [PMID: 34415303 PMCID: PMC8378403 DOI: 10.1093/jisesa/ieab061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Indexed: 06/13/2023]
Abstract
The gut microbiota of insects usually plays an important role in the development and reproduction of their hosts. The fecundity of Henosepilachna vigintioctopunctata (Fabricius) varies greatly when they develop on different host plants. Whether and how the gut microbiota regulates the fecundity of H. vigintioctopunctata was unknown. To address this question, we used 16S rRNA sequencing to analyze the gut microbiomes of H. vigintioctopunctata adults fed on two host plant species (Solanum nigrum and Solanum melongena) and one artificial diet. The development of the ovaries and testes was also examined. Our results revealed that the diversity and abundance of gut microorganisms varied significantly in insects reared on different diets. The gut microbiota of H. vigintioctopunctata raised on the two host plants was similar, with Proteobacteria being the dominant phylum in both groups, whereas Firmicutes was the dominant phylum in the group reared on the artificial diet. The predominant microbiota in the S. nigrum group were Acinetobacter soli and Acinetobacter ursingii (Acinetobacter, Moraxellaceae); Moraxella osloensis (Enhydrobacter, Moraxellaceae); and Empedobacter brevis (Empedobacter, Weeksellaceae). The microbiota in this group are associated with high lipid metabolism. In addition, the beetles' ovaries and testes were more highly developed in the S. nigrum group than in the other two groups. These findings provide valuable information for elucidating the complex roles the gut microbiota play in the fecundity of H. vigintioctopunctata, and may also contribute to developing future novel control strategies involving this economically important pest.
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Affiliation(s)
- Hanwen Li
- Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
- Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou 434025, Hubei, China
| | - Changwei Zhao
- Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
- Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou 434025, Hubei, China
| | - Yang Yang
- Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
- Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou 434025, Hubei, China
| | - Zhixiong Zhou
- Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
- Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou 434025, Hubei, China
| | - Jingwei Qi
- Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
- Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou 434025, Hubei, China
| | - Chuanren Li
- Institute of Entomology, College of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
- Hubei Engineering Research Center for Pest Forewarning and Management, Yangtze University, Jingzhou 434025, Hubei, China
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He L, Wang P, Schick SF, Huang A, Jacob P, Yang X, Xia Y, Snijders AM, Mao JH, Chang H, Hang B. Genetic background influences the effect of thirdhand smoke exposure on anxiety and memory in Collaborative Cross mice. Sci Rep 2021; 11:13285. [PMID: 34168244 PMCID: PMC8225773 DOI: 10.1038/s41598-021-92702-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/08/2021] [Indexed: 01/18/2023] Open
Abstract
Growing evidence indicates that thirdhand smoke (THS) exposure induces many adverse health effects. However, it is unclear how THS exposure affects behavior and how host genetic background modulates phenotypic changes. Here we used the Collaborative Cross (CC) mouse population-based model to assess behavioral alterations immediately after THS exposure from 4 to 9 weeks of age. We first measured anxiety-like behavior in six strains using light/dark box combined with a custom multivariate mouse tracking system. We developed an anxiety risk scoring system based on anxiety-related traits and then evaluated the THS impact on them. THS exposure significantly decreased anxiety risk in CC019 (P = 0.002) and CC051 (P = 0.009), but increased anxiety risk in CC036 (P < 0.001), while the other three strains did not show significant changes in anxiety-related traits. Such differences were driven by female mice for the six measures of anxiety-like behavior. Memory potential was measured in the same cohort of mice using the passive avoidance assay. Both THS-exposed male and female CC019 mice displayed significant memory loss compared to controls while no significant changes were found in the other five strains. This study provides strong evidence that THS exposure leads to strain-dependent changes in anxiety-like behavior and memory, suggesting that host genetic variations play a critical role in individual susceptibility to THS-induced effects.
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Affiliation(s)
- Li He
- Department of Internal Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Pin Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, China
| | - Suzyann F Schick
- Division of Occupational and Environmental Medicine, Department of Medicine, University of California, San Francisco, CA, 94143, USA
| | - Abel Huang
- Division of Occupational and Environmental Medicine, Department of Medicine, University of California, San Francisco, CA, 94143, USA
| | - Peyton Jacob
- Division of Cardiology, Department of Medicine, Clinical Pharmacology Program, University of California, San Francisco, CA, 94143, USA
| | - Xu Yang
- School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Yankai Xia
- School of Public Health, Nanjing Medical University, Nanjing, 211166, Jiangsu, China
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Bo Hang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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Zhang F, Weckhorst JL, Assié A, Hosea C, Ayoub CA, Khodakova AS, Cabrera ML, Vidal Vilchis D, Félix MA, Samuel BS. Natural genetic variation drives microbiome selection in the Caenorhabditis elegans gut. Curr Biol 2021; 31:2603-2618.e9. [PMID: 34048707 PMCID: PMC8222194 DOI: 10.1016/j.cub.2021.04.046] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023]
Abstract
Host genetic landscapes can shape microbiome assembly in the animal gut by contributing to the establishment of distinct physiological environments. However, the genetic determinants contributing to the stability and variation of these microbiome types remain largely undefined. Here, we use the free-living nematode Caenorhabditis elegans to identify natural genetic variation among wild strains of C. elegans that drives assembly of distinct microbiomes. To achieve this, we first established a diverse model microbiome that represents the strain-level phylogenetic diversity naturally encountered by C. elegans in the wild. Using this community, we show that C. elegans utilizes immune, xenobiotic, and metabolic signaling pathways to favor the assembly of different microbiome types. Variations in these pathways were associated with enrichment for specific commensals, including the Alphaproteobacteria Ochrobactrum. Using RNAi and mutant strains, we showed that host selection for Ochrobactrum is mediated specifically by host insulin signaling pathways. Ochrobactrum recruitment is blunted in the absence of DAF-2/IGFR and modulated by the competitive action of insulin signaling transcription factors DAF-16/FOXO and PQM-1/SALL2. Further, the ability of C. elegans to enrich for Ochrobactrum as adults is correlated with faster animal growth rates and larger body size at the end of development. These results highlight a new role for the highly conserved insulin signaling pathways in the regulation of gut microbiome composition in C. elegans.
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Affiliation(s)
- Fan Zhang
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Jessica L Weckhorst
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Quantitative and Computational Biosciences, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Ciara Hosea
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Development, Disease Models and Therapeutics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Christopher A Ayoub
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Anastasia S Khodakova
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Mario Loeza Cabrera
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Development, Disease Models and Therapeutics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Daniela Vidal Vilchis
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Marie-Anne Félix
- Ecole Normale Supérieure, IBENS, CNRS UMR8197, INSERM U1024, Paris, France
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Quantitative and Computational Biosciences, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Development, Disease Models and Therapeutics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
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He L, Zhou Y, Zhang Y, Hang B, Chang H, Schick SF, Celniker SE, Xia Y, Snijders AM, Mao J. Thirdhand cigarette smoke leads to age-dependent and persistent alterations in the cecal microbiome of mice. Microbiologyopen 2021; 10:e1198. [PMID: 34180593 PMCID: PMC8123915 DOI: 10.1002/mbo3.1198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 01/11/2023] Open
Abstract
The gut microbiome composition is influenced by many factors including environmental exposures. Here, we investigated the effect of thirdhand cigarette smoke (THS) and exposure age on gut microbiome diversity. C57BL/6 mice were exposed to THS at human exposure relevant levels for three weeks during three different life stages: postnatal (0-3 weeks of age), pubescent (4-7 weeks of age), and adult (9-12 weeks of age), respectively. Cecal microbiome profiles were assessed at 17 weeks of age by 16S rRNA gene sequencing. We found that age at THS exposure strongly influenced the cecal microbiome composition. Although postnatal THS exposure significantly influenced the microbial composition, pubescent and adulthood exposures only had minor effects. The microbiome of postnatally THS-exposed mice significantly increased several degradation pathways that regulate glycolysis and pyruvate decarboxylation, and significantly decreased coenzyme A biosynthesis and pyrimidine deoxyribonucleoside salvage. Our results indicate that mouse postnatal development is particularly susceptible to persistent THS exposure effects on the gut microbiome.
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Affiliation(s)
- Li He
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
- Department of HematologyZhongnan HospitalWuhan UniversityWuhanChina
| | - Yan‐Xia Zhou
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
- Marine CollegeShandong UniversityWeihaiChina
| | - Yuqing Zhang
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
- State Key Laboratory of Reproductive MedicineInstitute of ToxicologyNanjing Medical UniversityNanjingChina
| | - Bo Hang
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Hang Chang
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Suzaynn F. Schick
- Department of MedicineDivision of Occupational and Environmental MedicineUniversity of CaliforniaSan FranciscoCAUSA
| | - Susan E. Celniker
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Yankai Xia
- State Key Laboratory of Reproductive MedicineInstitute of ToxicologyNanjing Medical UniversityNanjingChina
| | - Antoine M. Snijders
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
| | - Jian‐Hua Mao
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCAUSA
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Wu B, Huang L, Chen J, Zhang Y, Wang J, He J. Gut microbiota of homologous Chinese soft-shell turtles (Pelodiscus sinensis) in different habitats. BMC Microbiol 2021; 21:142. [PMID: 33975559 PMCID: PMC8112038 DOI: 10.1186/s12866-021-02209-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 04/29/2021] [Indexed: 12/22/2022] Open
Abstract
Background Chinese soft-shell turtle (Pelodiscus sinensis) is an important commercial species for their high nutritional value and unique taste, but it has been a vulnerable species due to habitat loss. In this study, homologous juvenile turtles were allocated to lake, pond and paddy field to investigate the habitat effects on turtles. Results The growth, morphology and gut microbial communities were monitored during the 4 months cultural period. It showed higher growth rate of turtles in paddy field and pond. The appearance, visceral coefficients, gut morphology and microbial communities in turtles were distinct among different habitats. The microbial community richness on Chao1 was obviously lower in initial turtle guts from greenhouses, whereas it was relative higher in turtle guts sampled from paddy fields than ponds and lake. Significant differences on dominant microbes were found among initial and subsequent samples from different habitats. Firmicutes was the most abundant phylum in the guts of turtles sampled from the greenhouse initially, while Proteobacteria was the most abundant phylum after cultivation in different habitats, followed by Bacteroidetes. The microbial composition were distinct in different habitats at 60d, and the appearance of dominant phyla and genera was more driven by sampling time than habitats at 120d. Both the sampling time and habitats affected the appearance of dominant phyla and genera during the cultivation. The functional predictions indicated that both habitat type and sampling time had significant effects on metabolic pathways, especially amino acid and carbohydrate metabolism. Conclusions The turtles could adapt to natural lakes, artificial ponds and paddy fields. The gut microbial abundance was different among the habitats and sampling time. The species of microbes were significantly more diverse in paddy field specimens than in those from ponds and lakes. Rice-turtle coculture is a potential ecological and economic farming mode that plays important roles in wild turtle protection and food security. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02209-y.
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Affiliation(s)
- Benli Wu
- Key Laboratory of Aquaculture & Stock Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, No.40 Nongkenan Road, Luyang District, Hefei, 230031, Anhui Province, China
| | - Long Huang
- Key Laboratory of Aquaculture & Stock Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, No.40 Nongkenan Road, Luyang District, Hefei, 230031, Anhui Province, China
| | - Jing Chen
- Key Laboratory of Aquaculture & Stock Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, No.40 Nongkenan Road, Luyang District, Hefei, 230031, Anhui Province, China
| | - Ye Zhang
- Key Laboratory of Aquaculture & Stock Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, No.40 Nongkenan Road, Luyang District, Hefei, 230031, Anhui Province, China
| | - Jun Wang
- State Key Laboratory of Eco-hydraulic in Northwest Arid Region of China, Xi'an University of Technology, 710048, Xi'an, China
| | - Jixiang He
- Key Laboratory of Aquaculture & Stock Enhancement of Anhui Province, Fisheries Research Institute, Anhui Academy of Agricultural Sciences, No.40 Nongkenan Road, Luyang District, Hefei, 230031, Anhui Province, China.
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Pu Y, Tan Y, Qu Y, Chang L, Wang S, Wei Y, Wang X, Hashimoto K. A role of the subdiaphragmatic vagus nerve in depression-like phenotypes in mice after fecal microbiota transplantation from Chrna7 knock-out mice with depression-like phenotypes. Brain Behav Immun 2021; 94:318-326. [PMID: 33422641 DOI: 10.1016/j.bbi.2020.12.032] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/23/2020] [Accepted: 12/31/2020] [Indexed: 02/08/2023] Open
Abstract
The α7 subtype of the nicotinic acetylcholine receptor (α7 nAChR: coded by Chrna7) regulates the cholinergic ascending anti-inflammatory pathway involved in depression. We previously reported that Chrna7 knock-out (KO) mice show depression-like phenotypes through systemic inflammation. In this study, we investigated whether fecal microbiota transplantation (FMT) from Chrna7 KO mice causes depression-like phenotypes in mice treated with an antibiotic cocktail (ABX). Chrna7 KO mice with depression-like phenotypes show an abnormal gut microbiota composition, although the alpha diversity and beta diversity were not altered. FMT from Chrna7 KO mice caused depression-like phenotypes, systemic inflammation, and downregulation of synaptic proteins in the prefrontal cortex (PFC) in the ABX-treated mice compared to FMT from the control mice. The Principal component analysis based on the OTU level showed that the FMT group from the KO mice were different from the FMT group from the control mice. We found differences in abundance for several bacteria in the FMT group from the KO mice at the taxonomic level when compared with the other group. Interestingly, subdiaphragmatic vagotomy significantly blocked the development of depression-like phenotypes in the ABX-treated mice after FMT from Chrna7 KO mice. These data suggest that FMT from Chrna7 KO mice produce depression-like phenotypes in ABX-treated mice via the subdiaphragmatic vagus nerve. The brain-gut-microbiota axis association with the subdiaphragmatic vagus nerve plays an important role in the development of depression.
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Affiliation(s)
- Yaoyu Pu
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Yunfei Tan
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Youge Qu
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Lijia Chang
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Siming Wang
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Yan Wei
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Xingming Wang
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan
| | - Kenji Hashimoto
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba 260-8670, Japan.
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Bo TB, Kohl KD. Stabilization and optimization of host-microbe-environment interactions as a potential reason for the behavior of natal philopatry. Anim Microbiome 2021; 3:26. [PMID: 33785073 PMCID: PMC8011129 DOI: 10.1186/s42523-021-00087-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Many animals engage in a behavior known as natal philopatry, where after sexual maturity they return to their own birthplaces for subsequent reproduction. There are many proposed ultimate factors that may underlie the evolution of natal philopatry, such as genetic optimization, suitable living conditions, and friendly neighbors, which can improve the survival rates of offspring. However, here we propose that a key factor that has been overlooked could be the colonization of gut microbiota during early life and the effects these microorganisms have on host performance and fitness. In addition to the bacteria transmitted from the mother to offspring, microbes from the surrounding environment also account for a large proportion of the developing gut microbiome. While it was long believed that microbial species all have global distributions, we now know that there are substantial geographic differences and dispersal limitations to environmental microbes. The establishment of gut microbiota during early life has enormous impacts on animal development, including energy metabolism, training of the immune system, and cognitive development. Moreover, these microbial effects scale to influence animal performance and fitness, raising the possibility for natural selection to act on the integrated combination of gut microbial communities and host genetics (i.e. the holobiont). Therefore, in this paper, we propose a hypothesis: that optimization of host-microbe-environment interactions represents a potentially important yet overlooked reason for natal philopatry. Microbiota obtained by natal philopatry could help animals adapt to the environment and improve the survival rates of their young. We propose future directions to test these ideas, and the implications that this hypothesis has for our understanding of host-microbe interactions.
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Affiliation(s)
- Ting-Bei Bo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kevin D Kohl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
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Modulation of the immune response and metabolism in germ-free rats colonized by the probiotic Lactobacillus salivarius LI01. Appl Microbiol Biotechnol 2021; 105:1629-1645. [PMID: 33507355 DOI: 10.1007/s00253-021-11099-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/21/2020] [Accepted: 01/05/2021] [Indexed: 01/06/2023]
Abstract
The gut microbiota plays an important role in multifaceted physiological functions in the host. Previous studies have assessed the probiotic effects of Lactobacillus salivarius LI01. In this study, we aimed to investigate the potential effects and putative mechanism of L. salivarius LI01 in immune modulation and metabolic regulation through the monocolonization of germ-free (GF) Sprague-Dawley (SD) rats with L. salivarius LI01. The GF rats were separated into two groups and administered a gavage of L. salivarius LI01 or an equal amount of phosphate-buffered saline. The levels of serum biomarkers, such as interleukin (IL)-1α, IL-5, and IL-10, were restored by L. salivarius LI01, which indicated the activation of Th0 cell differentiation toward immune homeostasis. L. salivarius LI01 also stimulated the immune response and metabolic process by altering transcriptional expression in the ileum and liver. A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed significant enrichment of the 5'-adenosine monophosphate-activated protein kinase (AMPK) signaling pathway, which indicated that L. salivarius LI01 exerts an effect on energy accumulation. The LI01 group showed alterations in fecal carbohydrates accompanied by an increased body weight gain. In addition, L. salivarius LI01 produced indole-3-lactic acid (ILA) and enhanced arginine metabolism by rebalancing the interconversion between arginine and proline. These findings provide evidence showing that L. salivarius LI01 can directly impact the host by modulating immunity and metabolism. KEY POINTS : • Lactobacillus salivarius LI01 conventionalizes the cytokine profile and activates the immune response. • LI01 modulates carbohydrate metabolism and arginine transaction. • LI01 generates tryptophan-derived indole-3-lactic acid. • The cytochrome P450 family contributes to the response to altered metabolites.
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Host genetics and gut microbiota cooperatively contribute to azoxymethane-induced acute toxicity in Collaborative Cross mice. Arch Toxicol 2021; 95:949-958. [PMID: 33458792 DOI: 10.1007/s00204-021-02972-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/04/2021] [Indexed: 12/19/2022]
Abstract
Azoxymethane (AOM) is a widely used carcinogen to study chemical-induced colorectal carcinogenesis and is an agent for studying fulminant hepatic failure. The inter-strain susceptibility to acute toxicity by AOM has been reported, but its association with host genetics or gut microbiota remains largely unexplored. Here a cohort of genetically diverse Collaborative Cross (CC) mice was used to assess the contribution of host genetics and the gut microbiome to AOM-induced acute toxicity. We observed variation in AOM-induced acute liver failure across CC strains. Quantitative trait loci (QTL) analysis revealed three chromosome regions significantly associated with AOM toxicity. Genes located within these QTL, including peroxisome proliferator-activated receptor alpha (Ppara), were enriched for enzyme activator and nucleoside-triphosphatase regulator activity. We further demonstrated that the protein level of PPARα in liver tissues from sensitive strains was remarkably lower compared to levels in resistant strains, consistent with protective role of PPAR family in liver injury. We discovered that the abundance levels of gut microbial families Anaeroplasmataceae, Ruminococcaceae, Lactobacillaceae, Akkermansiaceae and Clostridiaceae were significantly higher in the sensitive strains compared to the resistant strains. Using a random forest classifier method, we determined that the relative abundance levels of these microbial families predicted AOM toxicity with the area under the receiver-operating curve (AUC) of 0.75. Combining the three genetic loci and five microbial families increased the predictive accuracy of AOM toxicity (AUC of 0.99). Moreover, we found that Ruminococcaceae and Lactobacillaceae acted as mediators between host genetics and AOM toxicity. In conclusion, this study shows that host genetics and specific microbiome members play a critical role in AOM-induced acute toxicity, which provides a framework for analysis of the health effects from environmental toxicants.
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Associations of Genetic Variants Contributing to Gut Microbiota Composition in Immunoglobin A Nephropathy. mSystems 2021; 6:6/1/e00819-20. [PMID: 33436510 PMCID: PMC7901477 DOI: 10.1128/msystems.00819-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The gut microbiota and host genetics are implicated in the pathogenesis of IgAN. Recent studies have confirmed that microbial compositions are heritable (microbiome quantitative trait loci [QTL]). The gut microbiota has been implicated in immunoglobin A nephropathy (IgAN) because the intestinal immune response is assumed to be one of the disease triggers. Since the microbial composition is heritable, we hypothesize that genetic variants controlling gut microbiota composition may be associated with susceptibility to IgAN or clinical phenotypes. A total of 175 gut-microbiome-associated genetic variants were retrieved from the Genome-Wide Association Study (GWAS) Catalog. Genetic associations were examined in 1,511 patients with IgAN and 4,469 controls. Subphenotype associations and microbiome annotations were undertaken for a better understanding of how genes shaped phenotypes. Likely candidate microbes suggested in genetic associations were validated using 16S rRNA gene sequencing in two independent data sets with 119 patients with IgAN and 45 controls in total. Nine genetic variants were associated with susceptibility to IgAN. Risk genotypes of LYZL1 were associated with higher serum levels of galactose-deficient IgA1 (Gd-IgA1). Other significant findings included the associations between the risk genotype of SIPA1L3 and early age at onset, PLTP and worse kidney function, and AL365503.1 and more severe hematuria. Besides, risk genotypes of LYZL1 and SIPA1L3 were associated with decreased abundances of Dialister and Bacilli, respectively. Risk genotypes of PLTP and AL365503.1 were associated with increased abundances of Erysipelotrichaceae and Lachnobacterium, respectively. 16S data validated a decreased tendency for Dialister and an increased tendency for Erysipelotrichaceae in IgAN. In this pilot study, our results provided preliminary evidence that the gut microbiota in IgAN was affected by host genetics and shed new light on candidate bacteria for future pathogenesis studies. IMPORTANCE The gut microbiota and host genetics are implicated in the pathogenesis of IgAN. Recent studies have confirmed that microbial compositions are heritable (microbiome quantitative trait loci [QTL]). The relationship between host genetics and the microbiota and the role of the microbiota in IgAN are unclear. We retrieved the GWAS Catalog and associated microbiome QTL in IgAN, observing that nine genetic variants were associated with IgAN susceptibility and some clinical phenotypes. In a consistent way, the decreased abundance of Dialister was associated with higher serum levels of Gd-IgA1, and 16S rRNA gene analysis confirmed the decreased abundance of Dialister in IgAN. These data provided preliminary evidence that the gut microbiota in IgAN was affected by host genetics, which is a new strategy for future pathogenesis and intervention studies.
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Gut microbiome partially mediates and coordinates the effects of genetics on anxiety-like behavior in Collaborative Cross mice. Sci Rep 2021; 11:270. [PMID: 33431988 PMCID: PMC7801399 DOI: 10.1038/s41598-020-79538-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/07/2020] [Indexed: 02/06/2023] Open
Abstract
Growing evidence suggests that the gut microbiome (GM) plays a critical role in health and disease. However, the contribution of GM to psychiatric disorders, especially anxiety, remains unclear. We used the Collaborative Cross (CC) mouse population-based model to identify anxiety associated host genetic and GM factors. Anxiety-like behavior of 445 mice across 30 CC strains was measured using the light/dark box assay and documented by video. A custom tracking system was developed to quantify seven anxiety-related phenotypes based on video. Mice were assigned to a low or high anxiety group by consensus clustering using seven anxiety-related phenotypes. Genome-wide association analysis (GWAS) identified 141 genes (264 SNPs) significantly enriched for anxiety and depression related functions. In the same CC cohort, we measured GM composition and identified five families that differ between high and low anxiety mice. Anxiety level was predicted with 79% accuracy and an AUC of 0.81. Mediation analyses revealed that the genetic contribution to anxiety was partially mediated by the GM. Our findings indicate that GM partially mediates and coordinates the effects of genetics on anxiety.
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Witjes VM, Boleij A, Halffman W. Reducing versus Embracing Variation as Strategies for Reproducibility: The Microbiome of Laboratory Mice. Animals (Basel) 2020; 10:E2415. [PMID: 33348632 PMCID: PMC7767075 DOI: 10.3390/ani10122415] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
Irreproducibility is a well-recognized problem in biomedical animal experimentation. Phenotypic variation in animal models is one of the many challenging causes of irreproducibility. How to deal with phenotypic variation in experimental designs is a topic of debate. Both reducing and embracing variation are highlighted as strategies for reproducibility. In this theoretical review, we use variation in mouse microbiome composition as an example to analyze this ongoing discussion, drawing on both animal research and philosophy of science. We provide a conceptual explanation of reproducibility and analyze how the microbiome affects mouse phenotypes to demonstrate that the role of the microbiome in irreproducibility can be understood in two ways: (i) the microbiome can act as a confounding factor, and (ii) the result may not be generalizable to mice harboring a different microbiome composition. We elucidate that reducing variation minimizes confounding, whereas embracing variation ensures generalizability. These contrasting strategies make dealing with variation in experimental designs extremely complex. Here, we conclude that the most effective strategy depends on the specific research aim and question. The field of biomedical animal experimentation is too broad to identify a single optimal strategy. Thus, dealing with variation should be considered on a case-by-case basis, and awareness amongst researchers is essential.
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Affiliation(s)
- Vera M. Witjes
- Institute for Science in Society, Faculty of Science, Radboud University, 6500 GL Nijmegen, The Netherlands;
| | - Annemarie Boleij
- Department of Pathology, Radboud Institute for Molecular Life Science (RIMLS), Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands;
| | - Willem Halffman
- Institute for Science in Society, Faculty of Science, Radboud University, 6500 GL Nijmegen, The Netherlands;
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Suppa A, Kvist J, Li X, Dhandapani V, Almulla H, Tian AY, Kissane S, Zhou J, Perotti A, Mangelson H, Langford K, Rossi V, Brown JB, Orsini L. Roundup causes embryonic development failure and alters metabolic pathways and gut microbiota functionality in non-target species. MICROBIOME 2020; 8:170. [PMID: 33339542 PMCID: PMC7780628 DOI: 10.1186/s40168-020-00943-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 11/09/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Research around the weedkiller Roundup is among the most contentious of the twenty-first century. Scientists have provided inconclusive evidence that the weedkiller causes cancer and other life-threatening diseases, while industry-paid research reports that the weedkiller has no adverse effect on humans or animals. Much of the controversial evidence on Roundup is rooted in the approach used to determine safe use of chemicals, defined by outdated toxicity tests. We apply a system biology approach to the biomedical and ecological model species Daphnia to quantify the impact of glyphosate and of its commercial formula, Roundup, on fitness, genome-wide transcription and gut microbiota, taking full advantage of clonal reproduction in Daphnia. We then apply machine learning-based statistical analysis to identify and prioritize correlations between genome-wide transcriptional and microbiota changes. RESULTS We demonstrate that chronic exposure to ecologically relevant concentrations of glyphosate and Roundup at the approved regulatory threshold for drinking water in the US induce embryonic developmental failure, induce significant DNA damage (genotoxicity), and interfere with signaling. Furthermore, chronic exposure to the weedkiller alters the gut microbiota functionality and composition interfering with carbon and fat metabolism, as well as homeostasis. Using the "Reactome," we identify conserved pathways across the Tree of Life, which are potential targets for Roundup in other species, including liver metabolism, inflammation pathways, and collagen degradation, responsible for the repair of wounds and tissue remodeling. CONCLUSIONS Our results show that chronic exposure to concentrations of Roundup and glyphosate at the approved regulatory threshold for drinking water causes embryonic development failure and alteration of key metabolic functions via direct effect on the host molecular processes and indirect effect on the gut microbiota. The ecological model species Daphnia occupies a central position in the food web of aquatic ecosystems, being the preferred food of small vertebrates and invertebrates as well as a grazer of algae and bacteria. The impact of the weedkiller on this keystone species has cascading effects on aquatic food webs, affecting their ability to deliver critical ecosystem services. Video Abstract.
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Affiliation(s)
- Antonio Suppa
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
- Department of Chemistry, Life Sciences and Environmental Sustainability University of Parma, Department of Life Sciences, Viale Usberti, 11/A, Parma, Italy
| | - Jouni Kvist
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Xiaojing Li
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
| | - Vignesh Dhandapani
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
| | - Hanan Almulla
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
| | | | - Stephen Kissane
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
| | - Jiarui Zhou
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
| | - Alessio Perotti
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
| | | | | | - Valeria Rossi
- Department of Chemistry, Life Sciences and Environmental Sustainability University of Parma, Department of Life Sciences, Viale Usberti, 11/A, Parma, Italy
| | - James B. Brown
- Environmental Bioinformatics, Centre for Computational Biology, School of Biosciences, University of Birmingham Edgbaston, Birmingham, B15 2TT UK
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Statistics Department, University of California, Berkeley, Berkeley, CA, 94720 USA, Preminon LLC, Rodeo, CA 94572 USA
| | - Luisa Orsini
- Environmental Genomics Group, School of Biosciences, the University of Birmingham, Birmingham, B15 2TT UK
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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