1
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Zhang ZJ, Cole CG, Coyne MJ, Lin H, Dylla N, Smith RC, Pappas TE, Townson SA, Laliwala N, Waligurski E, Ramaswamy R, Woodson C, Burgo V, Little JC, Moran D, Rose A, McMillin M, McSpadden E, Sundararajan A, Sidebottom AM, Pamer EG, Comstock LE. Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution. Cell Host Microbe 2024:S1931-3128(24)00323-8. [PMID: 39293438 DOI: 10.1016/j.chom.2024.08.016] [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: 03/08/2024] [Revised: 06/27/2024] [Accepted: 08/22/2024] [Indexed: 09/20/2024]
Abstract
Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome, with diverse impacts on human health. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, metabolomic, and horizontal gene transfer analyses. Families, genera, and species could be grouped based on many distinctive features. We also observed extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-species diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses represents a valuable resource to facilitate informed selection of strains for microbiome reconstitution.
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Affiliation(s)
- Zhenrun J Zhang
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA; Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave., Chicago, IL 60637, USA
| | - Cody G Cole
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA; Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave., Chicago, IL 60637, USA
| | - Michael J Coyne
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA; Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave., Chicago, IL 60637, USA
| | - Huaiying Lin
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Nicholas Dylla
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Rita C Smith
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Téa E Pappas
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Shannon A Townson
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Nina Laliwala
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Emily Waligurski
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA; Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave., Chicago, IL 60637, USA
| | - Ramanujam Ramaswamy
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Che Woodson
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Victoria Burgo
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Jessica C Little
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - David Moran
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Amber Rose
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Mary McMillin
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Emma McSpadden
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Anitha Sundararajan
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Ashley M Sidebottom
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA
| | - Eric G Pamer
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA; Department of Medicine, Section of Infectious Diseases & Global Health, University of Chicago Medicine, 5841 South Maryland Ave., Chicago, IL 60637, USA; Department of Pathology, University of Chicago Medicine, 5841 South Maryland Ave., Chicago, IL 60637, USA; Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave., Chicago, IL 60637, USA.
| | - Laurie E Comstock
- Duchossois Family Institute (DFI), University of Chicago, 900 E. 57th St., Chicago, IL 60637, USA; Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave., Chicago, IL 60637, USA.
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2
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Güven Gülhan Ü, Nikerel E, Çakır T, Erdoğan Sevilgen F, Durmuş S. Species-level identification of enterotype-specific microbial markers for colorectal cancer and adenoma. Mol Omics 2024; 20:397-416. [PMID: 38780313 DOI: 10.1039/d4mo00016a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Enterotypes have been shown to be an important factor for population stratification based on gut microbiota composition, leading to a better understanding of human health and disease states. Classifications based on compositional patterns will have implications for personalized microbiota-based solutions. There have been limited enterotype based studies on colorectal adenoma and cancer. Here, an enterotype-based meta-analysis of fecal shotgun metagenomic studies was performed, including 1579 samples of healthy controls (CTR), colorectal adenoma (ADN) and colorectal cancer (CRC) in total. Gut microbiota of healthy people were clustered into three enterotypes (Ruminococcus-, Bacteroides- and Prevotella-dominated enterotypes). Reference-based enterotype assignments were performed for CRC and ADN samples, using the supervised machine learning algorithm, K-nearest neighbors. Differential abundance analyses and random forest classification were conducted on each enterotype between healthy controls and CRC-ADN groups, revealing novel enterotype-specific microbial markers for non-invasive CRC screening strategies. Furthermore, we identified microbial species unique to each enterotype that play a role in the production of secondary bile acids and short-chain fatty acids, unveiling the correlation between cancer-associated gut microbes and dietary patterns. The enterotype-based approach in this study is promising in elucidating the mechanisms of differential gut microbiome profiles, thereby improving the efficacy of personalized microbiota-based solutions.
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Affiliation(s)
- Ünzile Güven Gülhan
- Department of Bioengineering, Gebze Technical University, Gebze, TR 41400, Turkey.
| | - Emrah Nikerel
- Department of Genetics and Bioengineering, Yeditepe University, Istanbul, TR 34755, Turkey
| | - Tunahan Çakır
- Department of Bioengineering, Gebze Technical University, Gebze, TR 41400, Turkey.
- PhiTech Bioinformatics, Gebze, TR 41470, Turkey
| | - Fatih Erdoğan Sevilgen
- The Institute for Data Science & Artificial Intelligence, Boğaziçi University, Istanbul, TR 34342, Turkey
- PhiTech Bioinformatics, Gebze, TR 41470, Turkey
| | - Saliha Durmuş
- Department of Bioengineering, Gebze Technical University, Gebze, TR 41400, Turkey.
- PhiTech Bioinformatics, Gebze, TR 41470, Turkey
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3
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Oles RE, Terrazas MC, Loomis LR, Neal MJ, Paulchakrabarti M, Zuffa S, Hsu CY, Vasquez Ayala A, Lee MH, Tribelhorn C, Belda-Ferre P, Bryant M, Zemlin J, Young J, Dulai P, Sandborn WJ, Sivagnanam M, Raffatellu M, Pride D, Dorrestein PC, Zengler K, Choudhury B, Knight R, Chu H. Pathogenic Bacteroides fragilis strains can emerge from gut-resident commensals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599758. [PMID: 38948766 PMCID: PMC11213024 DOI: 10.1101/2024.06.19.599758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Bacteroides fragilis is a prominent member of the human gut microbiota, playing crucial roles in maintaining gut homeostasis and host health. Although it primarily functions as a beneficial commensal, B. fragilis can become pathogenic. To determine the genetic basis of its duality, we conducted a comparative genomic analysis of 813 B. fragilis strains, representing both commensal and pathogenic origins. Our findings reveal that pathogenic strains emerge across diverse phylogenetic lineages, due in part to rapid gene exchange and the adaptability of the accessory genome. We identified 16 phylogenetic groups, differentiated by genes associated with capsule composition, interspecies competition, and host interactions. A microbial genome-wide association study identified 44 genes linked to extra-intestinal survival and pathogenicity. These findings reveal how genomic diversity within commensal species can lead to the emergence of pathogenic traits, broadening our understanding of microbial evolution in the gut.
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Affiliation(s)
- Renee E. Oles
- Department of Pathology, University of California, San Diego, La Jolla, CA
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | | | - Luke R. Loomis
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | - Maxwell J. Neal
- Department of Bioengineering, University of California, San Diego, La Jolla, CA
| | | | - Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA
| | - Chia-Yun Hsu
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | | | - Michael H. Lee
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Caitlin Tribelhorn
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Pedro Belda-Ferre
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - MacKenzie Bryant
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Jasmine Zemlin
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA
| | - Jocelyn Young
- Division of Gastroenterology, Hepatology and Nutrition, University of California, San Diego and Rady Children’s Hospital, San Diego, CA
| | - Parambir Dulai
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA
- Division of Gastroenterology, Northwestern University, Chicago, Illinois
| | - William J. Sandborn
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
| | - Mamata Sivagnanam
- Division of Gastroenterology, Hepatology and Nutrition, University of California, San Diego and Rady Children’s Hospital, San Diego, CA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, La Jolla, CA
| | - David Pride
- Department of Pathology, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Center for Innovative Phage Applications and Therapeutics (IPATH), University of California, San Diego, La Jolla, CA
- Center of Advanced Laboratory Medicine (CALM), University of California, San Diego, La Jolla, CA
| | - Pieter C. Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA
| | - Karsten Zengler
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
- Department of Bioengineering, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Program in Materials Science and Engineering, University of California, San Diego, La Jolla, CA
| | - Biswa Choudhury
- GlycoAnalytics Core, University of California San Diego, San Diego, CA
| | - Rob Knight
- Division of Host-Microbe Systems and Therapeutics, Department of Pediatrics, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA
- Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, La Jolla, CA
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4
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Abrahamsen HL, Sanford TC, Collamore CE, Johnstone BA, Coyne MJ, García-Bayona L, Christie MP, Evans JC, Farrand AJ, Flores K, Morton CJ, Parker MW, Comstock LE, Tweten RK. Distant relatives of a eukaryotic cell-specific toxin family evolved a complement-like mechanism to kill bacteria. Nat Commun 2024; 15:5028. [PMID: 38866748 PMCID: PMC11169675 DOI: 10.1038/s41467-024-49103-5] [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: 02/02/2024] [Accepted: 05/22/2024] [Indexed: 06/14/2024] Open
Abstract
Cholesterol-dependent cytolysins (CDCs) comprise a large family of pore-forming toxins produced by Gram-positive bacteria, which are used to attack eukaryotic cells. Here, we functionally characterize a family of 2-component CDC-like (CDCL) toxins produced by the Gram-negative Bacteroidota that form pores by a mechanism only described for the mammalian complement membrane attack complex (MAC). We further show that the Bacteroides CDCLs are not eukaryotic cell toxins like the CDCs, but instead bind to and are proteolytically activated on the surface of closely related species, resulting in pore formation and cell death. The CDCL-producing Bacteroides is protected from the effects of its own CDCL by the presence of a surface lipoprotein that blocks CDCL pore formation. These studies suggest a prevalent mode of bacterial antagonism by a family of two-component CDCLs that function like mammalian MAC and that are wide-spread in the gut microbiota of diverse human populations.
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Affiliation(s)
- Hunter L Abrahamsen
- Department of Microbiology & Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Tristan C Sanford
- Department of Microbiology & Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Casie E Collamore
- Department of Microbiology & Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Bronte A Johnstone
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Michael J Coyne
- Duchossois Family Institute and Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Leonor García-Bayona
- Duchossois Family Institute and Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Michelle P Christie
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jordan C Evans
- Department of Microbiology & Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Wheeler Bio, Oklahoma City, OK, 73104, USA
| | - Allison J Farrand
- Department of Microbiology & Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Wheeler Bio, Oklahoma City, OK, 73104, USA
| | - Katia Flores
- Duchossois Family Institute and Department of Microbiology, University of Chicago, Chicago, IL, USA
| | - Craig J Morton
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
- CSIRO Biomedical Manufacturing Program, Clayton, VIC, 3168, Australia
| | - Michael W Parker
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.
- Australian Cancer Research Foundation Rational Drug Discovery Centre, St Vincent's Institute of Medical Research, Fitzroy, VIC, 2065, Australia.
| | - Laurie E Comstock
- Duchossois Family Institute and Department of Microbiology, University of Chicago, Chicago, IL, USA.
| | - Rodney K Tweten
- Department of Microbiology & Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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5
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Kennedy NW, Comstock LE. Mechanisms of bacterial immunity, protection, and survival during interbacterial warfare. Cell Host Microbe 2024; 32:794-803. [PMID: 38870897 PMCID: PMC11216714 DOI: 10.1016/j.chom.2024.05.006] [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: 04/09/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 06/15/2024]
Abstract
Most bacteria live in communities, often with closely related strains and species with whom they must compete for space and resources. Consequently, bacteria have acquired or evolved mechanisms to antagonize competitors through the production of antibacterial toxins. Similar to bacterial systems that combat phage infection and mechanisms to thwart antibiotics, bacteria have also acquired and evolved features to protect themselves from antibacterial toxins. Just as there is a large body of research identifying and characterizing antibacterial proteins and toxin delivery systems, studies of bacterial mechanisms to resist and survive assault from competitors' weapons have also expanded tremendously. Emerging data are beginning to reveal protective processes and mechanisms that are as diverse as the toxins themselves. Protection against antibacterial toxins can be acquired by horizontal gene transfer, receptor or target alteration, induction of protective functions, physical barriers, and other diverse processes. Here, we review recent studies in this rapidly expanding field.
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Affiliation(s)
- Nolan W Kennedy
- Duchossois Family Institute and Department of Microbiology, University of Chicago, Chicago, IL 60637, USA
| | - Laurie E Comstock
- Duchossois Family Institute and Department of Microbiology, University of Chicago, Chicago, IL 60637, USA.
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6
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García-Bayona L, Said N, Coyne MJ, Flores K, Elmekki NM, Sheahan ML, Camacho AG, Hutt K, Yildiz FH, Kovács ÁT, Waldor MK, Comstock LE. A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.590671. [PMID: 38746121 PMCID: PMC11092513 DOI: 10.1101/2024.04.29.590671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Although horizontal gene transfer is pervasive in the intestinal microbiota, we understand only superficially the roles of most exchanged genes and how the mobile repertoire affects community dynamics. Similarly, little is known about the mechanisms underlying the ability of a community to recover after a perturbation. Here, we identified and functionally characterized a large conjugative plasmid that is one of the most frequently transferred elements among Bacteroidales species and is ubiquitous in diverse human populations. This plasmid encodes both an extracellular polysaccharide and fimbriae, which promote the formation of multispecies biofilms in the mammalian gut. We use a hybridization-based approach to visualize biofilms in clarified whole colon tissue with unprecedented 3D spatial resolution. These biofilms increase bacterial survival to common stressors encountered in the gut, increasing strain resiliency, and providing a rationale for the plasmid's recent spread and high worldwide prevalence.
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7
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Zhang ZJ, Cole CG, Coyne MJ, Lin H, Dylla N, Smith RC, Waligurski E, Ramaswamy R, Woodson C, Burgo V, Little JC, Moran D, Rose A, McMillin M, McSpadden E, Sundararajan A, Sidebottom AM, Pamer EG, Comstock LE. Comprehensive analyses of a large human gut Bacteroidales culture collection reveal species and strain level diversity and evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584156. [PMID: 38496653 PMCID: PMC10942478 DOI: 10.1101/2024.03.08.584156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome with diverse impacts on human health. While Bacteroidales strains and species are genomically and functionally diverse, order-wide comparative analyses are lacking. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, mobile gene, and metabolomic analyses. Families, genera, and species could be grouped based on many distinctive features. However, we also show extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-specific diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses can serve as a resource to facilitate informed selection of strains for microbiome reconstitution.
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Affiliation(s)
- Zhenrun J Zhang
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
| | - Cody G Cole
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
| | - Michael J Coyne
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
| | - Huaiying Lin
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Nicholas Dylla
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Rita C Smith
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Emily Waligurski
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
| | - Ramanujam Ramaswamy
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Che Woodson
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Victoria Burgo
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Jessica C Little
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - David Moran
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Amber Rose
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Mary McMillin
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Emma McSpadden
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Anitha Sundararajan
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Ashley M Sidebottom
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Medicine, Section of Infectious Diseases & Global Health, University of Chicago Medicine, 5841 South Maryland Ave, Chicago, IL, 60637, USA
- Department of Pathology, University of Chicago Medicine, 5841 South Maryland Ave, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
| | - Laurie E Comstock
- Duchossois Family Institute, University of Chicago, 900 E. 57th St, Chicago, IL, 60637, USA
- Department of Microbiology, Biological Sciences Division, University of Chicago, 5841 South Maryland Ave, Chicago, IL, 60637, USA
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8
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Liu Z, Good BH. Dynamics of bacterial recombination in the human gut microbiome. PLoS Biol 2024; 22:e3002472. [PMID: 38329938 PMCID: PMC10852326 DOI: 10.1371/journal.pbio.3002472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/14/2023] [Indexed: 02/10/2024] Open
Abstract
Horizontal gene transfer (HGT) is a ubiquitous force in microbial evolution. Previous work has shown that the human gut is a hotspot for gene transfer between species, but the more subtle exchange of variation within species-also known as recombination-remains poorly characterized in this ecosystem. Here, we show that the genetic structure of the human gut microbiome provides an opportunity to measure recent recombination events from sequenced fecal samples, enabling quantitative comparisons across diverse commensal species that inhabit a common environment. By analyzing recent recombination events in the core genomes of 29 human gut bacteria, we observed widespread heterogeneities in the rates and lengths of transferred fragments, which are difficult to explain by existing models of ecological isolation or homology-dependent recombination rates. We also show that natural selection helps facilitate the spread of genetic variants across strain backgrounds, both within individual hosts and across the broader population. These results shed light on the dynamics of in situ recombination, which can strongly constrain the adaptability of gut microbial communities.
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Affiliation(s)
- Zhiru Liu
- Department of Applied Physics, Stanford University, Stanford, California, United States of America
| | - Benjamin H. Good
- Department of Applied Physics, Stanford University, Stanford, California, United States of America
- Department of Biology, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub–San Francisco, San Francisco, California, United States of America
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9
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Bongiovanni TR, Latario CJ, Le Cras Y, Trus E, Robitaille S, Swartz K, Schmidtke D, Vincent M, Kosta A, Orth J, Stengel F, Pellarin R, Rocha EPC, Ross BD, Durand E. Assembly of a unique membrane complex in type VI secretion systems of Bacteroidota. Nat Commun 2024; 15:429. [PMID: 38200008 PMCID: PMC10781749 DOI: 10.1038/s41467-023-44426-1] [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: 06/08/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
The type VI secretion system (T6SS) of Gram-negative bacteria inhibits competitor cells through contact-dependent translocation of toxic effector proteins. In Proteobacteria, the T6SS is anchored to the cell envelope through a megadalton-sized membrane complex (MC). However, the genomes of Bacteroidota with T6SSs appear to lack genes encoding homologs of canonical MC components. Here, we identify five genes in Bacteroides fragilis (tssNQOPR) that are essential for T6SS function and encode a Bacteroidota-specific MC. We purify this complex, reveal its dimensions using electron microscopy, and identify a protein-protein interaction network underlying the assembly of the MC including the stoichiometry of the five TssNQOPR components. Protein TssN mediates the connection between the Bacteroidota MC and the conserved baseplate. Although MC gene content and organization varies across the phylum Bacteroidota, no MC homologs are detected outside of T6SS loci, suggesting ancient co-option and functional convergence with the non-homologous MC of Pseudomonadota.
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Affiliation(s)
- Thibault R Bongiovanni
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
| | - Casey J Latario
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Youn Le Cras
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Evan Trus
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Sophie Robitaille
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Kerry Swartz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
| | - Danica Schmidtke
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA
- Department of Microbiology, University of Washington, Seattle, WA, 98109, USA
| | - Maxence Vincent
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France
| | - Artemis Kosta
- Microscopy Core Facility, Institut de Microbiologie de la Méditerranée (IMM), FR3479, CNRS, Aix-Marseille University, Marseille, France
| | - Jan Orth
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Florian Stengel
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
- Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Riccardo Pellarin
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS & University of Lyon, 7 Passage du Vercors, 69007, Lyon, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Benjamin D Ross
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, 03755, USA.
- Department of Microbiology, University of Washington, Seattle, WA, 98109, USA.
| | - Eric Durand
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France.
- Laboratoire de Chimie Bactérienne (LCB), Institut de Microbiologie, Bioénergies et Biotechnologie (IM2B), Aix-Marseille Université - Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 7255, Institut national de la santé et de la recherche médicale (INSERM), Marseille, France.
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10
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Wang S, Mu L, Yu C, He Y, Hu X, Jiao Y, Xu Z, You S, Liu SL, Bao H. Microbial collaborations and conflicts: unraveling interactions in the gut ecosystem. Gut Microbes 2024; 16:2296603. [PMID: 38149632 PMCID: PMC10761165 DOI: 10.1080/19490976.2023.2296603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/14/2023] [Indexed: 12/28/2023] Open
Abstract
The human gut microbiota constitutes a vast and complex community of microorganisms. The myriad of microorganisms present in the intestinal tract exhibits highly intricate interactions, which play a crucial role in maintaining the stability and balance of the gut microbial ecosystem. These interactions, in turn, influence the overall health of the host. The mammalian gut microbes have evolved a wide range of mechanisms to suppress or even eliminate their competitors for nutrients and space. Simultaneously, extensive cooperative interactions exist among different microbes to optimize resource utilization and enhance their own fitness. This review will focus on the competitive mechanisms among members of the gut microorganisms and discuss key modes of actions, including bacterial secretion systems, bacteriocins, membrane vesicles (MVs) etc. Additionally, we will summarize the current knowledge of the often-overlooked positive interactions within the gut microbiota, and showcase representative machineries. This information will serve as a reference for better understanding the complex interactions occurring within the mammalian gut environment. Understanding the interaction dynamics of competition and cooperation within the gut microbiota is crucial to unraveling the ecology of the mammalian gut microbial communities. Targeted interventions aimed at modulating these interactions may offer potential therapeutic strategies for disease conditions.
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Affiliation(s)
- Shuang Wang
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- Department of Biopharmaceutical Sciences (State-Province Key Laboratories of Biomedicine-Pharmaceutics of China), College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
| | - Lingyi Mu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Chong Yu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yuting He
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Xinliang Hu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Yanlei Jiao
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Ziqiong Xu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shaohui You
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Shu-Lin Liu
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
| | - Hongxia Bao
- Genomics Research Center, Key Laboratory of Gut Microbiota and Pharmacogenomics of Heilongjiang Province, State-Province Key Laboratory of Biomedicine-Pharmaceutics of China, College of Pharmacy, Harbin Medical University, Harbin, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD) College of Pharmacy, Harbin Medical University, Harbin, China
- Harbin Medical University-University of Calgary Cumming School of Medicine Centre for Infection and Genomics, Harbin Medical University, Harbin, China
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11
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Dapa T, Xavier KB. Effect of diet on the evolution of gut commensal bacteria. Gut Microbes 2024; 16:2369337. [PMID: 38904092 PMCID: PMC11195494 DOI: 10.1080/19490976.2024.2369337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
The gut microbiota, comprising trillions of diverse microorganisms inhabiting the intestines of animals, forms a complex and indispensable ecosystem with profound implications for the host's well-being. Its functions include contributing to developing the host's immune response, aiding in nutrient digestion, synthesizing essential compounds, acting as a barrier against pathogen invasion, and influencing the development or regression of various pathologies. The dietary habits of the host directly impact this intricate community of gut microbes. Diet influences the composition and function of the gut microbiota through alterations in gene expression, enzymatic activity, and metabolome. While the impact of diet on gut ecology is well-established, the investigation into the relationship between dietary consumption and microbial genotypic diversity has been limited. This review provides an overview of the relationship between diet and gut microbiota, emphasizing the impact of host nutrition on both short- and long-term evolution in the mammalian gut. It is evident that the evolution of the gut microbiota occurs even on short timescales through the acquisition of novel mutations, within the gut bacteria of individual hosts. Consequently, we discuss the importance of considering alterations in bacterial genomic diversity when analyzing microbiota-dependent effects on host physiology. Future investigations into the various microbiota-related traits shall greatly benefit from a deeper understanding of commensal bacterial evolutionary adaptation.
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Affiliation(s)
- Tanja Dapa
- Andalusian Center for Developmental Biology (CABD), Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University/CSIC/Junta de Andalucía, Seville, Spain
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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12
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Robitaille S, Simmons EL, Verster AJ, McClure EA, Royce DB, Trus E, Swartz K, Schultz D, Nadell CD, Ross BD. Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria. Nat Ecol Evol 2023; 7:2092-2107. [PMID: 37884689 PMCID: PMC11099977 DOI: 10.1038/s41559-023-02230-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
Understanding the relationship between the composition of the human gut microbiota and the ecological forces shaping it is of great importance; however, knowledge of the biogeographical and ecological relationships between physically interacting taxa is limited. Interbacterial antagonism may play an important role in gut community dynamics, yet the conditions under which antagonistic behaviour is favoured or disfavoured by selection in the gut are not well understood. Here, using genomics, we show that a species-specific type VI secretion system (T6SS) repeatedly acquires inactivating mutations in Bacteroides fragilis in the human gut. This result implies a fitness cost to the T6SS, but we could not identify laboratory conditions under which such a cost manifests. Strikingly, experiments in mice illustrate that the T6SS can be favoured or disfavoured in the gut depending on the strains and species in the surrounding community and their susceptibility to T6SS antagonism. We use ecological modelling to explore the conditions that could underlie these results and find that community spatial structure modulates interaction patterns among bacteria, thereby modulating the costs and benefits of T6SS activity. Our findings point towards new integrative models for interrogating the evolutionary dynamics of type VI secretion and other modes of antagonistic interaction in microbiomes.
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Affiliation(s)
- Sophie Robitaille
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Emilia L Simmons
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Adrian J Verster
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Emily Ann McClure
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Darlene B Royce
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Evan Trus
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Kerry Swartz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Carey D Nadell
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
| | - Benjamin D Ross
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA.
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13
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Good BH, Rosenfeld LB. Eco-evolutionary feedbacks in the human gut microbiome. Nat Commun 2023; 14:7146. [PMID: 37932275 PMCID: PMC10628149 DOI: 10.1038/s41467-023-42769-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 10/20/2023] [Indexed: 11/08/2023] Open
Abstract
Gut microbiota can evolve within their hosts on human-relevant timescales, but little is known about how these changes influence (or are influenced by) the composition of their local community. Here, by combining ecological and evolutionary analyses of a large cohort of human gut metagenomes, we show that the short-term evolution of the microbiota is linked with shifts in its ecological structure. These correlations are not simply explained by expansions of the evolving species, and often involve additional fluctuations in distantly related taxa. We show that similar feedbacks naturally emerge in simple resource competition models, even in the absence of cross-feeding or predation. These results suggest that the structure and function of host microbiota may be shaped by their local evolutionary history, which could have important implications for personalized medicine and microbiome engineering.
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Affiliation(s)
- Benjamin H Good
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA.
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, 94158, USA.
| | - Layton B Rosenfeld
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
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14
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Cummins EA, Moran RA, Snaith AE, Hall RJ, Connor CH, Dunn SJ, McNally A. Parallel loss of type VI secretion systems in two multi-drug-resistant Escherichia coli lineages. Microb Genom 2023; 9. [PMID: 37970873 DOI: 10.1099/mgen.0.001133] [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] [Indexed: 11/19/2023] Open
Abstract
The repeated emergence of multi-drug-resistant (MDR) Escherichia coli clones is a threat to public health globally. In recent work, drug-resistant E. coli were shown to be capable of displacing commensal E. coli in the human gut. Given the rapid colonization observed in travel studies, it is possible that the presence of a type VI secretion system (T6SS) may be responsible for the rapid competitive advantage of drug-resistant E. coli clones. We employed large-scale genomic approaches to investigate this hypothesis. First, we searched for T6SS genes across a curated dataset of over 20 000 genomes representing the full phylogenetic diversity of E. coli. This revealed large, non-phylogenetic variation in the presence of T6SS genes. No association was found between T6SS gene carriage and MDR lineages. However, multiple clades containing MDR clones have lost essential structural T6SS genes. We characterized the T6SS loci of ST410 and ST131 and identified specific recombination and insertion events responsible for the parallel loss of essential T6SS genes in two MDR clones.
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Affiliation(s)
- Elizabeth A Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Robert A Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ann E Snaith
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rebecca J Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Christopher H Connor
- Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3000, Australia
| | - Steven J Dunn
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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15
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Abstract
A massive number of microorganisms, belonging to different species, continuously divide inside the guts of animals and humans. The large size of these communities and their rapid division times imply that we should be able to watch microbial evolution in the gut in real time, in a similar manner to what has been done in vitro. Here, we review recent findings on how natural selection shapes intrahost evolution (also known as within-host evolution), with a focus on the intestines of mice and humans. The microbiota of a healthy host is not as static as initially thought from the information measured at only one genomic marker. Rather, the genomes of each gut-colonizing species can be highly dynamic, and such dynamism seems to be related to the microbiota species diversity. Genetic and bioinformatic tools, and analysis of time series data, allow quantification of the selection strength on emerging mutations and horizontal transfer events in gut ecosystems. The drivers and functional consequences of gut evolution can now begin to be grasped. The rules of this intrahost microbiota evolution, and how they depend on the biology of each species, need to be understood for more effective development of microbiota therapies to help maintain or restore host health.
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Affiliation(s)
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Oeiras, Portugal.
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16
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Bosch DE, Abbasian R, Parajuli B, Peterson SB, Mougous JD. Structural disruption of Ntox15 nuclease effector domains by immunity proteins protects against type VI secretion system intoxication in Bacteroidales. mBio 2023; 14:e0103923. [PMID: 37345922 PMCID: PMC10470768 DOI: 10.1128/mbio.01039-23] [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: 04/25/2023] [Accepted: 05/03/2023] [Indexed: 06/23/2023] Open
Abstract
Bacteroidales use type VI secretion systems (T6SS) to competitively colonize and persist in the colon. We identify a horizontally transferred T6SS with Ntox15 family nuclease effector (Tde1) that mediates interbacterial antagonism among Bacteroidales, including several derived from a single human donor. Expression of cognate (Tdi1) or orphan immunity proteins in acquired interbacterial defense systems protects against Tde1-dependent attack. We find that immunity protein interaction induces a large effector conformational change in Tde nucleases, disrupting the active site and altering the DNA-binding site. Crystallographic snapshots of isolated Tde1, the Tde1/Tdi1 complex, and homologs from Phocaeicola vulgatus (Tde2/Tdi2) illustrate a conserved mechanism of immunity inserting into the central core of Tde, splitting the nuclease fold into two subdomains. The Tde/Tdi interface and immunity mechanism are distinct from all other polymorphic toxin-immunity interactions of known structure. Bacteroidales abundance has been linked to inflammatory bowel disease activity in prior studies, and we demonstrate that Tde and T6SS structural genes are each enriched in fecal metagenomes from ulcerative colitis subjects. Genetically mobile Tde1-encoding T6SS in Bacteroidales mediate competitive growth and may be involved in inflammatory bowel disease. Broad immunity is conferred by Tdi1 homologs through a fold-disrupting mechanism unique among polymorphic effector-immunity pairs of known structure. IMPORTANCE Bacteroidales are related to inflammatory bowel disease severity and progression. We identify type VI secretion system (T6SS) nuclease effectors (Tde) which are enriched in ulcerative colitis and horizontally transferred on mobile genetic elements. Tde-encoding T6SSs mediate interbacterial competition. Orphan and cognate immunity proteins (Tdi) prevent intoxication by multiple Tde through a new mechanism among polymorphic toxin systems. Tdi inserts into the effector central core, splitting Ntox15 into two subdomains and disrupting the active site. This mechanism may allow for evolutionary diversification of the Tde/Tdi interface as observed in colicin nuclease-immunity interactions, promoting broad neutralization of Tde by orphan Tdi. Tde-dependent T6SS interbacterial antagonism may contribute to Bacteroidales diversity in the context of ulcerative colitis.
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Affiliation(s)
- Dustin E. Bosch
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Romina Abbasian
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Bishal Parajuli
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - S. Brook Peterson
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Joseph D. Mougous
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
- Microbial Interactions and Microbiome Center, University of Washington, Seattle, Washington, USA
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17
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Sheahan ML, Coyne MJ, Flores K, Garcia-Bayona L, Chatzidaki-Livanis M, Sundararajan A, Holst AQ, Barquera B, Comstock LE. A ubiquitous mobile genetic element disarms a bacterial antagonist of the gut microbiota. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.553775. [PMID: 37662397 PMCID: PMC10473720 DOI: 10.1101/2023.08.25.553775] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
DNA transfer is ubiquitous in the gut microbiota, especially among species of Bacteroidales. In silico analyses have revealed hundreds of mobile genetic elements shared between these species, yet little is known about the phenotypes they encode, their effects on fitness, or pleiotropic consequences for the recipient's genome. Here, we show that acquisition of a ubiquitous integrative and conjugative element encoding an antagonistic system shuts down the native contact-dependent antagonistic system of Bacteroides fragilis . Despite inactivating the native antagonism system, mobile element acquisition increases fitness of the B. fragilis transconjugant over its progenitor by arming it with a new weapon. This DNA transfer causes the strain to change allegiances so that it no longer targets ecosystem members containing the same element yet is armed for communal defense.
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18
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Gong D, Adomako-Bonsu AG, Wang M, Li J. Three specific gut bacteria in the occurrence and development of colorectal cancer: a concerted effort. PeerJ 2023; 11:e15777. [PMID: 37554340 PMCID: PMC10405800 DOI: 10.7717/peerj.15777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/29/2023] [Indexed: 08/10/2023] Open
Abstract
Colorectal cancer (CRC), which develops from the gradual evolution of tubular adenomas and serrated polyps in the colon and rectum, has a poor prognosis and a high mortality rate. In addition to genetics, lifestyle, and chronic diseases, intestinal integrity and microbiota (which facilitate digestion, metabolism, and immune regulation) could promote CRC development. For example, enterotoxigenic Bacteroides fragilis, genotoxic Escherichia coli (pks+ E. coli), and Fusobacterium nucleatum, members of the intestinal microbiota, are highly correlated in CRC. This review describes the roles and mechanisms of these three bacteria in CRC development. Their interaction during CRC initiation and progression has also been proposed. Our view is that in the precancerous stage of colorectal cancer, ETBF causes inflammation, leading to potential changes in intestinal ecology that may provide the basic conditions for pks+ E. coli colonization and induction of oncogenic mutations, when cancerous intestinal epithelial cells can further recruit F. nucleatum to colonise the lesion site and F. nucleatum may contribute to CRC advancement by primarily the development of cancer cells, stemization, and proliferation, which could create new and tailored preventive, screening and therapeutic interventions. However, there is the most dominant microbiota in each stage of CRC development, not neglecting the possibility that two or even all three bacteria could be engaged at any stage of the disease. The relationship between the associated gut microbiota and CRC development may provide important information for therapeutic strategies to assess the potential use of the associated gut microbiota in CRC studies, antibiotic therapy, and prevention strategies.
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Affiliation(s)
- Dengmei Gong
- Institute of Zoonosis, College of Public Health, Zunyi Medical University, Zunyi, Guizhou, China
| | - Amma G Adomako-Bonsu
- Institute of Toxicology and Pharmacology, University Medical School Schleswig-Holstein, Kiel, Germany
| | - Maijian Wang
- Gastrointestinal Surgery, Affiliate Hospital of Zunyi Medical University, Zunyi, Guizhou, China
| | - Jida Li
- Institute of Zoonosis, College of Public Health, Zunyi Medical University, Zunyi, Guizhou, China
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19
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Singh RP, Kumari K. Bacterial type VI secretion system (T6SS): an evolved molecular weapon with diverse functionality. Biotechnol Lett 2023; 45:309-331. [PMID: 36683130 DOI: 10.1007/s10529-023-03354-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/14/2022] [Accepted: 01/05/2023] [Indexed: 01/24/2023]
Abstract
Bacterial secretion systems are nanomolecular complexes that release a diverse set of virulence factors/or proteins into its surrounding or translocate to their target host cells. Among these systems, type VI secretion system 'T6SS' is a recently discovered molecular secretion system which is widely distributed in Gram-negative (-ve) bacteria, and shares structural similarity with the puncturing device of bacteriophages. The presence of T6SS is an advantage to many bacteria as it delivers toxins to its neighbour pathogens for competitive survival, and also translocates protein effectors to the host cells, leading to disruption of lipid membranes, cell walls, and cytoskeletons etc. Recent studies have characterized both anti-prokaryotic and anti-eukaryotic effectors, where T6SS is involved in diverse cellular functions including favouring colonization, enhancing the survival, adhesive modifications, internalization, and evasion of the immune system. With the evolution of advanced genomics and proteomics tools, there has been an increase in the number of characterized T6SS effector arsenals and also more clear information about the adaptive significance of this complex system. The functions of T6SS are generally regulated at the transcription, post-transcription and post-translational levels through diverse mechanisms. In the present review, we aimed to provide information about the distribution of T6SS in diverse bacteria, any structural similarity/or dissimilarity, effectors proteins, functional significance, and regulatory mechanisms. We also tried to provide information about the diverse roles played by T6SS in its natural environments and hosts, and further any changes in the microbiome.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
| | - Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
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20
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Robitaille S, Simmons EL, Verster AJ, McClure EA, Royce DB, Trus E, Swartz K, Schultz D, Nadell CD, Ross BD. Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.20.529031. [PMID: 36865186 PMCID: PMC9980007 DOI: 10.1101/2023.02.20.529031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Understanding the relationship between the composition of the human gut microbiota and the ecological forces shaping it is of high importance as progress towards therapeutic modulation of the microbiota advances. However, given the inaccessibility of the gastrointestinal tract, our knowledge of the biogeographical and ecological relationships between physically interacting taxa has been limited to date. It has been suggested that interbacterial antagonism plays an important role in gut community dynamics, but in practice the conditions under which antagonistic behavior is favored or disfavored by selection in the gut environment are not well known. Here, using phylogenomics of bacterial isolate genomes and analysis of infant and adult fecal metagenomes, we show that the contact-dependent type VI secretion system (T6SS) is repeatedly lost from the genomes of Bacteroides fragilis in adults compare to infants. Although this result implies a significant fitness cost to the T6SS, but we could not identify in vitro conditions under which such a cost manifests. Strikingly, however, experiments in mice illustrated that the B. fragilis T6SS can be favored or disfavored in the gut environment, depending on the strains and species in the surrounding community and their susceptibility to T6SS antagonism. We use a variety of ecological modeling techniques to explore the possible local community structuring conditions that could underlie the results of our larger scale phylogenomic and mouse gut experimental approaches. The models illustrate robustly that the pattern of local community structuring in space can modulate the extent of interactions between T6SS-producing, sensitive, and resistant bacteria, which in turn control the balance of fitness costs and benefits of performing contact-dependent antagonistic behavior. Taken together, our genomic analyses, in vivo studies, and ecological theory point toward new integrative models for interrogating the evolutionary dynamics of type VI secretion and other predominant modes of antagonistic interaction in diverse microbiomes.
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Affiliation(s)
- Sophie Robitaille
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Emilia L. Simmons
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Adrian J. Verster
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Emily Ann McClure
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Darlene B. Royce
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Evan Trus
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Kerry Swartz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Daniel Schultz
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Carey D. Nadell
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Benjamin D. Ross
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
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21
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Type VI Secretion Systems: Environmental and Intra-host Competition of Vibrio cholerae. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:41-63. [PMID: 36792870 DOI: 10.1007/978-3-031-22997-8_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The Vibrio Type VI Secretion System (T6SS) is a harpoon-like nanomachine that serves as a defense system and is encoded by approximately 25% of all gram-negative bacteria. In this chapter, we describe the structure of the T6SS in different Vibrio species and outline how the use of different T6SS effector and immunity proteins control kin selection. We summarize the genetic loci that encode the structural elements that make up the Vibrio T6SSs and how these gene clusters are regulated. Finally, we provide insights into T6SS-based competitive dynamics, the role of T6SS genetic exchange in those competitive dynamics, and roles for the Vibrio T6SS in virulence.
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22
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Dapa T, Wong DP, Vasquez KS, Xavier KB, Huang KC, Good BH. Within-host evolution of the gut microbiome. Curr Opin Microbiol 2023; 71:102258. [PMID: 36608574 PMCID: PMC9993085 DOI: 10.1016/j.mib.2022.102258] [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: 11/06/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023]
Abstract
Gut bacteria inhabit a complex environment that is shaped by interactions with their host and the other members of the community. While these ecological interactions have evolved over millions of years, mounting evidence suggests that gut commensals can evolve on much shorter timescales as well, by acquiring new mutations within individual hosts. In this review, we highlight recent progress in understanding the causes and consequences of short-term evolution in the mammalian gut, from experimental evolution in murine hosts to longitudinal tracking of human cohorts. We also discuss new opportunities for future progress by expanding the repertoire of focal species, hosts, and surrounding communities, and by combining deep-sequencing technologies with quantitative frameworks from population genetics.
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Affiliation(s)
- Tanja Dapa
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Daniel Pgh Wong
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Kimberly S Vasquez
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Kerwyn Casey Huang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Benjamin H Good
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.
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23
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Robinson L, Liaw J, Omole Z, Corcionivoschi N, Hachani A, Gundogdu O. In silico investigation of the genus Campylobacter type VI secretion system reveals genetic diversity in organization and putative effectors. Microb Genom 2022; 8:mgen000898. [PMID: 36314601 PMCID: PMC9676060 DOI: 10.1099/mgen.0.000898] [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: 04/11/2022] [Accepted: 09/11/2022] [Indexed: 01/25/2023] Open
Abstract
Bacterial type VI secretion systems (T6SSs) are contractile nanomachines that deliver proteinic substrates into target prokaryotic or eukaryotic cells and the surrounding milieu. The genus Campylobacter encompasses 39 recognized species and 13 subspecies, with many belonging to a group known as ‘emerging Campylobacter pathogens’. Within Campylobacter , seven species have been identified to harbour a complete T6SS cluster but have yet to be comparatively assessed. In this study, using systematic bioinformatics approaches and the T6SS-positive Campylobacter jejuni 488 strain as a reference, we explored the genus-wide prevalence, similarity and make-up of the T6SS amongst 372 publicly available ‘complete’ Campylobacter genomes. Our analyses predict that approximately one-third of Campylobacter species possess a T6SS. We also putatively report the first identification of a T6SS in four species: Campylobacter cuniculorum, Campylobacter helveticus, Campylobacter armoricus and Campylobacter ornithocola . The Campylobacter T6SSs cluster into three distinct organizations (I–III), of which two break down into further variants. Thirty T6SS-containing genomes were found to harbour more than one vgrG gene, with Campylobacter lari strain NCTC 11845 possessing five. Analysis of the C. jejuni Pathogenicity Island-1 confirmed its conservation amongst T6SS-positive C. jejuni strains, as well as highlighting its diverse genetic composition, including additional putative effector–immunity pairs (e.g. PoNe and DUF1911 domains). Effector–immunity pairs were also observed neighbouring vgrG s in several other Campylobacter species, in addition to putative genes encoding nucleases, lysozymes, ATPases and a ferric ATP-binding cassette uptake system. These observations highlight the diverse genetic make-up of the T6SS within Campylobacter and provide further evidence of its role in pathogenesis.
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Affiliation(s)
- Luca Robinson
- National Heart and Lung Institute, Imperial College London, London, UK
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Janie Liaw
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Zahra Omole
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Nicolae Corcionivoschi
- Bacteriology Branch, Veterinary Sciences Division, Agri-Food and Biosciences Institute, Belfast, UK
- Bioengineering of Animal Resources, University of Life Sciences – King Mihai I of Romania from Timisoara, Timisoara, Romania
| | - Abderrahman Hachani
- The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, University of Melbourne, Melbourne, VIC, Australia
| | - Ozan Gundogdu
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
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In Silico Study of Cell Surface Structures of Parabacteroides distasonis Involved in Its Maintenance within the Gut Microbiota. Int J Mol Sci 2022; 23:ijms23169411. [PMID: 36012685 PMCID: PMC9409006 DOI: 10.3390/ijms23169411] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
The health-promoting Parabacteroides distasonis, which is part of the core microbiome, has recently received a lot of attention, showing beneficial properties for its host and potential as a new biotherapeutic product. However, no study has yet investigated the cell surface molecules and structures of P. distasonis that allow its maintenance within the gut microbiota. Moreover, although P. distasonis is strongly recognized as an intestinal commensal species with benefits for its host, several works displayed controversial results, showing it as an opportunistic pathogen. In this study, we reported gene clusters potentially involved in the synthesis of capsule, fimbriae-like and pili-like cell surface structures in 26 P. distasonis genomes and applied the new RfbA-typing classification in order to better understand and characterize the beneficial/pathogenic behavior related to P. distasonis strains. Two different types of fimbriae, three different types of pilus and up to fourteen capsular polysaccharide loci were identified over the 26 genomes studied. Moreover, the addition of data to the rfbA-type classification modified the outcome by rearranging rfbA genes and adding a fifth group to the classification. In conclusion, the strain variability in terms of external proteinaceous structure could explain the inter-strain differences previously observed of P. distasonis adhesion capacities and its potential pathogenicity, but no specific structure related to P. distasonis beneficial or detrimental activity was identified.
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A proteolytically activated antimicrobial toxin encoded on a mobile plasmid of Bacteroidales induces a protective response. Nat Commun 2022; 13:4258. [PMID: 35871068 PMCID: PMC9308784 DOI: 10.1038/s41467-022-31925-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 07/11/2022] [Indexed: 01/19/2023] Open
Abstract
Phocaeicola vulgatus is one of the most abundant and ubiquitous bacterial species of the human gut microbiota, yet a comprehensive analysis of antibacterial toxin production by members of this species has not been reported. Here, we identify and characterize a previously undescribed antibacterial protein. This toxin, designated BcpT, is encoded on a small mobile plasmid that is largely confined to strains of the closely related species Phocaeicola vulgatus and Phocaeicola dorei. BcpT is unusual in that it requires cleavage at two distinct sites for activation, and we identify bacterial proteases that perform this activation. We further identify BcpT's receptor as the Lipid A-core glycan, allowing BcpT to target species of other Bacteroidales families. Exposure of cells to BcpT induces a response involving an unusual sigma/anti-sigma factor pair that is likely triggered by cell envelope stress, resulting in the expression of genes that partially protect cells from multiple antimicrobial toxins.
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26
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Analysis of Effector and Immunity Proteins of the GA2 Type VI Secretion Systems of Gut Bacteroidales. J Bacteriol 2022; 204:e0012222. [PMID: 35735993 PMCID: PMC9295542 DOI: 10.1128/jb.00122-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Three distinct genetic architectures (GAs) of Type VI secretion systems (T6SSs) have been described in gut Bacteroidales species, each with unique genes and characteristics. Unlike the GA3 T6SSs, potent antagonism has not yet been demonstrated for the GA1 or GA2 T6SSs. We previously showed that the GA2 T6SS loci are contained on integrative and conjugative elements and that there are five subtypes. Collectively, GA2 are the most prevalent Bacteroidales T6SSs in the human populations analyzed. In this study, we provide a comprehensive bioinformatic analysis of the three variable regions of GA2 T6SS loci, which encode toxic effector and immunity proteins. In total, we identified 63 distinct effectors encoded within 31 nonredundant GA2 loci, 18 of which do not have described motifs or predicted functions. We provide experimental evidence for toxin activity for four different GA2 effectors, showing that each functions only when present in the periplasm, and experimentally confirm their cognate immunity proteins. Our data demonstrate that each GA2 locus encodes at least three distinct effectors with targets in both the cytoplasm and the periplasm. The data also suggest that the effectors of a given locus are loaded onto the tube by different mechanisms, which may allow all three effectors encoded within a single GA2 locus with distinct antibacterial activity to be loaded onto a single T6 tube, increasing the antagonistic effect. IMPORTANCE Humans are colonized with many gut Bacteroidales species at high density, allowing for extensive opportunities for contact-dependent antagonism. To begin to understand the antagonistic potential of the GA2 T6SSs of the gut Bacteroidales, we performed bioinformatic and experimental analyses of the three divergent regions containing the toxin effector and immunity genes. We show that each GA2 T6SS locus encodes at least three distinct toxic effectors including toxins linked to Rhs and Hcp with cytoplasmic targets, and unlinked effectors with targets in the periplasm. The diversity and modality of effectors exceeds that of the GA1 or GA3 T6SS loci (M. J. Coyne, K. G. Roelofs, and L. E. Comstock, BMC Genomics 17:58, 2016, https://doi.org/10.1186/s12864-016-2377-z) and suggests that these T6SSs have the potential to be potent antibacterial weapons in the human gut.
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Diversity and distribution of Type VI Secretion System gene clusters in bacterial plasmids. Sci Rep 2022; 12:8249. [PMID: 35581398 PMCID: PMC9113992 DOI: 10.1038/s41598-022-12382-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022] Open
Abstract
Type VI Secretion System (T6SS) is a nanomolecular apparatus that allows the delivery of effector molecules through the cell envelope of a donor bacterium to prokaryotic and/or eukaryotic cells, playing a role in the bacterial competition, virulence, and host interaction. T6SS is patchily distributed in bacterial genomes, suggesting an association with horizontal gene transfer (HGT). In fact, T6SS gene loci are eventually found within genomic islands (GIs), and there are some reports in plasmids and integrative and conjugative elements (ICEs). The impact that T6SS may have on bacteria fitness and the lack of evidence on its spread mechanism led us to question whether plasmids could represent a key mechanism in the spread of T6SS in bacteria. Therefore, we performed an in-silico analysis to reveal the association between T6SS and plasmids. T6SS was mined on 30,660 plasmids from NCBI based on the presence of at least six T6SS core proteins. T6SS was identified in 330 plasmids, all belonging to the same type (T6SSi), mainly in Proteobacteria (328/330), particularly in Rhizobium and Ralstonia. Interestingly, most genomes carrying T6SS-harboring plasmids did not encode T6SS in their chromosomes, and, in general, chromosomal and plasmid T6SSs did not form separate clades.
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28
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Unni R, Pintor KL, Diepold A, Unterweger D. Presence and absence of type VI secretion systems in bacteria. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35467500 DOI: 10.1099/mic.0.001151] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The type VI secretion system (T6SS) is a molecular puncturing device that enables Gram-negative bacteria to kill competitors, manipulate host cells and take up nutrients. Who would want to miss such superpowers? Indeed, many studies show how widespread the secretion apparatus is among microbes. However, it is becoming evident that, on multiple taxonomic levels, from phyla to species and strains, some bacteria lack a T6SS. Here, we review who does and does not have a type VI secretion apparatus and speculate on the dynamic process of gaining and losing the secretion system to better understand its spread and distribution across the microbial world.
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Affiliation(s)
- Rahul Unni
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany.,Institute for Experimental Medicine, Kiel University, Michaelisstraße 5, 24105 Kiel, Germany
| | - Katherine L Pintor
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Andreas Diepold
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Daniel Unterweger
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany.,Institute for Experimental Medicine, Kiel University, Michaelisstraße 5, 24105 Kiel, Germany
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29
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Bank NC, Singh V, Rodriguez-Palacios A. Classification of Parabacteroides distasonis and other Bacteroidetes using O- antigen virulence gene: RfbA-Typing and hypothesis for pathogenic vs. probiotic strain differentiation. Gut Microbes 2022; 14:1997293. [PMID: 35090379 PMCID: PMC8803095 DOI: 10.1080/19490976.2021.1997293] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Parabacteroides distasonis (Pdis) is the type species for the new Parabacteroides genus, and a gut commensal of the Bacteroidetes phylum. Emerging reports (primarily based on reference strain/ATCC-8503) concerningly propose that long-known opportunistic pathogen Pdis is a probiotic. We posit there is an urgent need to characterize the pathogenicity of Pdis strain-strain variability. Unfortunately, no methods/insights exist to classify Bacteroidetes for this purpose. Herein, we developed a virulence gene-based classification system for Pdis and Bacteroidetes to facilitate pathogenic-vs-probiotic characterization. We used DNA in silico methods to develop a system based on the virulence (lipopolysaccharide/bacterial wall) 'rfbA O-antigen-synthesis gene'. We then performed phylogenetic analysis of rfbA from fourteen Pdis complete genomes (21 genes), other Parabacteroides, Bacteroidetes, and Enterobacteriaceae; and proposed a PCR-based Restriction-Fragment Length Polymorphism method. Cluster analysis revealed that Pdis can be classified into four lineages (based on gene gaps/insertions) which we designated rfbA-Types I, II, III, and IV. In context, we found 14 additional rfbA-types (I-XVIII) interspersed with numerous Bacteroidetes and pathogenic Enterobacteriaceae forming three major "rfbA-superclusters." For laboratory rfbA-Typing implementation, we developed a PCR-primer strategy to amplify Pdis rfbA genes (100%-specificity) to conduct MboII-RFLP and sub-classify Pdis. In-silico primers for other Bacteroidetes are proposed/discussed. Comparative analysis of lipopolysaccharide/lipid-A gene lpxK confirmed rfbA as highly discriminant. In conclusion, rfbA-Typing classifies Bacteroidetes/Pdis into unique clusters/superclusters given rfbA copy/sequence variability. Analysis revealed that most pathogenic Pdis strains are single-copy rfbA-Type I . The relevance of the rfbA strain variability in disease might depend on their hypothetical modulatory interactions with other O-antigens/lipopolysaccharides and TLR4 lipopolysaccharide-receptors in human/animal cells.
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Affiliation(s)
- Nicholas C. Bank
- Division of Gastroenterology and Liver Disease, School of Medicine, Case Western Reserve University , Cleveland, United States
| | - Vaidhvi Singh
- Division of Gastroenterology and Liver Disease, School of Medicine, Case Western Reserve University , Cleveland, United States
| | - Alex Rodriguez-Palacios
- Division of Gastroenterology and Liver Disease, School of Medicine, Case Western Reserve University , Cleveland, United States,School of Medicine, Digestive Health Research Institute, Case Western Reserve University, Cleveland, United States,University Hospitals Research and Education Institute, University Hospitals Cleveland Medical Center, Cleveland, United States,CONTACT Alex Rodriguez-Palacios Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, United States; School of Medicine, Digestive Health Research Institute, Case Western Reserve University, Cleveland, United States; University Hospitals Research and Education Institute, University Hospitals Cleveland Medical Center, Cleveland, United States
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30
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Yan W, Hall AB, Jiang X. Bacteroidales species in the human gut are a reservoir of antibiotic resistance genes regulated by invertible promoters. NPJ Biofilms Microbiomes 2022; 8:1. [PMID: 35013297 PMCID: PMC8748976 DOI: 10.1038/s41522-021-00260-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 11/26/2021] [Indexed: 12/21/2022] Open
Abstract
Antibiotic-resistance genes (ARGs) regulated by invertible promoters can mitigate the fitness cost of maintaining ARGs in the absence of antibiotics and could potentially prolong the persistence of ARGs in bacterial populations. However, the origin, prevalence, and distribution of these ARGs regulated by invertible promoters remains poorly understood. Here, we sought to assess the threat posed by ARGs regulated by invertible promoters by systematically searching for ARGs regulated by invertible promoters in the human gut microbiome and examining their origin, prevalence, and distribution. Through metagenomic assembly of 2227 human gut metagenomes and genomic analysis of the Unified Human Gastrointestinal Genome (UHGG) collection, we identified ARGs regulated by invertible promoters and categorized them into three classes based on the invertase-regulating phase variation. In the human gut microbiome, ARGs regulated by invertible promoters are exclusively found in Bacteroidales species. Through genomic analysis, we observed that ARGs regulated by invertible promoters have convergently originated from ARG insertions into glycan-synthesis loci that were regulated by invertible promoters at least three times. Moreover, all three classes of invertible promoters regulating ARGs are located within integrative conjugative elements (ICEs). Therefore, horizontal transfer via ICEs could explain the wide taxonomic distribution of ARGs regulated by invertible promoters. Overall, these findings reveal that glycan-synthesis loci regulated by invertible promoters in Bacteroidales species are an important hotspot for the emergence of clinically-relevant ARGs regulated by invertible promoters.
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Affiliation(s)
- Wei Yan
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - A Brantley Hall
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, USA
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA.
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31
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Saa P, Urrutia A, Silva-Andrade C, Martín AJ, Garrido D. Modeling approaches for probing cross-feeding interactions in the human gut microbiome. Comput Struct Biotechnol J 2021; 20:79-89. [PMID: 34976313 PMCID: PMC8685919 DOI: 10.1016/j.csbj.2021.12.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/03/2021] [Accepted: 12/04/2021] [Indexed: 12/16/2022] Open
Abstract
Microbial communities perform emergent activities that are essentially different from those carried by their individual members. The gut microbiome and its metabolites have a significant impact on the host, contributing to homeostasis or disease. Food molecules shape this community, being fermented through cross-feeding interactions of metabolites such as lactate, acetate, and amino acids, or products derived from macromolecule degradation. Mathematical and experimental approaches have been applied to understand and predict the interactions between microorganisms in complex communities such as the gut microbiota. Rational and mechanistic understanding of microbial interactions is essential to exploit their metabolic activities and identify keystone taxa and metabolites. The latter could be used in turn to modulate or replicate the metabolic behavior of the community in different contexts. This review aims to highlight recent experimental and modeling approaches for studying cross-feeding interactions within the gut microbiome. We focus on short-chain fatty acid production and fiber fermentation, which are fundamental processes in human health and disease. Special attention is paid to modeling approaches, particularly kinetic and genome-scale stoichiometric models of metabolism, to integrate experimental data under different diet and health conditions. Finally, we discuss limitations and challenges for the broad application of these modeling approaches and their experimental verification for improving our understanding of the mechanisms of microbial interactions.
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Affiliation(s)
- Pedro Saa
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
- Institute for Mathematical and Computational Engineering, Pontificia Universidad Católica de Chile, Vicuña Mackenna, 4860 Santiago, Chile
| | - Arles Urrutia
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudia Silva-Andrade
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Alberto J. Martín
- Laboratorio de Biología de Redes, Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Daniel Garrido
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
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Bacteroidetocins Target the Essential Outer Membrane Protein BamA of Bacteroidales Symbionts and Pathogens. mBio 2021; 12:e0228521. [PMID: 34517753 PMCID: PMC8546649 DOI: 10.1128/mbio.02285-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Bacteroidetocins are a family of antibacterial peptide toxins that are produced by and target members of the phylum Bacteroidetes. To date, 19 bacteroidetocins have been identified, and four have been tested and shown to kill diverse Bacteroidales species (M. J. Coyne, N. Béchon, L. M. Matano, V. L. McEneany, et al., Nat Commun 10:3460, 2019, https://doi.org/10.1038/s41467-019-11494-1). Here, we identify the target and likely mechanism of action of the bacteroidetocins. We selected seven spontaneous mutants of four different genera, all resistant to bacteroidetocin A (Bd-A) and found that all contained mutations in a single gene, bamA. Construction of three of these bamA mutants in the wild-type (WT) strains confirmed they confer resistance to Bd-A as well as to other bacteroidetocins. We identified an aspartate residue of BamA at the beginning of exterior loop 3 (eL3) that, when altered, renders strains resistant to Bd-A. Analysis of a panel of diverse Bacteroidales strains showed a correlation between the presence of this aspartate residue and Bd-A sensitivity. Fluorescence microscopy and transmission electron microscopy (TEM) analysis of Bd-A-treated cells showed cellular morphological changes consistent with a BamA defect. Transcriptomic analysis of Bd-A-treated cells revealed gene expression changes indicative of cell envelope stress. Studies in mice revealed that bacteroidetocin-resistant mutants are outcompeted by their WT strain in vivo. Analyses of longitudinal human gut isolates showed that bamA mutations leading to bacteroidetocin resistance do not become fixed in the human gut, even in bacteroidetocin-producing strains and nonproducing coresident strains. Together, these data lend further support to the applicability of the bacteroidetocins as therapeutic peptides in the treatment of maladies involving Bacteroidales species.
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