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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Dong Q, Lin H, Allen MM, Garneau JR, Sia JK, Smith RC, Haro F, McMillen T, Pope RL, Metcalfe C, Burgo V, Woodson C, Dylla N, Kohout C, Sundararajan A, Snitkin ES, Young VB, Fortier LC, Kamboj M, Pamer EG. Virulence and genomic diversity among clinical isolates of ST1 (BI/NAP1/027) Clostridioides difficile. Cell Rep 2023; 42:112861. [PMID: 37523264 PMCID: PMC10627504 DOI: 10.1016/j.celrep.2023.112861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/01/2023] [Accepted: 07/07/2023] [Indexed: 08/02/2023] Open
Abstract
Clostridioides difficile produces toxins that damage the colonic epithelium, causing colitis. Variation in disease severity is poorly understood and has been attributed to host factors and virulence differences between C. difficile strains. We test 23 epidemic ST1 C. difficile clinical isolates for their virulence in mice. All isolates encode a complete Tcd pathogenicity locus and achieve similar colonization densities. However, disease severity varies from lethal to avirulent infections. Genomic analysis of avirulent isolates reveals a 69-bp deletion in the cdtR gene, which encodes a response regulator for binary toxin expression. Deleting the 69-bp sequence in virulent R20291 strain renders it avirulent in mice with reduced toxin gene transcription. Our study demonstrates that a natural deletion within cdtR attenuates virulence in the epidemic ST1 C. difficile isolates without reducing colonization and persistence. Distinguishing strains on the basis of cdtR may enhance the specificity of diagnostic tests for C. difficile colitis.
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Affiliation(s)
- Qiwen Dong
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA.
| | - Huaiying Lin
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Marie-Maude Allen
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Julian R Garneau
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Jonathan K Sia
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rita C Smith
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Fidel Haro
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Tracy McMillen
- Infection Control, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rosemary L Pope
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Carolyn Metcalfe
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Victoria Burgo
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Che Woodson
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Nicholas Dylla
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Claire Kohout
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | | | - Evan S Snitkin
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vincent B Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Louis-Charles Fortier
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Mini Kamboj
- Infection Control, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Eric G Pamer
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
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Dong Q, Lin H, Allen MM, Garneau JR, Sia JK, Smith RC, Haro F, McMillen T, Pope RL, Metcalfe C, Burgo V, Woodson C, Dylla N, Kohout C, Sundararajan A, Snitkin ES, Young VB, Fortier LC, Kamboj M, Pamer EG. Virulence and genomic diversity among clinical isolates of ST1 (BI/NAP1/027) Clostridioides difficile. bioRxiv 2023:2023.01.12.523823. [PMID: 36711955 PMCID: PMC9882218 DOI: 10.1101/2023.01.12.523823] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Clostridioides difficile (C. difficile) , a leading cause of nosocomial infection, produces toxins that damage the colonic epithelium and results in colitis that varies from mild to fulminant. Variation in disease severity is poorly understood and has been attributed to host factors (age, immune competence and intestinal microbiome composition) and/or virulence differences between C. difficile strains, with some, such as the epidemic BI/NAP1/027 (MLST1) strain, being associated with greater virulence. We tested 23 MLST1(ST1) C. difficile clinical isolates for virulence in antibiotic-treated C57BL/6 mice. All isolates encoded a complete Tcd pathogenicity locus and achieved similar colonization densities in mice. Disease severity varied, however, with 5 isolates causing lethal infections, 16 isolates causing a range of moderate infections and 2 isolates resulting in no detectable disease. The avirulent ST1 isolates did not cause disease in highly susceptible Myd88 -/- or germ-free mice. Genomic analysis of the avirulent isolates revealed a 69 base-pair deletion in the N-terminus of the cdtR gene, which encodes a response regulator for binary toxin (CDT) expression. Genetic deletion of the 69 base-pair cdtR sequence in the highly virulent ST1 R20291 C. difficile strain rendered it avirulent and reduced toxin gene transcription in cecal contents. Our study demonstrates that a natural deletion within cdtR attenuates virulence in the epidemic ST1 C. difficile strain without reducing colonization and persistence in the gut. Distinguishing strains on the basis of cdtR may enhance the specificity of diagnostic tests for C. difficile colitis.
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Affiliation(s)
- Qiwen Dong
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Huaiying Lin
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Marie-Maude Allen
- Department of Microbiology and Infectious Diseases, Universite de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Julian R. Garneau
- Department of Microbiology and Infectious Diseases, Universite de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Jonathan K. Sia
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Rita C. Smith
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Fidel Haro
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Tracy McMillen
- Infection Control, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Rosemary L. Pope
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
| | - Carolyn Metcalfe
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Victoria Burgo
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Che Woodson
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Nicholas Dylla
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Claire Kohout
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | | | - Evan S Snitkin
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Vincent B. Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Louis-Charles Fortier
- Department of Microbiology and Infectious Diseases, Universite de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Mini Kamboj
- Infection Control, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Eric G. Pamer
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
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