Identification of <named-content content-type="genus-species">Clostridioides difficile</named-content>-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly
ABSTRACT A major function of the gut microbiota is to provide colonization resistance, wherein pathogens are inhibited or suppressed below infectious levels. However, the fraction of gut microbiota required for colonization resistance remains unclear. We used culturomics to isolate a gut microbiota...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2020-02-01
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| Series: | mSystems |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mSystems.00620-19 |
| _version_ | 1818405903887499264 |
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| author | Sudeep Ghimire Chayan Roy Supapit Wongkuna Linto Antony Abhijit Maji Mitchel Chan Keena Andrew Foley Joy Scaria |
| author_facet | Sudeep Ghimire Chayan Roy Supapit Wongkuna Linto Antony Abhijit Maji Mitchel Chan Keena Andrew Foley Joy Scaria |
| author_sort | Sudeep Ghimire |
| collection | DOAJ |
| description | ABSTRACT A major function of the gut microbiota is to provide colonization resistance, wherein pathogens are inhibited or suppressed below infectious levels. However, the fraction of gut microbiota required for colonization resistance remains unclear. We used culturomics to isolate a gut microbiota culture collection comprising 1,590 isolates belonging to 102 species. This culture collection represents 34.57% of the taxonomic diversity and 70% functional capacity, as estimated by metagenomic sequencing of the fecal samples used for culture. Using whole-genome sequencing, we characterized species representatives from this collection and predicted their phenotypic traits, further characterizing isolates by defining nutrient utilization profiles and short-chain fatty acid production. When screened with a coculture assay, 66 species in our culture collection inhibited Clostridioides difficile. Several phenotypes, particularly, growth rate, production of SCFAs, and the utilization of mannitol, sorbitol, or succinate, correlated with C. difficile inhibition. We used a combinatorial community assembly approach to formulate defined bacterial mixes inhibitory to C. difficile. We tested 256 combinations and found that both species composition and blend size were important in inhibition. Our results show that the interaction of bacteria with one another in a mix and with other members of gut commensals must be investigated to design defined bacterial mixes for inhibiting C. difficile in vivo. IMPORTANCE Antibiotic treatment causes instability of gut microbiota and the loss of colonization resistance, thus allowing pathogens such as Clostridioides difficile to colonize and causing recurrent infection and mortality. Although fecal microbiome transplantation has been shown to be an effective treatment for C. difficile infection (CDI), a more desirable approach would be the use of a defined mix of inhibitory gut bacteria. The C. difficile-inhibiting species and bacterial combinations identified herein improve the understanding of the ecological interactions controlling colonization resistance against C. difficile and could aid in the design of defined bacteriotherapy as a nonantibiotic alternative against CDI. |
| first_indexed | 2024-12-14T09:03:27Z |
| format | Article |
| id | doaj.art-5c2f86ce500f4fbe802168f6b8c0e1cf |
| institution | Directory Open Access Journal |
| issn | 2379-5077 |
| language | English |
| last_indexed | 2024-12-14T09:03:27Z |
| publishDate | 2020-02-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj.art-5c2f86ce500f4fbe802168f6b8c0e1cf2022-12-21T23:08:46ZengAmerican Society for MicrobiologymSystems2379-50772020-02-015110.1128/mSystems.00620-19Identification of <named-content content-type="genus-species">Clostridioides difficile</named-content>-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community AssemblySudeep Ghimire0Chayan Roy1Supapit Wongkuna2Linto Antony3Abhijit Maji4Mitchel Chan Keena5Andrew Foley6Joy Scaria7Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USADepartment of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USADepartment of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USADepartment of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USADepartment of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USADepartment of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USADepartment of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USADepartment of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USAABSTRACT A major function of the gut microbiota is to provide colonization resistance, wherein pathogens are inhibited or suppressed below infectious levels. However, the fraction of gut microbiota required for colonization resistance remains unclear. We used culturomics to isolate a gut microbiota culture collection comprising 1,590 isolates belonging to 102 species. This culture collection represents 34.57% of the taxonomic diversity and 70% functional capacity, as estimated by metagenomic sequencing of the fecal samples used for culture. Using whole-genome sequencing, we characterized species representatives from this collection and predicted their phenotypic traits, further characterizing isolates by defining nutrient utilization profiles and short-chain fatty acid production. When screened with a coculture assay, 66 species in our culture collection inhibited Clostridioides difficile. Several phenotypes, particularly, growth rate, production of SCFAs, and the utilization of mannitol, sorbitol, or succinate, correlated with C. difficile inhibition. We used a combinatorial community assembly approach to formulate defined bacterial mixes inhibitory to C. difficile. We tested 256 combinations and found that both species composition and blend size were important in inhibition. Our results show that the interaction of bacteria with one another in a mix and with other members of gut commensals must be investigated to design defined bacterial mixes for inhibiting C. difficile in vivo. IMPORTANCE Antibiotic treatment causes instability of gut microbiota and the loss of colonization resistance, thus allowing pathogens such as Clostridioides difficile to colonize and causing recurrent infection and mortality. Although fecal microbiome transplantation has been shown to be an effective treatment for C. difficile infection (CDI), a more desirable approach would be the use of a defined mix of inhibitory gut bacteria. The C. difficile-inhibiting species and bacterial combinations identified herein improve the understanding of the ecological interactions controlling colonization resistance against C. difficile and could aid in the design of defined bacteriotherapy as a nonantibiotic alternative against CDI.https://journals.asm.org/doi/10.1128/mSystems.00620-19Clostridium difficilecoculturecolonization resistanceculturomicsfatty acidsmetagenomics |
| spellingShingle | Sudeep Ghimire Chayan Roy Supapit Wongkuna Linto Antony Abhijit Maji Mitchel Chan Keena Andrew Foley Joy Scaria Identification of <named-content content-type="genus-species">Clostridioides difficile</named-content>-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly mSystems Clostridium difficile coculture colonization resistance culturomics fatty acids metagenomics |
| title | Identification of <named-content content-type="genus-species">Clostridioides difficile</named-content>-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly |
| title_full | Identification of <named-content content-type="genus-species">Clostridioides difficile</named-content>-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly |
| title_fullStr | Identification of <named-content content-type="genus-species">Clostridioides difficile</named-content>-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly |
| title_full_unstemmed | Identification of <named-content content-type="genus-species">Clostridioides difficile</named-content>-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly |
| title_short | Identification of <named-content content-type="genus-species">Clostridioides difficile</named-content>-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly |
| title_sort | identification of named content content type genus species clostridioides difficile named content inhibiting gut commensals using culturomics phenotyping and combinatorial community assembly |
| topic | Clostridium difficile coculture colonization resistance culturomics fatty acids metagenomics |
| url | https://journals.asm.org/doi/10.1128/mSystems.00620-19 |
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