Identification of Clostridioides difficile-Inhibiting Gut Commensals Using Culturomics, Phenotyping, and Combinatorial Community Assembly.
Clostridium difficile
coculture
colonization resistance
culturomics
fatty acids
metagenomics
microbiome
nutrient competition
pathogen inhibition
phenotypic identification
Journal
mSystems
ISSN: 2379-5077
Titre abrégé: mSystems
Pays: United States
ID NLM: 101680636
Informations de publication
Date de publication:
04 Feb 2020
04 Feb 2020
Historique:
entrez:
6
2
2020
pubmed:
6
2
2020
medline:
6
2
2020
Statut:
epublish
Résumé
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
Identifiants
pubmed: 32019832
pii: 5/1/e00620-19
doi: 10.1128/mSystems.00620-19
pmc: PMC7002114
pii:
doi:
Types de publication
Journal Article
Langues
eng
Informations de copyright
Copyright © 2020 Ghimire et al.
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