Comparative metagenomics reveals the differential gut microbiota involved in bile acid metabolism in patients with crohn's disease.

Microbial communities in CD patients showed reduced abundance in metabolism-associated genes and lower species-function correlation compared to healthy controls.

• Study conducted with nine CD patients and nine healthy controls using comparative metagenomics
• Integrated metagenomic species profiling and functional annotation with species-function network analysis were employed
• Findings suggest 'a possible imbalance of microbial communities in CD group'
• Both reduced functional gene abundance and lower species-function correlations were predicted in CD patients

Three microbial species associated with bile salt hydrolase (BSH)-coding genes showed significantly lower abundance in CD patients.

• Anaerostipes hadrus-like showed significantly lower abundance in CD patients (P = 0.001317)
• Roseburia intestinalis-like showed significantly lower abundance in CD patients (P = 0.03542)
• Coprococcus catus-like showed significantly lower abundance in CD patients (P = 0.0005787)
• All three species are associated with bile salt hydrolase-coding genes

Ruminococcus gnavus-like, associated with 3α-HSDH- and 3β-HSDH-coding genes, demonstrated relatively higher abundance in CD patients.

• Ruminococcus gnavus-like showed higher abundance in CD patients (P = 0.0257)
• This species is related to both 3α-hydroxysteroid dehydrogenase (3α-HSDH)- and 3β-HSDH-coding genes
• This contrasts with the decreased abundance of BSH-associated species in the same CD group

Escherichia coli-like, associated with 7α-HSDH-coding genes, exhibited higher abundance in CD patients.

• Escherichia coli-like showed higher abundance in CD patients (P = 0.01044)
• This species is identified as the taxon associated with 7α-HSDH-coding genes
• Both E. coli-like and Ruminococcus gnavus-like showed elevated abundance, contrasting with decreased BSH-associated taxa

Network correlation analysis indicated potential associations between differential bile acid metabolism-related species and other co-occurring gut microbiota in CD patients.

• Species-function network analysis was used to characterize microbial community relationships
• Differential species involved in BA metabolism were found to have potential associations with other co-occurring gut microbiota
• The network analysis approach complemented the functional gene abundance and species profiling analyses
• These associations suggest broader microbial community-level disruption in BA metabolism beyond individual species changes