Clostridioides difficile infection is associated with differences in transcriptionally active microbial communities

Area of Science:

• Microbiology
• Genomics
• Infectious Diseases

Background:

• Clostridioides difficile infection (CDI) causes significant hospitalizations and costs in the US.
• Gut microbiome dysbiosis is implicated in CDI development and recurrence.
• Metatranscriptomics (MT) offers a powerful tool to study active microbial communities in CDI.

Purpose of the Study:

• To investigate differences in active microbial community composition and gene expression between CDI-positive (CDI+) and CDI-negative (CDI-) individuals using MT.
• To identify specific microbial taxa and genes associated with CDI status.
• To explore the role of the mycobiome and biofilm formation in CDI pathogenesis.

Main Methods:

• Utilized metatranscriptomics (MT) to analyze active microbial taxa and expressed genes in fecal samples from CDI+ (n=20) and CDI- (n=19) patients.
• Applied statistical analyses including Kruskal-Wallis and PERMANOVA to identify significant differences in diversity, composition, and gene expression.
• Performed differential feature analysis to pinpoint specific taxa and genes associated with CDI status.

Main Results:

• No significant differences in microbial richness or evenness were found between CDI+ and CDI- groups.
• Clustering analysis revealed significant differences in active microbial taxa and gene expression based on CDI status.
• Increased expression of opportunistic pathogens like Enterocloster bolteae and Ruminococcus gnavus was observed in CDI+ samples.
• Specific fungal taxa, including those in the Saccharomycetaceae family, showed differential gene expression.
• Clostridioides difficile expressed genes associated with biofilm formation, suggesting a role in antibiotic resistance and recurrence.

Conclusions:

• Metatranscriptomics effectively differentiates active microbial and functional profiles in CDI patients.
• Specific opportunistic pathogens and fungal taxa are significantly associated with CDI.
• The expression of biofilm-associated genes by C. difficile may contribute to treatment challenges.
• The mycobiome plays a crucial role in CDI pathogenesis, warranting further investigation.