Diversity of human colonic butyrate‐producing bacteria revealed by analysis of the butyryl‐CoA:acetate CoA‐transferase gene

TLDR

Butyrate‑producing bacteria are key to colon health, supplying energy to the epithelium and modulating host responses, and their functional groups can be profiled by analyzing the butyryl‑CoA:acetate CoA‑transferase gene. The study aimed to assess the diversity and culturability of colonic butyrate‑producing bacteria by designing degenerate primers to amplify the butyryl‑CoA:acetate CoA‑transferase gene from fecal samples of 10 healthy volunteers. The authors used degenerate primers to amplify the butyryl‑CoA:acetate CoA‑transferase gene and then applied thermal melt curve analysis of the PCR amplicons to qualitatively distinguish major butyrate‑producing groups based on DNA G+C content. Amplified sequences were 98% identical to known cultured butyrate‑producing bacteria, clustering into 12 OTUs, with four dominant OTUs corresponding to *Eubacterium rectale*, *Roseburia faecis*, *Eubacterium hallii*, and an unnamed species SS2/1; the remaining 12% of sequences represented 20 OTUs from putatively uncultured strains, and inulin ingestion significantly increased *Faecalibacterium prausnitzii* abundance (P = 0.019).

Abstract

Summary Butyrate‐producing bacteria play an important role in the human colon, supplying energy to the gut epithelium and regulating host cell responses. In order to explore the diversity and culturability of this functional group, we designed degenerate primers to amplify butyryl‐CoA:acetate CoA‐transferase sequences from faecal samples provided by 10 healthy volunteers. Eighty‐eight per cent of amplified sequences showed > 98% DNA sequence identity to CoA‐transferases from cultured butyrate‐producing bacteria, and these fell into 12 operational taxonomic units (OTUs). The four most prevalent OTUs corresponded to Eubacterium rectale , Roseburia faecis , Eubacterium hallii and an unnamed cultured species SS2/1. The remaining 12% of sequences, however, belonged to 20 OTUs that are assumed to come from uncultured butyrate‐producing strains. Samples taken after ingestion of inulin showed significant ( P = 0.019) increases in Faecalibacterium prausnitzii . Because several of the dominant butyrate producers differ in their DNA % G+C content, analysis of thermal melt curves obtained for PCR amplicons of the butyryl‐CoA:acetate CoA‐transferase gene provides a convenient and rapid qualitative assessment of the major butyrate producing groups present in a given sample. This type of analysis therefore provides an excellent source of information on functionally important groups within the colonic microbial community.