What are gut bacteria actively doing in healthy people?

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The human gut naturally hosts a large, dynamic bacterial community with major relevance to health. Metagenomics is expanding knowledge of this microbiome’s gene content and its functional and genetic variability. However, little is known about which bacteria are active in the gastrointestinal tract and what they do.

To identify the active members of the gut microbiome and their functions under healthy conditions, researchers performed a metatranscriptomic study on ten healthy volunteers. They sequenced microbial cDNAs obtained from each sample using 454 technology. Analysis of 16S transcripts revealed the phylogenetic structure—the pattern of related groups—of the active microbial community. Lachnospiraceae, Ruminococcaceae, Bacteroidaceae, Prevotellaceae, and Rickenellaceae were the predominant families detected in the active microbiota.

Characterization of mRNAs revealed a uniform functional pattern in healthy individuals. The main functional roles of the gut microbiota were carbohydrate metabolism, energy production and synthesis of cellular components. In contrast, housekeeping activities such as amino acid and lipid metabolism were underrepresented in the metatranscriptome.

The results offer new insights into the functions of the complex gut microbiota in healthy individuals. This RNA-based survey also detected small RNAs, which are important regulatory elements in prokaryotic physiology and pathogenicity.