Metatranscriptomic approach to analyze the functional human gut microbiota

PLoS One. 2011 Mar 8;6(3):e17447. doi: 10.1371/journal.pone.0017447.


The human gut is the natural habitat for a large and dynamic bacterial community that has a great relevance for health. Metagenomics is increasing our knowledge of gene content as well as of functional and genetic variability in this microbiome. However, little is known about the active bacteria and their function(s) in the gastrointestinal tract. We performed a metatranscriptomic study on ten healthy volunteers to elucidate the active members of the gut microbiome and their functionality under conditions of health. First, the microbial cDNAs obtained from each sample were sequenced using 454 technology. The analysis of 16S transcripts showed the phylogenetic structure of the active microbial community. Lachnospiraceae, Ruminococcaceae, Bacteroidaceae, Prevotellaceae, and Rickenellaceae were the predominant families detected in the active microbiota. The 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. Our results provide new insights into the functionality of the complex gut microbiota in healthy individuals. In this RNA-based survey, we also detected small RNAs, which are important regulatory elements in prokaryotic physiology and pathogenicity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / classification
  • Bacteria / genetics
  • Biodiversity
  • DNA, Complementary / genetics
  • Gastrointestinal Tract / microbiology*
  • Gene Expression Profiling / methods*
  • Humans
  • Metagenome / genetics*
  • Metagenomics / methods*
  • RNA, Messenger / classification
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA


  • DNA, Complementary
  • RNA, Messenger
  • RNA, Ribosomal, 16S