Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

Abstract

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.

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

“…More specifically, previous studies analysing functional 'omes', such as the metatranscriptomes or the metaproteomes, in gastrointestinal samples 9,[11][12][13][14][15][16][17] have found that functional genes predicted from metagenomes are not necessarily expressed 9,[11][12][13] . Furthermore, as the functional omes display higher variability and sensitivity to perturbation 9,[11][12][13] , these variations may better reflect disease-related changes in host-microbiome interactions 14,15 . For this reason, the integration of metagenomic, metatranscriptomic and metaproteomic data is expected to yield important insights into the human microbiome 18 , as it has for environmental microbial consortia 19,20 .…”

Rhizosphere microbiome assemblage is affected by plant development

“…Plant development influences the functional capacity of the rhizomicrobiome Metatranscriptomics analyses of mRNA have only recently been used as a means to study microbial communities at a functional level in distinct environments such as the human gut (Gosalbes et al, 2011), the mouse gut (Xiong et al, 2012) and 7 160 167 198 1 199 366 Phenolics 31 139 170 222 57 279 449 Sugars 51 0 51 0 82 82 133 Sugar Alcohols 0 47 47 85 6 91 138 The values indicate the number of significant (Po0.05) correlations.…”

Gut microbiota, the pharmabiotics they produce and host health

“…The genetic pathway responsible for the de novo synthesis of vitamin B 12 by L. reuteri has previously been described for two L. reuteri strains (103) . More recently, the presence of bifidobacterial genes, predicted to be involved in the biosynthesis of several B vitamins has been identified in bifidobacteria residing in faecal samples of adult subjects (104)(105)(106) .…”