Metatranscriptomics: Monitoring Gut Microbiome Activity in Response to Diet

Abstract

The study of the gut microbiome—the collection of microflora within the intestinal tract—is growing in popularity as associations are found between diet and nutrition, gut microflora activity, and host health and disease. However, current metagenomic and ribosomal profiling approaches are unable to capture changes in activity within the gut microbiome populations. In this environment, shifts in diet or nutritional intake may not result in microbiome population changes, but may instead influence the activity of the existing microbial community. Metatranscriptomics—the study of microbial population activity based on RNA‐seq data—offers detailed data on the gene expression of all microbes within the sampled community. Unfortunately, current approaches for processing raw metatranscriptome data rely either on restricted databases, a fully in‐house analysis server, or use metagenome‐based approaches that have not been fully evaluated for use in processing metatranscriptomic datasets.We have created a new bioinformatics pipeline, SAMSA (Simple Analysis of Metatranscriptome Sequence Annotations), designed specifically for metatranscriptome dataset analysis, with options for either in‐house or external server‐based computational processing. Designed for use by researchers with relatively little bioinformatics experience, SAMSA offers a breakdown of metatranscriptome activity by organism or transcript function, and is fully open source. We have also determined a series of “best practices” for metatranscriptome preprocessing and sequencing for the most accurate analysis results. Using publicly available data, we have demonstrated that SAMSA offers summary analysis of both the organism activity and transcript‐level expression within a metatranscriptome, as well as identifying the most significant expression changes between control and experimental populations. We expect that SAMSA will shed new light on expression changes within the gut microbiome, providing a deeper understanding of how this community reacts to dietary modulation.Support or Funding InformationFunded in part by the Peter J. Shields Endowed Chair in Dairy Food Science (D.M.) S.W. was supported by a fellowship under the Training Program in Biomolecular Technology (NIGMS‐NIH T32‐GM008799) at the University of California, Davis.