Differential functional profiling from community RNA-Seq of environmental field samples

The utilization of RNA-Seq for the study of biological processes in species communities under a changing environment is a challenging task. Techniques that have been developed to identify differential expression in single species with known genomes cannot be directly applied. We introduce MeandeR (Metatranscriptomic analysis of differential expression in R) which implements a complete workflow for differential functional profiling of community RNA-Seq data using the KEGG database. We have integrated a fast tool for functional and phylogenetic classification of sequence reads together with state-of-the-art methods for differential expression analysis to provide a quick overview on functional changes within the context of biological pathways. We applied the tool to investigate the functional profile of field collected samples. Our results on a comparison of root communities from different forest types indicate that our approach can highlight biologically relevant differences in functional profiles of mixed species RNA-Seq data.