METHOD Open Access Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes

We have developed a process for transcriptome analysis of bacterial communities that accommodates both intact and fragmented starting RNA and combines efficient rRNA removal with strand-specific RNA-seq. We applied this approach to an RNA mixture derived from three diverse cultured bacterial species and to RNA isolated from clinical stool samples. The resulting expression profiles were highly reproducible, enriched up to 40-fold for non-rRNA transcripts, and correlated well with profiles representing undepleted total RNA. Background Microbial communities are known to play significant roles in human health, development, and disease [1-4], and DNA sequencing is an effective approach to charac-terize the structure and potential function of these com-munities. While sequencing of the 16S ribosomal RNA (rRNA) gene has been invaluable for identifying bacter-ial species and taxa in complex communities [5], shot-gun sequencing of metagenomes provides a much riche