Dynamic nature of viral and bacterial communities in human faeces during ex vivo incubation

In this study we used freshly collected faeces from eight healthy volunteers. To simulate extended colonic retention of faeces, intact samples were aliquoted and placed into anaerobic incubator at 37C shortly after collection, without addition of any media, diluents or substrates. Aliquots were removed for analysis at different timepoints. Virome (phageome) and microbiome composition were assessed by shotgun metagenomic and 16S rRNA amplicon library sequencing. All samples showed significant and steady changes over time. There was a steady increase in virome richness and subject specific blooms and collapses of certain phage and bacterial populations. Samples collected from Prevotella-rich individuals showed a striking collapse of Prevotella populations accompanied by a decrease in specific Petitvirales and increase of specific Crassvirales phages.