Diversity and abundance of single-stranded DNA viruses in human faeces

The human gut is a nutrient-rich environment where a large number of microbes reside, including viruses. While the symbiotic contribution of gut microbes to human physiology and predisposition to diseases has been well-studied, little is known about the role of viruses especially single-stranded DNA (ssDNA) viruses, despite their important ecological role within the microbial community. In this study, we investigated the abundance and diversity of DNA viruses on faecal samples from five healthy individuals through the combination of serial-filtration and CsCl-gradient ultracentrifugation. Virus abundance ranged from 108 to 109 per gram of faeces, and virus-to-bacterium ratios were much lower (less than 0.1) than those observed in aquatic environments. Viral DNA was extracted and randomly amplified using phi29 polymerase and analyzed through high-throughput 454 pyrosequencing. Among 400 133 sequences, an average of 86.2% viromes were previously uncharacterized when compared to public databases. Among previously-known viruses, double-stranded DNA podophages (52–74%), siphophages (11–30%) and myophages (1–4%), and ssDNA microphages (3–9%) were major constituents of human faecal viromes. A phylogenetic analysis of twenty-four large contigs of microphages based on conserved capsid protein sequences revealed five distinct newly-discovered evolutionary microphage groups that were distantly related to previously-known microphages. Moreover, putative capsid protein sequences of five contigs were closely related to prophage-like sequences in the genomes of three Bacteroides and three Prevotella strains, suggesting that Bacteroides and Prevotella may be the source of infecting microphages in their hosts.