Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces

Abstract

In this study, we investigated the abundance and diversity of single-stranded DNA (ssDNA) viruses in fecal samples from five healthy individuals through a combination of serial filtration and CsCl gradient ultracentrifugation. Virus abundance ranged from 10 8 to 10 9 per gram of feces, and virus-to-bacterium ratios were much lower (less than 0.1) than those observed in aquatic environments (5 to 10). 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 in public databases. Among previously known viruses, double-stranded DNA podophages (52 to 74%), siphophages (11 to 30%), myophages (1 to 4%), and ssDNA microphages (3 to 9%) were major constituents of human fecal viromes. A phylogenetic analysis of 24 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 are the sources of infecting microphages in their hosts.

Viruses in a 14th-Century Coprolite

“…Viral metagenomics has already been successfully applied to the exploration of modern environmental specimens sampled from marine water, freshwater, stromatolites and thrombolites, and soil (1-4) and to modern human-associated specimens collected from the liver, blood, nasopharyngeal aspirates, and stool (5-9). The DNA viromes generated from modern stools have been demonstrated to be dominated by bacteriophages (10, 11) and to be less diverse than environmental samples (8,12).Viral metagenomics does not require culturing viruses or a priori knowledge of the sequences that will be targeted, which allows for the identification of new, unknown or unexpected viruses and for the global assessment of the virome. Viral metagenomics is thus particularly suitable for paleomicrobiological studies, as little is known about which viruses are characteristic of ancient specimens.…”

Health and environmental applications of gut microbiome: a review

“…In another study focused on DNA virus diversity in a healthy 1-week-old infant, low diversity of viral community was observed, which was composed mainly of Caudovirales order of phages, and the viral community changed dramatically between 1 and 2 weeks of age [100]. Recent investigations utilizing extremely deep metagenomic sequencing have also confirmed the predominance of bacteriophages, affiliated to the families Siphoviridae, Myoviridae, Podoviridae and Microviridae in human faecal matters, some of which evolve at a rapid rate, as compared to the others, leading to great inter-individual diversity [45,46,102,103]. An extensive review of different family of viruses detected in different parts of the human body has been published elsewhere [99].…”

The animal gut as a melting pot for horizontal gene transfer

“…Other overrepresented functions could not be detected, most likely due to the lack of proper database representation. These studies also identified sequences of prophages, indicating that transduction is one of the mechanisms by which HGT occurs in these systems (Breitbart et al 2003;Reyes et al 2010;Kim et al 2011;Minot et al 2011;Berg Miller et al 2012;Ross et al 2013). …”

“…Several studies have attempted to characterize the mammalian GI tract virome using similar techniques (Breitbart et al 2003;Reyes et al 2010;Kim et al 2011;Minot et al 2011;Berg Miller et al 2012;Ross et al 2013). In this case, one of the main challenges encountered by investigators was the extremely low similarity of the obtained sequences to known genes in the different databases.…”