Alison S. Waller, David M. Kristensen, Takuji Yamada, Jens Roat Kultima, Shinichi Sunagawa,
Eugene V. Koonin, Peer Bork
This webpage contains supplementary materials for the article:
Classification and Quantification of Bacteriophage Taxa in Human Gut MetagenomesLink to paper:
Bacteriophages play key roles in microbial communities, to a large extent shaping the taxonomic and functional composition of the microbiome, but data on the connections between phage diversity and the composition of communities is scarce. Using taxon-specific marker genes, we identified and monitored 20 viral taxa in 252 human gut metagenomic samples, mostly at the level of genera. On average, 5 phage taxa were identified in each sample, with up to three of these being highly abundant. The abundances of most phage taxa vary by up to 4 orders of magnitude between the samples, and several taxa that are highly abundant in some samples are absent in others. Significant correlations exist between the abundances of some phage taxa and human host metadata: for example, Group 936 lactococal phages are more prevalent and abundant in Danish samples than in samples from Spain or the USA. Quantification of phages that exist as integrated prophages revealed that the abundance profiles of prophages are highly individual-specific and remain unique to an individual over a one year time period, and prediction of prophage lysis across the samples identified hundreds of prophages that are apparently active in the gut and vary across the samples, in terms of presence and lytic state. Finally, a prophage-host network of the human gut was established and includes numerous novel host-phage associations. .
Right-click (control-click on a Mac) on the link and choose " Save Link As.. " to save the document to your computerProphages found in reference bacterial genomes that are present in the 252 gut metagenomic samples:
For additional information of the constuction of the clade-specific viral marker genes please see the related article:
Orthologous gene clusters and taxon signature genes for viruses of prokaryotes