Diversity and abundance of single-stranded DNA viruses in human feces - PubMed (original) (raw)

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

Min-Soo Kim et al. Appl Environ Microbiol. 2011 Nov.

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 10⁸ to 10⁹ 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.

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Figures

Fig. 1.

Fig. 1.

Relative abundance of viral families in five human gut viromes. Viral sequences were compared to public databases (SEED nr, CAMERA nr, and CAMERA viral protein databases). Viral sequences were classified into viral families based on best matches. (A) Distribution of viral families based on sequence matches. (B) Distribution of viral families corrected by the phi29 polymerase bias and normalized by genome size.

Fig. 2.

Fig. 2.

Transmission electron micrographs showing diverse viral morphologies in human feces. Scale bars are shown on the bottom of each panel.

Fig. 3.

Fig. 3.

Abundance of viruses and bacteria in human feces determined by fluorescence staining with confocal laser-scanning microscopy.

Fig. 4.

Fig. 4.

Phylogenetic tree generated by the neighbor-joining algorithm of capsid protein sequences from fecal samples, cultured isolates, and environmental samples. Environmental sequences from previous studies of the Sargasso Sea (1), Highborne Cay (12), and Antarctic lake (28), 15 known sequences from cultured isolates (Chlamydia phages, Bdellovibrio phages, and Spiroplasma phages [in green] and Enterobacteria phages), and the predicted sequences from three Bacteroides and three Prevotella strains were aligned with the fecal sequences. Partial sequences of capsid protein were used for the phylogenetic analysis. Sequences were enveloped by their origins, and subgroups from fecal samples were intestinal microphages I, II, III, and IV and Bacteroides microphages. Filled and empty circles at internal nodes indicate bootstrap values greater than 90 and 50%, respectively. The scale bar represents 0.2 amino acid substitutions per site.

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