2011/09/24 by Min‐Soo Kim, Min-Soo Kim, Eun‐Jin Park +4 · 254 citations
Agricultural and Biological Sciences · Environmental Science · Medicine · #Amplicon #Bacteria #Bacteriophage #Bacteriophages and microbial interactions #Bacteroides #Biology #DNA #DNA sequencing #Escherichia coli #Feces #Gene #Genetics #Genome #Human virome #Lytic cycle #Microbiology #Phylogenetic tree #Phylogenetics #Plant Virus Research Studies #Podoviridae #Polymerase chain reaction #Prophage #Siphoviridae #Viral gastroenteritis research and epidemiology #Virus
paper · open access · doi:10.1128/aem.06331-11
published in Applied and Environmental Microbiology 77(22), 8062-8070 (American Society for Microbiology)
openalex publication_date 2011/09/24 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/29
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.