Viral diversity and dynamics in an infant gut

College of Marine Sciences, University of South Florida, 140 Seventh Avenue South, Saint Petersburg, FL 33701, USA.
Research in Microbiology (Impact Factor: 2.71). 06/2008; 159(5):367-73. DOI: 10.1016/j.resmic.2008.04.006
Source: PubMed


Metagenomic sequencing of DNA viruses from the feces of a healthy week-old infant revealed a viral community with extremely low diversity. The identifiable sequences were dominated by phages, which likely influence the diversity and abundance of co-occurring microbes. The most abundant fecal viral sequences did not originate from breast milk or formula, suggesting a non-dietary initial source of viruses. Certain sequences were stable in the infant's gut over the first 3 months of life, but microarray experiments demonstrated that the overall viral community composition changed dramatically between 1 and 2 weeks of age.

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    • "When it comes to annotation of virome sequence data, a major stumbling block is the lack of available phage genome sequences against which contigs can be compared, plus the large number of viral genes that are currently not represented in sequence databases. For example, studies of the human faecal virome have reported that between 66% and 98% of the generated sequences have no significant hits with GenBank sequences (Breitbart et al., 2008; Reyes et al., 2010; Minot et al., 2011). There are few, if any, available sequences for human-gut-associated lytic phages so there is a need to isolate and genomically characterize phages from gastrointestinal sources, rather than relying on the assumption that phages found in sewage are primarily of human gut origin. "
    Dataset: peerj-1061

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    • "Each of the array amplicons was sequenced to determine the spacer content of the strains, which provided a record of acquisition events that are highly ordinal and sequence-specific. Bacteria inhabiting the gastrointestinal and genito-urinary tracts are exposed to many foreign DNA elements, mainly bacteriophages and plasmids (Breitbart et al., 2008; Minot et al., 2011). In an attempt to specifically identify and document exposure to foreign DNA, we matched spacer sequence to known plasmid and bacteriophage protospacers from the NCBI database using BLAST. "
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