Article

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: 2.83). 06/2008; 159(5):367-73. DOI: 10.1016/j.resmic.2008.04.006
Source: PubMed

ABSTRACT 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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    • "Dehalococcoides-containing microbial consortium Characterization of prophages in prokaryotic genomes Waller et al., 2012 GTAs c and Rhodobacter capsulatus Encapsulation of GTAs Hynes et al., 2012 Coccolithoviruses and Emiliania huxleyi Viral diversity and gene expression during infection Allen and Wilson, 2008 Cyanophages and Prochlorococcus Phage and host transcriptome dynamics Lindell et al., 2007 Cyanophages and Synechococcus Comparative phage genomics Millard et al., 2009 Feces of new borns Diversity and dynamics of the viral assemblage Breitbart et al., 2008 Archaea-dominated acidic hot spring samples Identification of CRISPRs spaces within the viral metagenome Snyder et al., 2010 Candidatus Accumulibacter phosphatis-enriched sludge Phage expression and dynamics Kunin et al., 2008 Hypersaline sample Expression of the viral assemblage Santos et al., 2011 "
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    ABSTRACT: The interactions between viruses and their microbial hosts play a central role in the control of microbial communities in nature. However, the study of such interactions within the uncultured majority is technically very challenging. Here, we review how microarray tools can be used to analyze the interactions between viruses and their microbial hosts in nature, away from laboratory pure culture-based models.We show examples of how DNA arrays have been used to study the expression of viral assemblages in natural samples, and to assign viruses to hosts within uncultured communities. Finally, we briefly discuss the possibilities of protein and glycan arrays to gain insight into the ways microbes interact with their viruses.
    06/2014; 2. DOI:10.3389/fevo.2014.00031
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    • "In the gut of mammals, bacterial density increases along the digestive tract, from an almost sterile situation in the stomach, up to 10 10 – 10 11 per gram of material in the colon or in feces (Berg, 1996). Compared with this dense bacterial population in the terminal part of the gut, VLP concentrations in feces appear to be much lower: estimates of 10 8 per gram of feces in infant is reported (Breitbart et al., 2008), and another report in adults estimates values between 10 8 and 10 9 per gram of feces (Kim et al., 2011). In the bovine ruminal fluid, counts between 10 7 and 10 8 VLP/ml have been reported (Letarov and Kulikov, 2009) and references therein. "
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    Frontiers in Cellular and Infection Microbiology 03/2014; 4:39. DOI:10.3389/fcimb.2014.00039 · 2.62 Impact Factor
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