| The human gut virome: inter-individual variation and dynamic response to diet. | |
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MedLine Citation:
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PMID: 21880779 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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Immense populations of viruses are present in the human gut and other body sites. Understanding the role of these populations (the human "virome") in health and disease requires a much deeper understanding of their composition and dynamics in the face of environmental perturbation. Here, we investigate viromes from human subjects on a controlled feeding regimen. Longitudinal fecal samples were analyzed by metagenomic sequencing of DNA from virus-like particles (VLP) and total microbial communities. Assembly of 336 Mb of VLP sequence yielded 7175 contigs, many identifiable as complete or partial bacteriophage genomes. Contigs were rich in viral functions required in lytic and lysogenic growth, as well as unexpected functions such as viral CRISPR arrays and genes for antibiotic resistance. The largest source of variance among virome samples was interpersonal variation. Parallel deep-sequencing analysis of bacterial populations showed covaration of the virome with the larger microbiome. The dietary intervention was associated with a change in the virome community to a new state, in which individuals on the same diet converged. Thus these data provide an overview of the composition of the human gut virome and associate virome structure with diet. |
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Authors:
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Samuel Minot; Rohini Sinha; Jun Chen; Hongzhe Li; Sue A Keilbaugh; Gary D Wu; James D Lewis; Frederic D Bushman |
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Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't Date: 2011-08-31 |
Journal Detail:
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Title: Genome research Volume: 21 ISSN: 1549-5469 ISO Abbreviation: Genome Res. Publication Date: 2011 Oct |
Date Detail:
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Created Date: 2011-10-03 Completed Date: 2012-01-23 Revised Date: 2012-04-02 |
Medline Journal Info:
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Nlm Unique ID: 9518021 Medline TA: Genome Res Country: United States |
Other Details:
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Languages: eng Pagination: 1616-25 Citation Subset: IM |
Affiliation:
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Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA. |
Export Citation:
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APA/MLA Format Download EndNote Download BibTex |
| MeSH Terms | |
Descriptor/Qualifier:
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Adolescent Adult Bacteria / virology Bacteriophages / genetics* Contig Mapping Diet, Fat-Restricted* Diet, High-Fat* Drug Resistance, Bacterial Feces / microbiology, virology Gastrointestinal Tract / microbiology*, virology Genes, Bacterial Genes, Viral High-Throughput Nucleotide Sequencing Humans Metagenome Open Reading Frames RNA, Ribosomal, 16S / genetics Repetitive Sequences, Nucleic Acid Sequence Analysis, DNA Virion / isolation & purification Young Adult |
| Grant Support | |
ID/Acronym/Agency:
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AI39368/AI/NIAID NIH HHS; P30 DK050306/DK/NIDDK NIH HHS; S10RR024525/RR/NCRR NIH HHS; UL1RR024134/RR/NCRR NIH HHS |
| Chemical | |
Reg. No./Substance:
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0/RNA, Ribosomal, 16S |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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