title: Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome.
abstract: Viruses are the most abundant biological entities on the planet and play an important role in balancing microbes within an ecosystem and facilitating horizontal gene transfer. Although bacteriophages are abundant in rumen environments, little is known about the types of viruses present or their interaction with the rumen microbiome. We undertook random pyrosequencing of virus-enriched metagenomes (viromes) isolated from bovine rumen fluid and analysed the resulting data using comparative metagenomics. A high level of diversity was observed with up to 28,000 different viral genotypes obtained from each environment. The majority (~78%) of sequences did not match any previously described virus. Prophages outnumbered lytic phages approximately 2:1 with the most abundant bacteriophage and prophage types being associated with members of the dominant rumen phyla (Firmicutes and Proteobacteria). Metabolic profiling based on SEED subsystems revealed an enrichment of sequences with putative functional roles in DNA and protein metabolism, but a surprisingly low proportion of sequences assigned to carbohydrate and amino acid metabolism. We expanded our analysis to include previously described metagenomic data and 14 reference genomes. Clustered regularly interspaced short palindromic repeats (CRISPR) were detected in most of the microbial genomes, suggesting previous interactions between viral and microbial communities.
authors: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr, Urbana, IL 61801, USA.
authors: Margret E
authors: ME
authors: Berg Miller
authors: Carl J
authors: CJ
authors: Yeoman
authors: Nicholas
authors: N
authors: Chia
authors: Susannah G
authors: SG
authors: Tringe
authors: Florent E
authors: FE
authors: Angly
authors: Robert A
authors: RA
authors: Edwards
authors: Harry J
authors: HJ
authors: Flint
authors: Raphael
authors: R
authors: Lamed
authors: Edward A
authors: EA
authors: Bayer
authors: Bryan A
authors: BA
authors: White
mesh_terms: D000818:Animals; D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification / Q000821:virology*; D001435:Bacteriophages / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D044822:Biodiversity; D002417:Cattle; D019295:Computational Biology; D004269:DNA, Bacterial / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D005838:Genotype; D020071:Interspersed Repetitive Sequences; D055029:Inverted Repeat Sequences; D055442:Metabolome; D054892:Metagenome; D012417:Rumen / Q000382:microbiology* / Q000821:virology*; D017422:Sequence Analysis, DNA
chemical_list: D004269:DNA, Bacterial; D004279:DNA, Viral