Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen 英文参考文献.docVIP

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Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen 英文参考文献.doc

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Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen 英文参考文献

NextGenerationSequencingtoDefineProkaryoticand FungalDiversityintheBovineRumen DerrickE.Fouts1*.,SebastianSzpakowski1.,JanakiPurushe1¤a,ManolitoTorralba1, RichardC.Waterman2,MichaelD.MacNeil2¤b,LeesonJ.Alexander2,KarenE.Nelson1 1TheJ.CraigVenterInstitute(JCVI),Rockville,Maryland,UnitedStatesofAmerica,2FortKeoghLivestockandRangeResearchLaboratory,USDAAgriculturalResearch Service,MilesCity,Montana,UnitedStatesofAmerica Abstract AcombinationofSangerand454sequencesofsmallsubunitrRNAlociwereusedtointerrogatemicrobialdiversityinthe bovinerumenof12cowsconsumingaforagediet.Observedbacterialspeciesrichness,basedontheV1–V3regionofthe 16S rRNA gene, was between 1,903 to 2,432 species-level operational taxonomic units (OTUs) when 5,520 reads were sampled per animal. Eighty percent of species-level OTUs were dominated by members of the order Clostridiales, Bacteroidales,ErysipelotrichalesandunclassifiedTM7.AbundanceofPrevotellaspeciesvariedwidelyamongthe12animals. Archaealspeciesrichness,alsobasedon16SrRNA,wasbetween8and13OTUs,representing5genera.Themajorityof archaealOTUs(84%)foundinthisstudywerepreviouslyobservedinpublicdatabaseswithonlytwonewOTUsdiscovered. Observedrumenfungalspeciesrichness,basedonthe18SrRNAgene,wasbetween21and40OTUswith98.4–99.9%of OTUs represented by more than one read, using Good’s coverage. Examination of the fungal community identified numerous novel groups. Prevotella and Tannerella were overrepresented in the liquid fraction of the rumen while ButyrivibrioandBlautiaweresignificantlyoverrepresentedinthesolidfractionoftherumen.Nostatisticaldifferencewas observedbetweentheliquidandsolidfractionsinbiodiversityofarchaeaandfungi.Thesurveyofmicrobialcommunities andanalysisofcross-domaincorrelationssuggestedthereisafargreaterextentofmicrobialdiversityinthebovinerumen than previously appreciated, and that next generation sequencing technologies promise to reveal novel species, interactions and pathways that can be studied further in order to better understan