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dc.contributor.authorWilkinson, Toby J.
dc.contributor.authorHuws, Sharon A.
dc.contributor.authorEdwards, Joan E.
dc.contributor.authorKingston-Smith, Alison H.
dc.contributor.authorSiu-Ting, Karen
dc.contributor.authorHughes, Martin
dc.contributor.authorRubino, Francesco
dc.contributor.authorFriedersdorff, Maximillian
dc.contributor.authorCreevey, Christopher J.
dc.date.accessioned2019-07-23T10:45:51Z
dc.date.available2019-07-23T10:45:51Z
dc.date.issued2018-05-25
dc.identifier.citationWilkinson TJ, Huws SA, Edwards JE, Kingston-Smith AH, Siu-Ting K, Hughes M, Rubino F, Friedersdorff M and Creevey CJ (2018) CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software. Front. Microbiol. 9:1095. doi: 10.3389/fmicb.2018.01095en_US
dc.identifier.urihttp://hdl.handle.net/11019/1685
dc.descriptionpeer-revieweden_US
dc.description.abstractMetataxonomic 16S rDNA based studies are a commonplace and useful tool in the research of the microbiome, but they do not provide the full investigative power of metagenomics and metatranscriptomics for revealing the functional potential of microbial communities. However, the use of metagenomic and metatranscriptomic technologies is hindered by high costs and skills barrier necessary to generate and interpret the data. To address this, a tool for Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was developed for inferring the functional potential of an observed microbiome profile, based on 16S data. This allows functional inferences to be made from metataxonomic 16S rDNA studies with little extra work or cost, but its accuracy relies on the availability of completely sequenced genomes of representative organisms from the community being investigated. The rumen microbiome is an example of a community traditionally underrepresented in genome and sequence databases, but recent efforts by projects such as the Global Rumen Census and Hungate 1000 have resulted in a wide sampling of 16S rDNA profiles and almost 500 fully sequenced microbial genomes from this environment. Using this information, we have developed “CowPI,” a focused version of the PICRUSt tool provided for use by the wider scientific community in the study of the rumen microbiome. We evaluated the accuracy of CowPI and PICRUSt using two 16S datasets from the rumen microbiome: one generated from rDNA and the other from rRNA where corresponding metagenomic and metatranscriptomic data was also available. We show that the functional profiles predicted by CowPI better match estimates for both the meta-genomic and transcriptomic datasets than PICRUSt, and capture the higher degree of genetic variation and larger pangenomes of rumen organisms. Nonetheless, whilst being closer in terms of predictive power for the rumen microbiome, there were differences when compared to both the metagenomic and metatranscriptome data and so we recommend, where possible, functional inferences from 16S data should not replace metagenomic and metatranscriptomic approaches. The tool can be accessed at http://www.cowpi.org and is provided to the wider scientific community for use in the study of the rumen microbiome.en_US
dc.description.sponsorshipTW, AK-S, MF, and CC were supported by a Biotechnology and Biological Sciences Research Council (BBSRC Global Challenges Research Fund for Biological and Data and Resources; BBS/OS/GC/000011B). CC and AK-S were also supported by a BBSRC Institute Strategic Programme Grant, Rumen Systems Biology (BB/E/W/10964A01). KS-T was supported by a fellowship from the ELEVATE Irish Research Council-MSCA cofund program (ELEVATEPD/2014/69). The metatranscriptomic sequencing was carried out by The Genome Analysis Centre (TGAC) under the Capacity and Capability Challenge (CCC) program.
dc.description.sponsorshipTW, AK-S, MF, and CC were supported by a Biotechnology and Biological Sciences Research Council (BBSRC Global Challenges Research Fund for Biological and Data and Resources; BBS/OS/GC/000011B). CC and AK-S were also supported by a BBSRC Institute Strategic Programme Grant, Rumen Systems Biology (BB/E/W/10964A01). KS-T was supported by a fellowship from the ELEVATE Irish Research Council-MSCA cofund program (ELEVATEPD/2014/69). The metatranscriptomic sequencing was carried out by The Genome Analysis Centre (TGAC) under the Capacity and Capability Challenge (CCC) program.
dc.language.isoenen_US
dc.publisherFrontiersen_US
dc.relation.ispartofseriesFrontiers in Microbiology;
dc.rightsAttribution-NonCommercial-ShareAlike 3.0 United States*
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/3.0/us/*
dc.subjectPICRUSten_US
dc.subjectrumenen_US
dc.subjectCowPIen_US
dc.subjectfunctionen_US
dc.subject16S ampliconen_US
dc.titleCowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Softwareen_US
dc.typeArticleen_US
dc.identifier.doihttps://dx.doi.org/10.3389/fmicb.2018.01095
dc.contributor.sponsorBiotechnology and Biological Sciences Research Councilen_US
dc.contributor.sponsorBBSRC Institute Strategic Programme Granten_US
dc.contributor.sponsorIrish Research Councilen_US
dc.contributor.sponsorMarie Skłodowska-Curie Actionsen_US
dc.contributor.sponsorGrantNumberBBS/OS/GC/000011Ben_US
dc.contributor.sponsorGrantNumberBB/E/W/10964A01en_US
dc.contributor.sponsorGrantNumberELEVATEPD/2014/69en_US
refterms.dateFOA2019-07-23T10:45:52Z


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