The Human Gut Chip "HuGChip'', an explorative phylogenetic microarray for determining gut microbiome diversity at family level

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dc.contributor.authorTottey, William
dc.contributor.authorDenonfoux, Jeremie
dc.contributor.authorJaziri, Faouzi
dc.contributor.authorParisot, Nicolas
dc.contributor.authorMissaoui, Mohiedine
dc.contributor.authorHill, David
dc.contributor.authorBorrel, Guillaume
dc.contributor.authorPeyretaillade, Eric
dc.contributor.authorAlric, Monique
dc.contributor.authorHarris, Hugh Michael B.
dc.contributor.authorJeffery, Ian B.
dc.contributor.authorClaesson, Marcus J.
dc.contributor.authorO'Toole, Paul W.
dc.contributor.authorPeyret, Pierre
dc.contributor.authorBrugère, Jean-François
dc.contributor.funderEuropean Commissionen
dc.contributor.funderDepartment of Agriculture, Fisheries and Food, Irelanden
dc.contributor.funderHealth Research Boarden
dc.contributor.funderAPC Microbiome Institute, College of Medicine and Health, University College Corken
dc.date.accessioned2016-02-17T11:46:18Z
dc.date.available2016-02-17T11:46:18Z
dc.date.issued2013
dc.description.abstractEvaluating the composition of the human gut microbiota greatly facilitates studies on its role in human pathophysiology, and is heavily reliant on culture-independent molecular methods. A microarray designated the Human Gut Chip (HuGChip) was developed to analyze and compare human gut microbiota samples. The PhylArray software was used to design specific and sensitive probes. The DNA chip was composed of 4,441 probes (2,442 specific and 1,919 explorative probes) targeting 66 bacterial families. A mock community composed of 16S rRNA gene sequences from intestinal species was used to define the threshold criteria to be used to analyze complex samples. This was then experimentally verified with three human faecal samples and results were compared (i) with pyrosequencing of the V4 hypervariable region of the 16S rRNA gene, (ii) metagenomic data, and (iii) qPCR analysis of three phyla. When compared at both the phylum and the family level, high Pearson's correlation coefficients were obtained between data from all methods. The HuGChip development and validation showed that it is not only able to assess the known human gut microbiota but could also detect unknown species with the explorative probes to reveal the large number of bacterial sequences not yet described in the human gut microbiota, overcoming the main inconvenience encountered when developing microarrays.en
dc.description.sponsorshipEuropean Commission (EU and Auvergne Council PhD studentships); Department of Agriculture, Fisheries and Food, Ireland (ELDERMET consortium); Health Research Board (FHRI Award to ELDERMET project)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleide62544
dc.identifier.citationTottey W, Denonfoux J, Jaziri F, Parisot N, Missaoui M, Hill D, et al. (2013) The Human Gut Chip “HuGChip”, an Explorative Phylogenetic Microarray for Determining Gut Microbiome Diversity at Family Level. PLoS ONE 8(5): e62544. doi:10.1371/journal.pone.0062544en
dc.identifier.doi10.1371/journal.pone.0062544
dc.identifier.issn1932-6203
dc.identifier.issued5en
dc.identifier.journaltitlePLOS ONEen
dc.identifier.urihttps://hdl.handle.net/10468/2377
dc.identifier.volume8en
dc.language.isoenen
dc.publisherPublic Library of Scienceen
dc.rights© 2013 Tottey et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are crediteden
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectHuman intestinal microbiotaen
dc.subjectGastrointestinal tracten
dc.subjectOligonucleotide probesen
dc.subjectSequence dataen
dc.subjectmcrA geneen
dc.subjectEcologyen
dc.subjectARBen
dc.subjectEnvironmenten
dc.subjectCommunitiesen
dc.subjectMetabolismen
dc.titleThe Human Gut Chip "HuGChip'', an explorative phylogenetic microarray for determining gut microbiome diversity at family levelen
dc.typeArticle (peer-reviewed)en
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