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The Approach to Sample Acquisition and Its Impact on the Derived Human Fecal Microbiome and VOC Metabolome

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dc.contributor.author Couch, Robin D.
dc.contributor.author Navarro, Karl
dc.contributor.author Sikaroodi, Masoumeh
dc.contributor.author Gillevet, Pat
dc.contributor.author Forsyth, Christopher B.
dc.contributor.author Mutlu, Ece
dc.contributor.author Engen, Phillip A.
dc.contributor.author Keshavarzian, Ali
dc.date.accessioned 2015-10-29T16:20:26Z
dc.date.available 2015-10-29T16:20:26Z
dc.date.issued 2013-11-18
dc.identifier.citation Couch RD, Navarro K, Sikaroodi M, Gillevet P, Forsyth CB, et al. (2013) The Approach to Sample Acquisition and Its Impact on the Derived Human Fecal Microbiome and VOC Metabolome. PLoS ONE 8(11): e81163. doi:10.1371/journal.pone.0081163 en_US
dc.identifier.uri https://hdl.handle.net/1920/10001
dc.description.abstract Recent studies have illustrated the importance of the microbiota in maintaining a healthy state, as well as promoting disease states. The intestinal microbiota exerts its effects primarily through its metabolites, and metabolomics investigations have begun to evaluate the diagnostic and health implications of volatile organic compounds (VOCs) isolated from human feces, enabled by specialized sampling methods such as headspace solid-phase microextraction (hSPME). The approach to stool sample collection is an important consideration that could potentially introduce bias and affect the outcome of a fecal metagenomic and metabolomic investigation. To address this concern, a comparison of endoscopically collected (in vivo) and home collected (ex vivo) fecal samples was performed, revealing slight variability in the derived microbiomes. In contrast, the VOC metabolomes differ widely between the home collected and endoscopy collected samples. Additionally, as the VOC extraction profile is hyperbolic, with short extraction durations more vulnerable to variation than extractions continued to equilibrium, a second goal of our investigation was to ascertain if hSPME-based fecal metabolomics studies might be biased by the extraction duration employed. As anticipated, prolonged extraction (18 hours) results in the identification of considerably more metabolites than short (20 minute) extractions. A comparison of the metabolomes reveals several analytes deemed unique to a cohort with the 20 minute extraction, but found common to both cohorts when the VOC extraction was performed for 18 hours. Moreover, numerous analytes perceived to have significant fold change with a 20 minute extraction were found insignificant in fold change with the prolonged extraction, underscoring the potential for bias associated with a 20 minute hSPME.
dc.description.sponsorship This study was supported by NIH grant 1RC2AA019405. Publication of this article was funded in part by the George Mason University Libraries Open Access Publishing Fund. en_US
dc.language.iso en_US en_US
dc.publisher Public Library of Science en_US
dc.rights Attribution 3.0 United States *
dc.rights.uri http://creativecommons.org/licenses/by/3.0/us/ *
dc.subject metabolomics en_US
dc.subject metabolites en_US
dc.subject endoscopy en_US
dc.subject microbiome en_US
dc.subject volatile organic compounds en_US
dc.subject esters en_US
dc.subject gastrointestinal tract en_US
dc.subject drug metabolism en_US
dc.title The Approach to Sample Acquisition and Its Impact on the Derived Human Fecal Microbiome and VOC Metabolome en_US
dc.type Article en_US
dc.identifier.doi http://dx.doi.org/10.1371/journal.pone.0081163


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