Impacts of seasonal housing and teat preparation on raw milk microbiota: a high-throughput sequencing study

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dc.contributor.author Doyle, Conor J.
dc.contributor.author Gleeson, David
dc.contributor.author O'Toole, Paul W.
dc.contributor.author Cotter, Paul D.
dc.date.accessioned 2017-05-18T14:00:06Z
dc.date.available 2017-05-18T14:00:06Z
dc.date.issued 2016-11-04
dc.identifier.citation Doyle, C. J., Gleeson, D., O'Toole, P. W. and Cotter, P. D. (2017) 'Impacts of Seasonal Housing and Teat Preparation on Raw Milk Microbiota: a High-Throughput Sequencing Study', Applied and Environmental Microbiology, 83(2). doi:10.1128/aem.02694-16 en
dc.identifier.volume 83 en
dc.identifier.issued 2 en
dc.identifier.startpage e02694-16 en
dc.identifier.issn 0099-2240,
dc.identifier.uri http://hdl.handle.net/10468/3995
dc.identifier.doi 10.1128/aem.02694-16
dc.description.abstract In pasture-based systems, changes in dairy herd habitat due to seasonality results in the exposure of animals to different environmental niches. These niches contain distinct microbial communities that may be transferred to raw milk, with potentially important food quality and safety implications for milk producers. It is postulated that the extent to which these microorganisms are transferred could be limited by the inclusion of a teat preparation step prior to milking. High-throughput sequencing on a variety of microbial niches on farms was used to study the patterns of microbial movement through the dairy production chain and, in the process, to investigate the impact of seasonal housing and the inclusion/exclusion of a teat preparation regime on the raw milk microbiota from the same herd over two sampling periods, i.e., indoor and outdoor. Beta diversity and network analyses showed that environmental and milk microbiotas separated depending on whether they were sourced from an indoor or outdoor environment. Within these respective habitats, similarities between the milk microbiota and that of teat swab samples and, to a lesser extent, fecal samples were apparent. Indeed, SourceTracker identified the teat surface as the most significant source of contamination, with herd feces being the next most prevalent source of contamination. In milk from cows grazing outdoors, teat prep significantly increased the numbers of total bacteria present. In summary, sequence-based microbiota analysis identified possible sources of raw milk contamination and highlighted the influence of environment and farm management practices on the raw milk microbiota. IMPORTANCE: The composition of the raw milk microbiota is an important consideration from both a spoilage perspective and a food safety perspective and has implications for milk targeted for direct consumption and for downstream processing. Factors that influence contamination have been examined previously, primarily through the use of culture-based techniques. We describe here the extensive application of high-throughput DNA sequencing technologies to study the relationship between the milk production environment and the raw milk microbiota. The results show that the environment in which the herd was kept was the primary driver of the composition of the milk microbiota composition. en
dc.description.sponsorship Teagasc (Teagasc Walsh Fellowship (2013030), Internal Teagasc funding (RMIS6364)) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher American Society for Microbiology en
dc.rights © 2016 American Society for Microbiology. All Rights Reserved. This is the Accepted manuscript version of the article published in its final form in Appl. Environ. Microbiol. doi: 10.1128/AEM.02694-16 en
dc.subject Farm practices en
dc.subject Food chain en
dc.subject Food safety en
dc.subject Metagenomics en
dc.subject Microbial source tracking en
dc.subject Raw milk microbiota en
dc.title Impacts of seasonal housing and teat preparation on raw milk microbiota: a high-throughput sequencing study en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Paul O'Toole, Microbiology, University College Cork, Cork, Ireland. +353-21-490-3000 Email: pwotoole@ucc.ie en
dc.internal.availability Full text available en
dc.date.updated 2017-05-18T13:40:57Z
dc.description.version Accepted Version en
dc.internal.rssid 395506662
dc.contributor.funder Teagasc en
dc.description.status Peer reviewed en
dc.identifier.journaltitle Applied and Environmental Microbiology en
dc.internal.copyrightchecked No !!CORA!! en
dc.internal.licenseacceptance Yes en
dc.internal.IRISemailaddress pwotoole@ucc.ie en


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