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dc.contributor.authorBowen, Jenna M.*
dc.contributor.authorMcCabe, Matthew*
dc.contributor.authorLister, Susan J.*
dc.contributor.authorCormican, Paul*
dc.contributor.authorDewhurst, Richard J.*
dc.date.accessioned2019-05-30T14:50:38Z
dc.date.available2019-05-30T14:50:38Z
dc.date.issued2018-10-08
dc.identifier.citationBowen JM, McCabe MS, Lister SJ, Cormican P, Dewhurst RJ. Evaluation of Microbial Communities Associated With the Liquid and Solid Phases of the Rumen of Cattle Offered a Diet of Perennial Ryegrass or White Clover. Frontiers in Microbiology 2018;9(2389); doi http://dx.doi.org/10.3389/fmicb.2018.02389.en_US
dc.identifier.urihttp://hdl.handle.net/11019/1662
dc.descriptionpeer-revieweden_US
dc.descriptionThe Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fmicb.2018.02389/full#supplementary-materialen_US
dc.description.abstractRumen microbiota plays an important role in animal productivity, methane production and health. Several different locations have been used to obtain rumen samples (i.e., liquid-phase samples, solid-phase samples, buccal swabs) in previous studies. Here we assess differences in the rumen microbiota between solid- and liquid-phases of the rumen under differing dietary conditions (white clover vs. perennial ryegrass); there were 4 sample types: liquid-associated/grass (LG), solid-associated/grass (SG), liquid-associated/clover (LC), and solid-associated/clover (SC). Four Holstein-Friesian cows were strip grazed on pure stands of perennial ryegrass or white clover in a change-over design experiment with 3 periods (each lasting for 3 weeks). Solid- and liquid- phase microbes were obtained following total rumen evacuation on the penultimate day of each period. DNA was extracted and multiplexed libraries sequenced using 16S next generation sequencing (Illumina MiSeq). Demultiplexed sequences underwent quality control and taxonomic profiles were generated for each sample. Statistical analysis for the effects of diet and phase was conducted both overall [using non-metric multidimensional scaling (NMDS) and diversity indices] and for individual taxa. Separation of both diet and phase was observed NMDS, with significant effects of diet (P < 0.001) and phase (P < 0.001) being observed. Regardless of diet, Prevotella was most abundant in the liquid samples. When assessing differences between phases, the majority of statistically significant taxa (predominantly from Archaea and the order Clostridiales) were found at higher relative abundances in solid-phase samples. Diversity (Shannon Index) was lower in the liquid-phase samples, possibly because of the higher relative abundance of Prevotella. A presence vs. absence approach, followed by Chi-squared testing, was adopted. Differences between phases (LG vs. LC, LC vs. LG, SG vs. SC, and SC vs. SG) and differences between phases for the clover diet (LC vs. SC and SC vs. LC) were significant (P < 0.001); differences between phases for the grass diet were non-significant. Sampling technique has a profound impact on reported microbial communities, which must be taken into consideration, particularly as archaea may be underestimated in the liquid-phase.en_US
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.subjectRumenen_US
dc.subjectMicrobiotaen_US
dc.subjectCattleen_US
dc.subjectLiquid phaseen_US
dc.subjectSolid phaseen_US
dc.titleEvaluation of Microbial Communities Associated With the Liquid and Solid Phases of the Rumen of Cattle Offered a Diet of Perennial Ryegrass or White Cloveren_US
dc.typeArticleen_US
dc.identifier.doihttps://doi.org/10.3389/fmicb.2018.02389
dc.contributor.sponsorTeagasc Walsh Fellowship Programmeen_US
refterms.dateFOA2019-05-30T14:50:39Z


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