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      Faecal Microbiota of Forage-Fed Horses in New Zealand and the Population Dynamics of Microbial Communities following Dietary Change

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          Abstract

          The effects of abrupt dietary transition on the faecal microbiota of forage-fed horses over a 3-week period were investigated. Yearling Thoroughbred fillies reared as a cohort were exclusively fed on either an ensiled conserved forage-grain diet (“Group A”; n = 6) or pasture (“Group B”; n = 6) for three weeks prior to the study. After the Day 0 faecal samples were collected, horses of Group A were abruptly transitioned to pasture. Both groups continued to graze similar pasture for three weeks, with faecal samples collected at 4-day intervals. DNA was isolated from the faeces and microbial 16S and 18S rRNA gene amplicons were generated and analysed by pyrosequencing. The faecal bacterial communities of both groups of horses were highly diverse (Simpson’s index of diversity >0.8), with differences between the two groups on Day 0 ( P<0.017 adjusted for multiple comparisons). There were differences between Groups A and B in the relative abundances of four genera, BF311 (family Bacteroidaceae; P = 0.003), CF231 (family Paraprevotellaceae; P = 0.004), and currently unclassified members within the order Clostridiales ( P = 0.003) and within the family Lachnospiraceae ( P = 0.006). The bacterial community of Group A horses became similar to Group B within four days of feeding on pasture, whereas the structure of the archaeal community remained constant pre- and post-dietary change. The community structure of the faecal microbiota (bacteria, archaea and ciliate protozoa) of pasture-fed horses was also identified. The initial differences observed appeared to be linked to recent dietary history, with the bacterial community of the forage-fed horses responding rapidly to abrupt dietary change.

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          Relationship between condition score, physical measurements and body fat percentage in mares.

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            Structure of the archaeal community of the rumen.

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              Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities

              Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2014
                10 November 2014
                : 9
                : 11
                : e112846
                Affiliations
                [1 ]Institute of Veterinary, Animal, and Biomedical Sciences, College of Sciences, Massey University, Palmerston North 4442, New Zealand
                [2 ]AgResearch Ltd, Grasslands Research Centre, Palmerston North 4442, New Zealand
                Agriculture and Agri-Food Canada, Canada
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: KAF CWR EKG DGT. Performed the experiments: KAF DGT. Analyzed the data: KAF SK CFB. Contributed reagents/materials/analysis tools: KAF SK ENB. Wrote the paper: KAF SK CWR EKG CFB ENB DGT. Obtained funding: KAF ENB DGT. Designed and conducted the laboratory component of the study: KAF SK ENB.

                Article
                PONE-D-14-04594
                10.1371/journal.pone.0112846
                4226576
                25383707
                50c6df5d-62c5-464e-944c-bd4d7cc75367
                Copyright @ 2014

                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 credited.

                History
                : 29 January 2014
                : 17 October 2014
                Page count
                Pages: 15
                Funding
                This study was funded by the Massey University Internal Research Funding (DGT) and AgResearch CORE (A17976) funds (ENB). An educational fellowship from the Ministry of Business Innovation and Employment: Science and Innovation Group ( www.msi.govt.nz) and a Massey University Doctoral Scholarship ( www.massey.ac.nz) provided financial assistance for the duration of the doctoral study (KAF). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Agriculture
                Animal Management
                Ecology
                Community Ecology
                Community Structure
                Biodiversity
                Microbial Ecology
                Microbiology
                Veterinary Science
                Veterinary Anatomy
                Animal Digestive Anatomy
                Veterinary Diseases
                Veterinary Bacteriology
                Veterinary Medicine
                Livestock Care
                Veterinary Microbiology
                Ecology and Environmental Sciences

                Uncategorized
                Uncategorized

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