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"id": "MGYS00005578",
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"accession": "MGYS00005578",
"samples-count": 28,
"bioproject": "PRJEB39336",
"is-private": false,
"last-update": "2020-08-07T18:45:07",
"secondary-accession": "ERP122840",
"centre-name": "VETERINARY Faculty",
"public-release-date": null,
"study-abstract": "Changes to the gut microbiota have been associated with an increased incidence of disease in many species. This is particularly important during the process of domestication, where captive animals commonly suffer from gastrointestinal (GI) pathophysiology. Horses are a prime example of a domesticated species which suffers from a high incidence of (often life-threatening) GI disease. Some of the most significant factors affecting the gut microbiota in horses are diet, stress and drug administration, all of which are associated with the process of domestication. There are no studies, to date, which describe the effect of increasing levels of domestication on the equine microbiota whilst controlling effectively for confounding variables. Here we aimed to do this by measuring the GI microbiota of adult female Exmoor ponies under 3 management conditions, representing different levels of domestication. Faecal samples were collected from 29 ponies in the South West of the UK; ponies were categorised as Feral (n=10), Semi-Feral (n=10) and Domesticated (n=9), based on their management conditions. Diet was recorded and faecal counts were egg taken from all animals to assess parasite infection status. DNA was extracted and microbial composition identified via high-throughput sequencing of bacterial 16S rRNA gene. Bacterial communities were dominated by Firmicutes (36.71%) and Bacteroidetes (30.99%). Profound stepwise changes in global microbial community structure were seen in the transition from Feral -Semi-Feral- Domesticated groups these changes were significant in a large number of bacterial phyla and at multiple taxonomic levels. In particular increases in members of the phylum Proteobacteria and Tenericutes were associated with the domesticated group; and increases in Methanobacteria were seen in the Feral group. Faecal egg counts were significantly different between groups, and regression between FEC and individual components of the microbiome revealed that a number of taxa associated with domestication level were also associated with parasite burden. Functional predictions based on microbiome data revealed increased amino acid and lipid metabolism in domesticated group, versus increased energy metabolism in feral group. Interestingly the semi-feral group had a wide variation in FEC and microbial alpha diversity and functional predictions were associated with disease pathways. In this study we have shown significant stepwise changes to GI microbiota due to domestication standardised in one breed of equine. A number of these changes were linked to parasite burden and, based on previous studies, the remainder are likely associated with diet. If we assume that the feral population has a more natural phenotype, akin to that with which horses have evolved, the data can potentially be used to provide bacterial markers of balanced gut homeostasis in domestic Exmoor ponies, and provide candidate markers in other equine breeds.\n\nAuthors: Bull K, Davies G, Meier S, Peachey L",
"study-name": "The composition of the equine microbiota undergoes a stepwise change in response to increasing levels of domestication",
"data-origination": "SUBMITTED"
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