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PeerJ. 2019 Apr 3;7:e6687. doi: 10.7717/peerj.6687. eCollection 2019.

A longitudinal study of the faecal microbiome and metabolome of periparturient mares.

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Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Leahurst campus, Wirral, UK.
Department of Surgery, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Al Sharquiya, Egypt.
Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK.
Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK.
Computational Biology Facility, Institute of Integrative Biology, University of Liverpool, Liverpool, UK.
Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, UK.
TopSpec Equine Ltd, Middle Park Farm, North Yorkshire, UK.



Periparturient mares are at increased risk of colic including large colon volvulus, which has a high mortality rate. Alterations in colonic microbiota related to either physiological or management changes, or both, that occur at this time have been suggested as potential causes for increased colic risk in this population of horses. Although the effect of management changes on the horse faecal microbiota has been investigated, limited work has been conducted to investigate changes in faecal microbiota structure and function in the periparturient period. The objectives of the current study were to investigate temporal stability of the faecal microbiota and volatile organic compounds (VOCs) of the faecal metabolome in periparturient mares.


Faecal samples were collected weekly from five pregnant mares from 3 weeks pre-foaling to 7 weeks post-foaling. The microbiome data was generated by PCR amplification and sequencing of the V1-V2 regions of the bacterial 16S rRNA genes, while the VOC profile was characterised using headspace solid phase microextraction gas chromatography mass spectrometry.


The mare faecal microbiota was relatively stable over the periparturient period and most variation was associated with individual mares. A small number of operational taxonomic units were found to be significantly differentially abundant between samples collected before and after foaling. A total of 98 VOCs were identified. The total number of VOCs did not vary significantly between individual mares, weeks of sample collection and feeds available to the mares. Three VOCs (decane, 2-pentylfuran, and oct-2-ene) showed significant increase overtime on linear mixed effects modelling analysis. These results suggest that the mare faecal microbiota is structurally and functionally stable during the periparturient period. The findings also suggest that if changes in the gut microbiota are related to development of colic postpartum, altered risk may be due to inherent differences between individual mares. VOCs offer a cost-effective means of looking at the functional changes in the microbiome and warrant further investigation in mares at risk of colic.


Colic; Horse; Mare; Metabolome; Microbiome; Microbiota; VOCs

Conflict of interest statement

The authors declare that they have no competing interests. Sarah J. Stoneham was employed by the Cheshire Equine Clinic during the period of sample collection and she is currently employed as an equine nutritionist by TopSpec Equine Ltd. North Yorkshire, UK.

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