Scotland's Rural College Characterisation of the faecal bacterial community in adult and elderly horses fed a high fibre, high oil or high starch diet using 454 pyrosequencing Dougal,

Faecal samples were collected from seventeen animals, each fed three different diets (high fibre, high fibre with a starch rich supplement and high fibre with an oil rich supplement). DNA was extracted and the V1–V2 regions of 16SrDNA were 454pyrosequenced to investigate the faecal microbiome of the horse. The effect of age was also considered by comparing mature (8 horses aged 5–12) versus elderly horses (9 horses aged 19–28). A reduction in diversity was found in the elderly horse group. Significant differences between diets were found at an OTU level (52 OTUs at corrected Q,0.1). The majority of differences found were related to the Firmucutes phylum (37) with some changes in Bacteroidetes (6), Proteobacteria (3), Actinobacteria (2) and Spirochaetes (1). For the forage only diet,with no added starch or oil, we found 30/2934 OTUs (accounting for 15.9% of sequences) present in all horses. However the core (i.e. present in all horses) associated with the oil rich supplemented diet was somewhat smaller (25/3029 OTUs, 10.3% ) and the core associated with the starch rich supplemented diet was even smaller (15/2884 OTUs, 5.4% ). The core associated with samples across all three diets was extremely small (6/5689 OTUs accounting for only 2.3% of sequences) and dominated by the order Clostridiales, with the most abundant family being Lachnospiraceae. In conclusion, forage based diets plus starch or oil rich complementary feeds were associated with differences in the faecal bacterial community compared with the forage alone. Further, as observed in people, ageing is associated with a reduction in bacterial diversity. However there was no change in the bacterial community structure in these healthy animals associated with age. Citation: Dougal K, de la Fuente G, Harris PA, Girdwood SE, Pinloche E, et al. (2014) Characterisation of the Faecal Bacterial Community in Adult and Elderly Horses Fed a High Fibre, High Oil or High Starch Diet Using 454 Pyrosequencing. PLoS ONE 9(2): e87424. doi:10.1371/journal.pone. 0087424 Editor: A. Mark Ibekwe, U. S. Salinity Lab, United States of America Received August 22, 2013; Accepted December 20, 2013; Published February 4, 2014 Copyright: 2014 Dougal et al. 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. Funding: This research was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) Case studentship (BB/G017271/1). No additional external funding was received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: Patricia A. Harris is employed by one of the funders of this research (WALTHAM Centre for Pet Nutrition, Melton Mowbray, Leicestershire. LE14 4RT). The authors confirm that this does not alter their adherence to all the PLOS ONE policies on sharing data and materials. * E-mail: cjn@aber.ac. uk