Characterisation of the faecal bacterial community in adult and elderly horses fed a high fibre, high oil or high starch diet using 454 Pyrosequencing

Faecal samples were collected from seventeen animals fed three different diets (high fibre, high fibre supplemented with starch and high fibre supplemented with oil). DNA was extracted and the V1-V2 regions of 16SrDNA were 454-pyrosequenced 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 and four OTUs were identified as significantly different from the adult group (P<0.001).These OTUs were predominantly in the order Clostridiales and were decreased in the elderly group. Significant differences between diets were also found at an OTU level (36 OTUs at P<0.001). The majority of differences found for both diet and age were related to the Firmucutes phylum (28) with some Bacteroidetes (4), Proteobacteria (2), Spirochaetes (1) and Actinobacteria (1). With a high fibre 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 a high oil supplemented diet was somewhat smaller (25/3029 OTUs, 10.3% ) and the core associated with a high oil 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, addition of starch or fat to the diet produced changes in the faecal bacterial community. Further, as observed in people, ageing is associated with a reduction in bacterial diversity and a change in the bacterial community structure.