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

Abstract

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 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. 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.

Figure 1. Phyla identified and relative proportion of each associated with different diets and age of horse.

Data shown from the bacteria community in faeces from horses fed three diets; Hay- high fibre diet, Oil- high oil diet, CHO- high starch diet. Horses fed these diets were also assigned to two age groups adult or elderly.

Figure 2. Phylogenetic tree showing significant OTUs (corrected P<0.1) for diet.

Tree shows only those OTUs found to be significant (corrected P<0.1) and was built using UPGMA. The coloured outer ring indicates the bacterial phyla each OTU belongs to while the outer circles show the relative abundances of each OTU for the different diets; 1 layer of circles for Hay- high fibre diet,1 for Oil- high oil diet and 1 for CHO- high starch diet.

Figure 3. The core bacterial community associated with different diets and age of horse.

The core community for All is defined as those OTUs (clustered at 97% similarity) present in all animals for all diets and which abundances are 0.1% (or greater) of the total number of sequences. The core for each of the three diets is defined as those OTUs (clustered at 97% similarity) present in all samples from each individual diet and which abundances are 0.1% (or greater) of the total number of sequences for each diet. The lower pale blue section of the bar indicates the proportion that is not part of the core. The remaining individual coloured sections represent each OTU of which the core is comprised; All (6), HAY(30), CHO (15), OIL(25). For details of classification and abundance of individual OTU’s see table S6.