Effect of age and the individual on the gastrointestinal microbiome of ponies fed a high-starch diet. Barley challenge

Bacteria residing in the gastrointestinal tract of all mammals are crucial for the digestion of dietary nutrients. Bacterial community composition is modified by age and diet in other species. Horses are adapted to consuming a high-fibre diet, although modern husbandry practices has increased the use of high energy, often high starch containing, feeds (eg. cereals). The current study assessed the impact of age on the faecal microbiome of ponies transitioning from a hay-based diet to a high-starch diet. Over two years (May to November), 23 Welsh Section A pony mares were evaluated (Controls, n = 6/year, 5-15 years; Aged, n = 6 Year 1; n = 5 Year 2, ≥19 years). Across 30-weeks, animals were randomly assigned to a single 5-week period of study, when they were individually fed the same hay to maintenance (2% body mass as daily dry matter intake) for 4-weeks. During the final week, 2g starch per kg body mass (micronized steam-flaked barley) was incorporated into the diet (3-day transition and 5 days at maximum). Faecal samples were collected for 11 days (final 3 days hay and 8 days hay + barley feeding) and bacterial communities determined using Next Generation Sequencing of amplified V1–V2 hypervariable regions of 16S rRNA. The dietary transition resulted in increases in Candidatus Saccharibacteria and Firmicutes and a reduction in Fibrobactres phyla abundance. Changes at the genus level were dominated by increases in Streptococcus abundance but this was not consistent across individual animals and was not associated with any outset animal phenotype parameter. Bacterial diversity was reduced during dietary transition in those Streptococcus ‘responders’. Faecal pH and VFA concentrations were modified by diet but considerable inter-individual variation was present. Age had a minimal effect on the microbiome response to diet. When all samples were considered, the core microbiome comprised of a single OTU, 0.56% of recovered sequences. The current study describes compositional changes in the faecal microbiome associated with the transition from a fibre-based to a high-starch diet in ponies and emphasises the individual nature of dietary responses, which may reflect functional differences in the bacterial populations present in the hindgut