Using culture ‘omics to explore the microbial structure and function in an equid in vitro digestion model

The in vitro gas production system (GPS), developed to estimate degradation of ruminant feedstuffs, has been adapted for equine use. This study aimed to characterise the bacterial community profile and metabolome of donor faeces and faecal inoculum within the GPS when fermenting the same diet as faecal donors. Six Welsh ponies on identical diets were faecal donors with samples collected for microbiome profiling and system inoculation. Gas production (manual pressure transducer technique) was performed for 156 h with 2 replicate bottles from each donor harvested at 8,20,28 and 36 h. Faecal and inoculum samples were subject to PMAxx for viability PCR, 16S rRNA sequencing and 1^H NMR metabonomics. Time in the GPS effected bacterial community profile, metabolic phenotype and predicted metabolic pathways. Collectively a system dysbiosis was observed at 8 h. End point metabolic profile was similar to the donor faeces but GP fibre degrading microbiota better reflected previously reported literature on rumen microbiota, rather than those found in horses. The GPS estimates dry matter digestibility similar to in vivo digestibility, resulting in a similar metabolic profile to donor faeces. However, the GPS either favours rumen dwelling microbiota or demonstrates functional microbial redundancy compared to the donor faeces of equids.