Composition of rabbit caecal microbiota and the effects of dietary quercetin supplementation and sex thereupon

The purpose of this study was to add to the current understanding of rabbit caecal microbiota. This involved describing its microbial composition and linking this to live performance parameters, as well as determining the effects of dietary quercetin (Qrc) supplementation (2 g/kg feed) and sex on the microbial population. The weight gain and feed conversion ratio of twelve New Zealand White rabbits was measured from 5 to 12 wk old, blood was sampled at 11 wk old for the determination of serum hormone levels, and the rabbits were slaughtered and caecal samples collected at 13 wk old. Ion 16STM metagenome sequencing was used to determine the microbiota profile. The dominance of Firmicutes (72.01±1.14% of mapped reads), Lachnospiraceae (23.94±1.01%) and Ruminococcaceae (19.71±1.07%) concurred with previous reports, but variation both between studies and individual rabbits was apparent beyond this. Significant correlations between microbial families and live performance parameters were found, suggesting that further research into the mechanisms of these associations could be useful. Negative correlations with the caecal flavonoid content were found, but the latter was not affected by diet, and the effects of quercetin supplementation on the microbiota were very limited, possibly due to the absorption of the quercetin-aglycone from the gastrointestinal tract prior to the caecum. Nonetheless, Clostridiales Family XIII. Incertae Sedis was more abundant in the quercetin-supplemented rabbits (Control: 0.003±0.003%; Qrc: 0.020±0.000; P=0.005), as was the genus Anaerofustis (Control: 0.000±0.002; Qrc: 0.010±0.002; P=0.003). Serum cortisol levels were higher in females, and several microbial families differed between the sexes. Most were more abundant in female rabbits, including the most abundant, the family Eubacteriaceae (Male: 2.93±0.40; Female: 4.73±0.40; P=0.01).