Effect of diet on structural resiliencies of rumen microbiota in cows
Résumé
Improving the ruminant digestive physiology by manipulating the rumen microbiota requires understanding the structural and functional resiliencies of microbiota in adult animals and the role of the host’s phenotype. Six rumen cannulated dry dairy cows were fed a corn silage (CS) diet for 5 weeks followed by a hay (H) diet for 5 weeks. Then, during a week labelled w0, the host-microbiota link was experimentally disrupted by collecting, pooling and homogenizing the rumen contents of the 6 cows and refilling each rumen with the homogenized microbiota mixture. The cows were kept on the H diet for 12 additional weeks and finally on the CS diet for 5 weeks. Using 16S-rDNA sequencing and Frogs pipeline, rumen microbiota composition was analyzed immediately after disruption at w0 and twice at the end of the 4 diet periods (w-6; w-1; w+11, w+16). Microbiota α-diversity (richness) was higher on H diet than on CS diet, was highest just after disruption (w0) and stabilized on H diets at a higher level at w+11 than at w-1. In contrast, richness were similar at the end of the two CS diet periods. PCoA based on Bray-Curtis distance at ASV-like level revealed along the first two principal coordinates a clear clustering by week and diet. Microbiota communities were clearly modified when diets were switched. After disruption, community structures did not return to the initial state when cows were fed the H diet but were restored with the CS diet. It suggests that structural resilience of the microbiota is diet-dependent.