Study of the possibility of modulating the composition of the gastrointestinal microbiome of rabbits fed fermented rapeseed meal

Abstract Understanding digestive functions and the role of microorganisms in the prevention of gastrointestinal and systemic diseases may be a strategy for preventing intestinal dysbiosis during critical periods of animal rearing, strengthening the immune system and reducing herd mortality. The aim of the study was to determine the effect of the addition of fermented rapeseed meal (FRSM) to the diet of rabbits on the composition of the bacterial microbiota of the caecal contents. The experiment was conducted using 40 35-day-old rabbits ( Oryctolagus cuniculus ) assigned to four groups of 10 animals each. Animals in the control group (group C) were fed a standard diet, while the experimental groups received 4% (group E1), 8% (group E2) or 12% (group E3) dried FRSM in place of the previously used soybean meal (SBM). After 120 days, six rabbits (three males and three females), of average size and intended for slaughter, were selected from each group. The contents of the caecum were collected from these animals for metagenomic analysis. The research showed that the microbiome of the caecum of rabbits shows low diversity at higher phylogenetic levels, but is highly diverse at lower levels. The study showed no directly proportional relationship between the various groups of microorganisms inhabiting the digestive tract and the share of fermented rapeseed meal used in the diet. To the best of our knowledge, this is the first study to characterize the microbiome of rabbits fed diets with the inclusion of fermented feed components.