Bacterial profile from caecal contents and soft faeces in growing rabbits given diets differing in soluble and insoluble fibre levels

To verify if non-invasive collection of soft faeces (SF) from rabbits can be used as an index of bacterial biodiversity in caecal contents (CC), 24 weaned rabbits were given diets with low (LI) and high (HI) levels of insoluble fibre (neutral detergent fibre, NDF) and low (LS) and high (HS) levels of soluble fibre (neutral detergent soluble fibre, NDSF). After 21 days, animals were fitted with neck collars for SF collection. Two days later, animals were slaughtered and CC sampled. Total bacterial concentration quantified by real time PCR (log₁₀ ng DNA/mg DM) was higher in SF than CC (2.615 vs. 2.383). Among diets, in CC it was (P = 0.059) lowest in LILS diet, whereas in SF it decreased (P = 0.025) with the NDF level. DGGE profiles showed that structure of bacterial communities of SF was close to that of CC; however, similarity was higher in LI than HI diets (0.82 vs. 0.74). Diversity indexes in CC decreased with NDSF (P < 0.05), whereas the effect of NDF (P < 0.05) was also appreciated in SF. Soft faeces can be an alternative to surgery or slaughter techniques to monitor changes in caecal bacterial community; however, high dietary NDF may decrease similarity between both communities.