Effects of replacing barley maize by citrus pulp in a dairy sheep diet on microbial populations in RUSITEC fermenters

Citrus pulp is a by-product highly available in the Mediterranean area. It is rich in rapidly degradable carbohydrates and it has been used in ruminant diets replacing partially the cereals with no negative effects on animal performance, but there is little information of its effects on microbial populations in the rumen. Two 50:50 forage:concentrate diets were used, with the concentrate containing either maize (20% fresh matter basis) or being totally replaced by citrus pulp. Four Rusitec fermenters were used in a cross-over design with two 14-day incubation periods, and three rumen-cannulated Merino sheep were used as ruminal content donors for inoculating the system. Samples of liquid and solid digesta were collected from the fermenters at the end of each incubation run. DNA was extracted and the abundance of bacteria and protozoa, as well as the relative abundance of fungi and archaea, were assessed by qPCR. Bacterial diversity was analysed using Automated Ribosomal Intergenic Spacer Analysis (ARISA). Data were processed using R with the vegan package. The number of peaks detected in the ARISA electropherograms and the Shannon’s index were not affected by the inclusion of citrus pulp in the diet (P>0.05). When representing the principal coordinates analysis based on Bray-Curtis distance, samples clearly grouped according to diet, suggesting different bacterial community composition. Abundance of bacterial and protozoa populations were similar in both diets in the solid digesta (P>0.05), but the presence of citrus pulp in the diet tended to increase the abundance of bacteria (P=0.099) and increased protozoa abundance (P=0.041) in the liquid digesta. Relative abundance of archaea increased in the liquid digesta of the citrus pulp diet (P=0.024), but there were no differences between diets (P>0.05) in the solid digesta. Finally, fungi populations were affected by diet, with higher relative abundance in both solid and liquid digesta (P=0.001 and P=0.022) for the citrus pulp diet compared to the one containing maize. In conclusion, replacing maize by citrus pulp in a dairy sheep diet promoted changes in microbial populations and a greater abundance of microorganisms, especially in the liquid digesta of Rusitec fermenters, which might be related to the high sugar content of citrus pulp.