Characterization of bacterial microbiota composition along the gastrointestinal tract in rabbits

The microbiota is extremely important for the animal’s health but, to date, knowledge on the intestinal microbiota of the rabbit is very limited. This study aimed to describe bacterial populations that inhabit the different gastrointestinal compartments of the rabbit: stomach, duodenum, jejunum, ileum, caecum, and colon. Samples of the luminal content from all compartments of 14 healthy New White Zealand rabbits were collected at slaughter and analysed using next generation 16S rRNA Gene Sequencing. The findings uncovered considerable differences at taxonomic levels among the regions of the digestive tract. Firmicutes were the most abundant phylum in all the sections (45.9%), followed by Bacteroidetes in the large intestine (38.9%) and Euryarchaeota in the foregut (25.9%). Four clusters of bacterial populations were observed along the digestive system: (i) stomach, (ii) duodenum and jejunum, (iii) ileum, and (iv) large intestine. Caecum and colon showed the highest richness and diversity in bacterial species while the highest variability was found in upper digestive tract. The knowledge of the physiological microbiota of healthy rabbits could be important to preserve the health and welfare of the host as well as to find strategies to manipulate the gut microbiota in order to promote also productive performance.