Characterization of Bacterial Microbiota Composition along the Gastrointestinal Tract in Rabbits.

Abstract

Simple SummaryEach animal hosts a large community of bacteria, protozoa, fungi, and algae that colonize every surface of the body. The microbiota is defined as the complex microbial community that inhabits a specific anatomic region of animals and interacts with it, developing symbiotic relationships. In this regard, the intestinal microbiota has a vital impact on metabolism, digestive activity, immune development, resistance to infections, health, and welfare of the host. Therefore, knowing its characteristics is important for understanding its action in these specific functions. This study provides a comprehensive map of the most common bacterial communities that colonize different parts of the rabbit gastrointestinal tract (stomach, duodenum, jejunum, ileus, caecum, and colon) while using a modern methodological approach and comparing it with the studies that have been conducted to date on other animal species and human beings. It could be the starting point for further research on gut microbiota modulation with the ultimate goal to promote the health and welfare, in order to prevent or treat gastrointestinal diseases, decrease antibiotic use, and increase the productive performance of rabbit.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 analyzed using next generation 16S rRNA Gene Sequencing. The findings uncovered considerable differences in the taxonomic levels among the regions of the digestive tract. Firmicutes were the most abundant phylum in all of 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 the upper digestive tract. Knowledge of the physiological microbiota of healthy rabbits could be important for preserving the health and welfare of the host as well as for finding strategies to manipulate the gut microbiota in order to also promote productive performance.