Characterization of Bacterial Microbiota Composition along the Gastrointestinal Tract in Rabbits

The mammal's gastrointestinal system is colonized by different microbial populations that live in a symbiotic relationship among them and with the host. The characteristic microbial community that occupies a well-defined habitat and has distinct physio-chemical properties is defined as microbiota. There are great differences in the structure and functions of the digestive tract among herbivores. Three categories can be identified: (i) ruminants, such as cattle and camelids, which have anterior digestive fermentative activity (rumen); (ii) posterior fermenters, such as horses and rodents, which have the large intestine (caecum and colon) as fermentation chamber; and, (iii) caecotrope animals, such as rabbits and hares, which rely on caecotrophy. Anyway, to date, only a few studies regarding the composition of the microbiota that inhabits the different sections of the gastrointestinal tract of healthy rabbits are available. Hence, better knowledge and a complete microbial mapping of all different parts of the gastrointestinal tract are necessary for promoting the health and welfare of the rabbit, whose market is going through a period of difficulty and it is the subject of animal welfare issues.This study investigated the microbial composition and diversity of the microbiota present in different tracts of the digestive system of adult rabbit (i.e., stomach, duodenum, jejunum, ileum, caecum, and colon) by 16S rRNA gene amplicon sequencing from 14 healthy New White Zealand rabbits.