Diversity and Co-Occurrence Pattern Analysis of Cecal and Jejunal Microbiota in Two Rabbit Breeds

The microbial population that inhabits specific niches in the body, developing symbiotic relationships with the host, is called the microbiota. This complex ecosystem of microbial communities is involved in important physiological processes in the host, such as nutrient digestion and absorption, immune system development, intestinal permeability, and both direct and indirect protection against the development of dangerous or pathogenic bacteria. The gut microbiota plays an important role in healthy animals but can also be a cause of pathology.Recently, this technology has also been used in domestic rabbits (Oryctolagus cuniculus) that are monogastric, hindgut-fermenting herbivores and rely on cecotrophy. The rabbit is a very interesting species because it is considered, at the same time, a farm animal, a pet, and also a laboratory animal. The composition of the microbiota of different intestinal tracts has been evaluated in livestock, laboratory, pet, and shelter rabbits, finding a different microbiota composition in the diverse gastrointestinal tracts.The present study aimed at comparing, using a 16S rRNA-based analysis, the microbial populations in the jejunum and cecum of two breeds of rabbits: the Native Middle Egypt Rabbit - NMER (NM) as a local breed with a light body weight and the Giant Flander (GF) as an exotic breed with a heavy body weight. In addition, histology, scanning electron microscope (SEM) examinations, and biochemical parameters were used to compare NM with GF rabbits.