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

Simple Summary A large population of bacteria, protozoa, fungi, and algae colonizes an animal's body surface. The complex community of microbes that occupies a specific area of the organism and develops symbiotic relationships with the host is referred to as the microbiota. In this context, the gut microbiota plays an important physiological role as it influences the digestion and absorption of nutrients, the development and maturation of the immune system, and thus the growth, resistance to disease, and welfare of the animal. For these reasons, it is important to know the role of the microbiota in these specific functions, as well as which factors can impact the composition of bacterial populations, because changes in the microbiota can result in both beneficial and detrimental effects (dysbiosis) on the host. This study, in addition to providing information on the composition of the microbiota in the jejunum and cecum of rabbits, also evaluates the effect of breed and different growth rates using a modern methodological approach. Since the effect of these factors on the modulation of the gut microbiota has been little studied, this research could be the starting point for new experimental investigations aimed at enhancing rabbit productivity and welfare. This study aimed to evaluate the productive performance and microbiota variation in the jejunum and cecum of two rabbit breeds with different growth rates. This study was carried out on Native Middle-Egypt Breed (NMER) and Giant Flanders (GF) rabbits from 5 weeks to 12 weeks of age. Twenty NMER (NM) and GF male rabbits were slaughtered, and the jejunum and cecum tracts were collected to assay gut microbiota composition via 16S ribosomal RNA (rRNA) gene sequencing and histology examination. At 12 weeks of age, daily weight gain, villus height in the jejunum, total protein, and albumin were higher in GF rabbits than in NMER rabbits. Also, the jejunal villi of GF were well arranged in their dense borders. The microbiota between the jejunum and cecum was significantly different in terms of Beta-diversity. A significant correlation between Enterococcus (jejunum NM samples) and Lactobacillus (cecum GF samples) with body weight and weight gain was found (p < 0.05). Moreover, Escherichia-Shigella in the cecum of NM was significantly correlated with weight gain (p < 0.05). The most abundant genera identified in the jejunal and cecal contents of GF were generally beneficial microbiota. They may also play a role in reducing the pathogenic effects of Escherichia coli in these rabbits.