Abstract
Epizootic rabbit enteropathy (ERE) is reproduced successfully in the present study by feeding rabbits a low-fibre diet, and high-throughput sequencing and quantitative real-time PCR (qPCR) analysis were applied to examine the microbial variations in the stomach, small intestine and caecum. The evenness was disturbed and the richness was decreased in the ERE groups. When the rabbits were suffering from ERE, the abundance of the Firmicutes was decreased in three parts of the digestive tract, whereas the Proteobacteria was increased in the stomach and caecum, the Bacteroidetes and Verrucomicrobia were increased in the small intestine. Correlation analysis showed that the reduced concentrations of TVFA and butyrate in the caeca of the ERE group were attributed to the decreased abundances of genera such as Lactobacillus, Alistipes and other fibrolytic bacteria and butyrate- producing bacteria such as Eubacterium and Faecalibacterium. It is concluded that, in terms of microorganisms, the overgrowth of Bacteroides fragilis, Clostridium perfringen, Enterobacter sakazakii and Akkermansia muciniphila and inhibition of Bifidobacterium spp. and Butyrivibrio fibrisolvens in the stomach, small intestine and caecum resulted in a decrease in butyrate yield, leading to the incidence of ERE, and the probability of developing ERE could be manipulated by adjusting the dietary fibre level.
Highlights
Epizootic rabbit enteropathy (ERE) is reproduced successfully in the present study by feeding rabbits a low-fibre diet, and high-throughput sequencing and quantitative real-time PCR analysis were applied to examine the microbial variations in the stomach, small intestine and caecum
The overall operational taxonomic units (OTUs) number, species richness indices (Chao[1], Ace index), and diversity index (Shannon index) in ERE rabbits were significantly lower (P < 0.01) than those in normal rabbits (Table 1). These results indicated that the bacteria in the caecum had higher phylogenetic richness than the bacteria in the stomach and small intestine, and the ERE rabbits had lower bacterial diversity and species richness than normal rabbits
The α-diversity and quantitative real-time PCR (qPCR) data showed that the caecal samples had higher species richness and a more abundant bacterial population than the stomach and small intestine samples in normal rabbits, which was in line with previous studies[18]
Summary
Epizootic rabbit enteropathy (ERE) is reproduced successfully in the present study by feeding rabbits a low-fibre diet, and high-throughput sequencing and quantitative real-time PCR (qPCR) analysis were applied to examine the microbial variations in the stomach, small intestine and caecum. Examination of the microbes in the gastrointestinal tract of ERE rabbits may facilitate the detection of pathogenic bacteria and the comprehension of the aetiopathogenesis of ERE. This experiment aimed to determine what bacteria might be responsible for the occurrence of ERE by comparing the microbial composition in the stomach, small intestine and caecum between healthy and ERE rabbits. Relationships between microbial genera and fermentation parameters including the VFA molar proportion, were identified
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