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Diarrhea is a syndrome of digestive disorders in young rabbits and may lead to secondary infections resulting in reduced immunity and higher mortality in baby rabbits, with serious impacts on rabbit farming. In this study, we investigated the effects of diarrhea on the health of baby rabbits in terms of intestinal mucosal development, immune function, and intestinal microbial diversity. We found that the duodenal villus length and the villus/crypt ratio in rabbits with diarrhea were significantly reduced compared with those in healthy rabbits ( P  < 0.01). Rabbits with diarrhea had significantly lower concentrations of acetic acid ( P  < 0.05), higher pH levels ( P  < 0.05), and higher levels of ammonia nitrogen ( P  < 0.01) in the cecum. Moreover, diarrhea in baby rabbits led to significantly reduced levels of total serum protein ( P  < 0.05) and markedly increased levels of alkaline phosphatase, urea nitrogen, TNF- α , and IL-6 ( P  < 0.05). Transcriptional analysis of peptidoglycan recognition proteins (PGRPs, including  PGLYRP-1 ,  PGLYRP-2 , and  PGLYRP-3 ) using real-time PCR revealed that diarrhea induced the upregulation of PGRPs in the cecum and duodenum. Furthermore, through pyrosequencing of the 16S rRNA V4 region in cecum samples, we found that the total number and diversity of microbes were not significantly different between healthy rabbits and those with diarrhea, though there were noticeable differences in the prevalences of  Clostridium ,  Roseburia,  and  Alistipes . Our results will contribute to a better understanding of the pathological mechanisms of diarrhea in young rabbits.

Impacts of diarrhea on the immune system, intestinal environment, and expression of PGRPs in New Zealand rabbits