The harmful effects of
diarrhea on the growth performance of rabbits have been well documented, but the details of the potential mechanism of intestinal
diarrhea when
antibiotics are stopped are still unclear. Here, PacBio sequencing technology was used to sequence the full length
16S rRNA gene of the microbiota of intestinal content samples, in order to characterize the bacterial communities in the small intestine (duodenum and jejunum) and large intestine (colon and cecum) in normal Hyplus rabbits and those with
diarrhea. The histopathological examination showed that intestinal
necrosis occurred in different degrees in the
diarrhea group, and that the mucosal epithelium was shed and necrotic, forming erosion, and the clinical manifestation was
necrosis. However, the intestinal tissue structure of the normal group was normal. The results revealed that there were significant differences in bacterial communities and structure between the
diarrhea and normal groups of four intestinal segments (p < 0.05). In general, 16 bacterial phyla, 144 bacterial genera and 22 metabolic pathways were identified in the two groups. Tax4Fun functional prediction analysis showed that KEGG related to
amino acid metabolism and energy metabolism was enriched in the large intestines of rabbits with
diarrhea, whereas lipid metabolism was more abundant in the small intestine of rabbits with
diarrhea. In conclusion, the change in the relative abundance of the identified dominant microbiota, which could deplete key anti-inflammatory metabolites and lead to bacterial imbalance and
diarrhea, resulted in
diarrhea in Hyplus rabbits that stopped using
antibiotics.