Abstract: Diarrhea caused by different pathogens can lead to changes in the structural characteristics of intestinal flora of calves. In order to study the diversity of intestinal flora, 38 fresh faecal samples were collected from three large-scale cattle farms in western Inner Mongolia, including 30 diarrhoea faecal samples and 8 healthy faecal samples. The diarrhoea-associated pathogens were tested by PCR and then the samples were divided into three groups, the healthy group (HC), the bovine rotavirus (BRV)-infected diarrhoea group (DC_a) and the Escherichia-Shigella infection diarrhoea group (DC_b). Total DNA was extracted and the highly variable V3-V4 region of the bacterial 16S rDNA gene was amplified by PCR using universal primers, sequenced by the Illumina NovaSeq platform and the sequencing results were analyzed by bioinformatics. The results of α diversity index showed that there was a significant difference in intestinal microbial diversity between diarrhea and healthy calves, and the α diversity index of DC_b group was significantly lower than that of the other two groups(P<0.05). At phyla level, the dominant phyla in the three groups were Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria, but their relative abundance were significantly different. In DC_b group, Firmicutes were significantly decreased (P<0.05) and Actinobacteria were significantly increased (P<0.05). At the genus level, the dominant genera and relative abundance of the three groups were different. PICRUSt2 function prediction analysis showed that compared with HC group, DC_a group significantly decreased mannose-degradation, galactose degradation, sugar and vitamin biosynthesis and other related metabolic pathways. DC_b was significantly enriched in hexitol degradation and L-tryptophan biosynthesis. This study showed that the difference between healthy calves and diarrhoeic calves was significant (P<0.05) in the intestinal flora of the phylum Firmicutes and Actinomycetes; Not only the pathogenic bacteria in the phylum Aspergillus can cause diarrhoea in calves but also lead to an inflammatory response in the intestine; Family Rumexcoccus has multiple functions and it is difficult to infer functional differences between genera from amplicon sequencing data; It can also be concluded that diarrhoea is closely related to energy and nutrient metabolism and amino acid metabolism.

Key words: calf diarrhea, intestinal flora, diversity, 16S rDNA sequencing