Three sampling strategies with a 16s rRNA high-throughput sequencing and gene expression assay (by RT-PCR) were designed, to better understand the host and probiotics effect on gut microbiota in sheep. Sampling: (1) colon contents and back-fat tissues from small-tailed Han sheep (SHS), big-tailed Hulun Buir sheep (BHBS), and short-tailed Steppe sheep (SHBS) (n = 12, 14, 12); (2) jejunum, cecum and colon contents, and feces from Tan sheep (TS, n = 6); (3) feces from TS at 4 time points (nonfeeding, 30 and 60 feeding days, and stop feeding 30 days) with probiotics supplementation (n = 7). The results indicated SHS had the highest Firmicutes abundance, the thinnest back-fat, and the lowest expression of C/EBPβ, C/EBPδ, ATGL, CFD, and SREBP1. Some bacteria orders and families could be potential biomarkers for sheep breeds with a distinct distribution of bacterial abundance, implying the host genotype is predominant in shaping unique microbiota under a shared environment. The microbiota diversity and Bifidobacterial populations significantly changed after 60 days of feeding but restored to its initial state, with mostly colonies, after 30 days ceased. The microbiota composition was greatly different between the small and large intestines, but somewhat different between the large intestine and feces; feces may be reliable for studying large intestinal microbiota in ruminants.

Cryptosporidium spp., Enterocytozoon bieneusi, and Giardia duodenalis are zoonotic pathogens commonly found in the intestinal tract of mammalian hosts including livestock and humans. The prevalence of these eukaryote microorganisms in domestic animals and their interaction with intestinal microbiota are not yet fully recognized. We analyzed the intestinal microbiota composition with metagenomics and functional characterization with Cluster of Orthologous (COG) in Bactrian camels, which were raised on Qinghai-Tibet Plateau, Northwest China. Thus, fecal samples were collected from the animals to determine the parasite infection and the profile of microbiota. Analysis of intestinal microbiota at genus level revealed important features of interaction between parasites infection and bacterial community. Coprococcus and Prevotella were more abundant while Akkermansia had lower relative abundance with E. bieneusi infection. Bacteria of Akkermansia, Lactococcus, Oxalobacter, Sphaerochaeta, Paludibacter, Fibrobacter, Anaerovibrio, Pseudomonas, Mogibacterium, Pseudoramibacter_Eubacterium, YRC22, Flexispira, SMB53, AF12, and Roseburia genera were found under-presented and Oscillospira genus over-presented when G. duodenalis infection was present. Meanwhile, Cryptosporidium spp. and E. bieneusi co-infected animals showed lower relative abundance of Allobaculum, Rikenella, Shuttleworthia, Epulopiscium, Bilophila, Dorea, Fibrobacter, and TG5. Results demonstrate important interaction between the intestinal parasites and microbiota, and provide informative link for understanding the co-evolution of zoonotic pathogens and bacteria in domestic animals.