| Summary: | <i>Cryptosporidium</i> spp., <i>Enterocytozoon bieneusi</i>, and <i>Giardia duodenalis</i> 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. <i>Coprococcus</i> and <i>Prevotella</i> were more abundant while <i>Akkermansia</i> had lower relative abundance with <i>E. bieneusi</i> infection. Bacteria of <i>Akkermansia</i>, <i>Lactococcus</i>, <i>Oxalobacter</i>, <i>Sphaerochaeta</i>, <i>Paludibacter</i>, <i>Fibrobacter</i>, <i>Anaerovibrio</i>, <i>Pseudomonas</i>, <i>Mogibacterium</i>, <i>Pseudoramibacter_Eubacterium</i>, <i>YRC22</i>, <i>Flexispira</i>, <i>SMB53</i>, <i>AF12</i>, and <i>Roseburia</i> genera were found under-presented and <i>Oscillospira</i> genus over-presented when <i>G. duodenalis</i> infection was present. Meanwhile, <i>Cryptosporidium</i> spp. and <i>E. bieneusi</i> co-infected animals showed lower relative abundance of <i>Allobaculum</i>, <i>Rikenella</i>, <i>Shuttleworthia</i>, <i>Epulopiscium</i>, <i>Bilophila</i>, <i>Dorea</i>, <i>Fibrobacter</i>, and <i>TG5</i>. 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.
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