Metagenomic analysis of the gut microbiota in Cryptosporidium-infected Tibetan sheep.

Cryptosporidium are important causative parasitic protozoa that cause gastrointestinal discomfort and diarrhea in humans and animals, posing a huge threat to public health. Ruminants serve as the main source of Cryptosporidium infection. However, the relationship between this intestinal parasite and host gut microbiota in Tibetan sheep remains almost unknown. In the present study, using nested PCR targeting the SSU rRNA gene, we detected Cryptosporidium in 9% (38/420) of fecal samples. The positive rate was significantly higher in 4-7 month-old lambs than in adult sheep. Infection of Cryptosporidium spp. was associated with limited overall structural and functional alterations of the host gut microbiota, characterized by increased the relative abundance of Escherichia and reduced functional pathways related to amino acid biosynthesis and nucleotide/nucleoside biosynthesis. Additionally, the data indicates that age served as a primary determinant of the gut microbiota, whereas Cryptosporidium load showed no significant association with microbial variation. Machine learning model analysis revealed that these differential microbial features could effectively discriminate between infected and uninfected animals. These findings elucidate that Cryptosporidium infection is associated with specific and limited gut microbiota alterations in sheep.