Cryptosporidium is one of the six major pathogens causing diarrhea worldwide, and it poses many hazards. To study the effect of Cryptosporidium infection on the intestinal fungal community of the host, this study focused on yaks and collected fecal samples from the infected group (CP, n=6) and the control group (CO, n=6). The structure and composition of the intestinal fungal community were analyzed using ITS amplicon sequencing technology. A significant decline in fungal diversity and evenness after infection was indicated by results showing that the Shannon index, Simpson index, and Pielou evenness of the infected group were significantly lower than those of the control group (P<0.05). Beta diversity analysis (PCoA, NMDS, and UPGMA clustering tree) revealed that the two groups of samples could be clearly separated, and the samples of the infected group were more closely clustered. Both groups were dominated at the phylum level, and these are Ascomycota and Basidiomycota, but the relative abundance of the Ascomycota phylum in the infected group (79.09%) was higher than that in the control group (64.82%). At the class level, the infected group enriched Leotiomycetes and Tremellomycetes. At the order level, Thelebolales (61.57%) and Filobasidiales (18.60%) were dominant in the infected group, while Pleosporales (39.57%) and Coniochaetales (6.27%) were dominant in the control group. At the genus level, Naganishia (46.84%) was significantly enriched in the infected group, while Neoascochyta (6.86%), Neostagonospora (5.69%), and others were higher in the control group. LDA analysis and the Wilcox test further confirmed the statistical significance of the above differential taxonomic units. Cryptosporidium infection can significantly alter the variety and composition of the intestinal fungal community, forming a fungal structure characterized by the amplification of opportunistic fungi such as Naganishia.

To Cite This Article: Shi B, Xu C, Cidanzhuoga, Almutairi MH, 2026. Evaluation of the impact of Cryptosporidium infection on the fungi in the intestines of yaks. Pak Vet J, 46(7): 1772-1781. http://dx.doi.org/10.29261/pakvetj/2026.170