Analysis of gut microbiota with cryptosporidiosis based on fecal condition in neonatal dairy calves on a farm in Japan

Cryptosporidiosis is a major cause of diarrhea and is associated with high morbidity in calves. Changes in the gut microbiota exacerbate diarrhea caused by Cryptosporidium parvum infection in neonatal and weaned calves. However, information on the gut microbiota of neonatal calves with C. parvum infection is scarce, and research into the microbiome of calves is essential for developing preventive and therapeutic interventions. This study aimed to elucidate the gut microbiota of neonatal calves with cryptosporidiosis. We collected 31 fecal samples from 31 neonatal calves on a dairy farm with or without C. parvum antigen [CP(+) or CP(−)] using a kit and analyzed the differences in the microbiota between diarrheal (D) and normal (N) fecal samples with C. parvum infection based on the fecal score. The analyses revealed the α diversity indexes of fecal microbiota in CP(+)-N samples were higher than that in CP(+)-D samples. Megasphaera spp. and other rumen microbes were identified, and significantly associated with CP(+)-N samples compared with CP(+)-D samples by linear discriminant analysis effect size (LEfSe). We conclude that the specific gut microbiota could characterize fecal microbiota in calves with neonatal cryptosporidiosis without clinical symptoms.