Development of the Intestinal Microbiota of Dairy Calves and Changes Associated with Cryptosporidium spp. Infection in Brazil

<i>Cryptosporidium</i> spp. is one of the most important pathogens infecting nursing calves worldwide. This study aimed to investigate the intestinal microbiota of dairy calves during the first month of life and the impact of diarrhea caused by <i>Cryptosporidium</i> on a Brazilian farm. Fecal samples from 30 calves were collected during the first month of life, and fecal scores were recorded. Samples from the second, third, and fourth days of life were analyzed by DNA sequencing of the 16S rRNA gene. In addition, samples of sixteen calves positive for <i>Cryptosporidium</i> spp. were retrospectively chosen according to the development of diarrhea: four and two days before diarrhea, at the onset of diarrhea, after four days of diarrhea, at the end of diarrhea, and after six days of diarrhea resolution. Diarrhea was observed in all calves (100%), starting at day 5 of life, and all calves tested positive for <i>Cryptosporidium</i> in at least one sample. The microbiota richness increased with age but was retarded by diarrhea. Compositional changes associated with <i>Cryptosporidium</i> infection included increases in <i>Fusobacterium, Prevotella</i>, and <i>Peptostreptococcus</i>, as well as decreases in <i>Collinsella</i> and Lachnospiraceae. In conclusion, <i>Cryptosporidium</i> infection has the potential to decrease richness and change the composition of the intestinal microbiota of dairy calves.