Progression of the faecal microbiome in preweaning dairy calves that develop cryptosporidiosis

Abstract

Background Cryptosporidiosis is a diarrheal disease that commonly affects calves under 6-weeks-old. The causative agent, Cryptosporidium parvum, has been associated with the abundance of specific taxa in the faecal microbiome during active infection. However, the long-term impact of these microbiome shifts, and potential effects on calf growth and health have not yet been explored. Methods 346 calves from three dairy farms had one faecal swab collected during the first week of life (W1). Thereafter, sampled calves were monitored for diarrhoeal disease and those that suffered a diarrhoea event were tested for C. parvumby lateral flow test (LFT). Calves that experienced diarrhoea and tested positive for C. parvum by LFT were assigned to the Cryptosporidium-positive (Cp+) group (n=32). Matched healthy (H) controls with no history of diarrhoea were selected from the remaining cohort (n=33). The selected subset of calves (n=65) were observed until weaning, collecting a faecal swab, at approximately Week 5 (W5) and Week 10 (W10) after birth, resulting in a total of 191 samples (W1; n=65, W5; n=64, W10; n=62). 16S rRNA gene amplicon sequencing was performed on all extracted samples. Results Analysis of the longitudinal microbiome showed significant changes in the microbial diversity and composition across all three time points. Whilst Firmicuteswere elevated in the Cp+ group at W5 compared to the H group, no other significant differences were detected between H and Cp+ groups. Whilst the core microbiota showed some taxa were exclusive to each group, the role of these taxa in health and disease has yet to be determined. Antibiotics were also found to have an impact on the relative abundance of some taxa. Though there was a difference in daily live weight gain between H and Cp+ groups, it did not reach significance at either W5 and W10, suggesting that Cp+ calves can catch up to their healthy counterparts once the infection has resolved. Conclusions The findings of this study illustrate the changes in the microbial diversity and composition during the preweaning period in dairy calves. The results also indicate that the faecal microbiome is not predictive of cryptosporidiosis and imply that cryptosporidiosis doesn’t cause long-term gut dysbiosis. This study furthers our understanding of the parasite-microbiome relationship and its impact on the bovine host.