Cryptosporidiosis is one of the leading causes of diarrhoea in young calves worldwide. Caused by the protozoan parasite Cryptosporidium parvum, the disease affects not only animal welfare but also farm productivity, contributing to treatment costs, reduced growth rates, and, in severe cases, calf mortality. While acute infection is known to disrupt the gut microbiome, questions remain about whether these changes persist after infection and whether the microbiome can predict disease susceptibility.
A recent study by researchers at the University of Liverpool and their collaborators sought to address these questions by conducting one of the largest longitudinal studies of the calf faecal microbiome to date.
Study design: following calves from birth to weaning
The study enrolled 346 Holstein dairy calves across three UK farms. Faecal swabs were collected in the first week of life, again around week five (typically after diarrhoeal events had resolved), and finally at week ten during weaning.
During the study period, 32 calves developed diarrhoea and tested positive for C. parvum, forming the Cryptosporidium-positive (Cp+) group. These were compared to 33 healthy controls (H) that showed no signs of diarrhoea across the study. This careful matching of calves by age, farm, and treatment history helped control for confounding factors such as management practices and antibiotic usage.
The samples were processed for 16S rRNA gene amplicon sequencing, enabling detailed analysis of bacterial diversity and composition across timepoints. Alongside microbiome profiling, calves were monitored for health outcomes, including body condition, daily live weight gain, and respiratory health, providing a broader view of how infection impacted their development.
Microbiome development and the impact of infection
The calf fecal microbiome became more diverse with age. Both alpha diversity (species richness and evenness) and shifts in beta diversity (community composition) reflected a natural progression in microbial colonisation during the preweaning period. Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria were the dominant phyla, with specific genera such as Escherichia/Shigella and Bacteroides abundant early in life, before giving way to Ruminococcaceae, Lachnospiraceae, and Prevotella at later stages.
When comparing healthy calves with those that developed cryptosporidiosis, the researchers found only limited differences. At week five, infected calves had a slightly higher abundance of Firmicutes than controls, but this distinction had disappeared by week ten. No particular microbial profile before infection predicted which calves would develop diarrhoea.
In terms of health outcomes, infected calves had lower body condition scores at week five, but this difference was no longer significant by week ten. Daily live weight gain and respiratory health did not differ significantly between groups, suggesting that calves were able to recover after infection.
The role of antibiotics and treatments
One aspect the study also highlighted was the influence of antibiotics and anti-cryptosporidial treatments. On one farm, antibiotics such as trimethoprim/sulfadiazine, amoxicillin/clavulanic acid, and tulathromycin were administered in response to outbreaks of other diseases. These treatments were associated with changes in the relative abundance of certain bacterial taxa, although most were present at low levels.
Similarly, halofuginone lactate, used either prophylactically or therapeutically against C. parvum, was associated with shifts in the abundance of some genera.
While these effects were not always consistent, they emphasise the importance of considering farm-level management and treatment practices when interpreting microbiome data.
Ensuring robust and reproducible results
Microbiome studies are inherently complex, with many steps where technical variation can affect results. To ensure their findings were reliable, the research team incorporated ZymoBIOMICS Microbial Community Standards as positive controls during sequencing.
These standards, consisting of a defined mixture of microbial DNA, allowed the researchers to check for sequencing biases, validate DNA extraction and amplification steps, and ensure that the differences they observed reflected genuine biological patterns rather than artefacts of sample processing. The inclusion of standards provided confidence that the microbiome changes described were both reproducible and biologically meaningful.
Limitations of the study
The authors acknowledge several limitations. Diagnoses of cryptosporidiosis relied on lateral flow testing, which, while rapid and practical for on-farm use, is not 100% sensitive or specific. The influence of antibiotics and halofuginone treatment was difficult to fully disentangle from the effects of infection itself. Body weight data were only available from one farm, limiting the statistical power for growth comparisons, and a small number of samples were lost in transit.
Despite these constraints, the findings were consistent with the team’s earlier metagenomic work and align with other longitudinal studies of calf gut microbiome development.
Conclusions: resilience of the calf microbiome
This study provides important insights into the resilience of the calf gut microbiome. While C. parvum infection disrupts calf health in the short term, it does not appear to have lasting effects on microbial diversity or composition once infection resolves. The microbiome continues along its natural developmental trajectory, suggesting that calves are able to restore microbial balance after illness.
For the dairy industry, these findings are encouraging, offering reassurance that cryptosporidiosis, though damaging during acute disease, does not cause long-term disruption to the gut microbial communities critical for calf growth and immune development. For the scientific community, the study highlights the importance of robust design, careful control of variables, and the use of validated microbial standards to ensure trustworthy conclusions in microbiome research.
References
Hares, M.F., Griffiths, B.E., Barningham, L. et al. Progression of the faecal microbiome in preweaning dairy calves that develop cryptosporidiosis. anim microbiome 7, 3 (2025). https://doi.org/10.1186/s42523-024-00352-1