Progression of the faecal microbiome in preweaning dairy calves that develop cryptosporidiosis. [Dataset]

Abstract

The aim of this study was to determine how the bacterial diversity and composition of the faecal microbiome in healthy and Cryptosporidium-positive calves changed between birth and weaning. The objective was to ascertain taxa which are associated with the pre-/post-infection or healthy faecal microbiome, which could further our understanding of the host-parasite-microbiome relationship, and therefore assist in the development of novel therapeutics.

Citation

HARES, M.F., GRIFFITHS, B.E., BARNINGHAM, L., VAMOS, E.E., GREGORY, R., DUNCAN, J.S., OIKONOMOU, G., STEWART, C.J. and COOMBES, J.L. 2025. Progression of the faecal microbiome in preweaning dairy calves that develop cryptosporidiosis. [DATASET]. Animal microbiome [online], 7, article number 3. Available from: https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-024-00352-1#Sec19

• Acceptance Date: Nov 3, 2024
• Online Publication Date: Jan 6, 2025
• Publication Date: Dec 31, 2025
• Deposit Date: Jan 16, 2025
• Publicly Available Date: Jan 16, 2025
• Publisher: Springer
• DOI: https://doi.org/10.1186/s42523-024-00352-1
• Keywords: Cryptosporidium parvum; Bovine cryptosporidiosis; Calf diarrhoea/diarrhea; Longitudinal; Faecal/fecal microbiome; 16S rRNA gene amplicon sequencing
• Public URL: https://rgu-repository.worktribe.com/output/2662862
• Related Public URLs: https://rgu-repository.worktribe.com/output/2661951 (Journal article that this supplementary material is associated with)
• Type of Data: TXT files, XLSX file, PPTX file and PDF file.
• Collection Date: Nov 30, 2020
• Collection Method: Three hundred and forty-six (346) female Holstein dairy calves from three commercial dairy farms, based in North Wales and Cheshire, UK (Farm 1, 2, and 3), were enrolled on to the study during the first week of life. Calves had rectal swabs collected at three time-points; preweaning pre-C. parvum infection (Week 1; n=65), then at preweaning post-C. parvum infection (Week 5±2; n=65), and during the weaning stage post-infection (Week 10±2; n=64); classified hereafter as W1, W5, W10, respectively. All calves were enrolled on the study within 2 months, with the collection of all samples taking place across a period of 4 months between July and November 2020. Prior to the development of clinical signs of cryptosporidiosis, one faecal swab sample (Sterilin Regular Nylon Flocked Swabs 552 C, Scientific Laboratory Supplies, UK) was collected from each of the 346 calves during the first week of life (W1), and snap frozen on dry ice directly after the sampling. DNA extraction of faecal swab samples (n=191) was carried out using the DNeasy® PowerLyzer® Powersoil® Kit (QIAGEN, UK) as per the manufacturer's instructions with the following exceptions. All analysis of the resulting OTU and taxonomy tables was carried out in mothur 1.47.0 and RStudio with R version 4.3.1, using the following R packages: vegan 2.6-4, phyloseq 1.44.0, pairwiseAdonis 0.4.1, VennDiagram 1.7.3, emmeans 1.8.9, and MaAsLin2 1.15.1. 16S rRNA gene amplicon sequencing was performed in order to ascertain how the diversity of the calf faecal microbiome changed between birth and weaning in calves that developed cryptosporidiosis compared to healthy controls. To summarise, C. parvum infection had minimal impact on the microbial diversity and composition of the calf faecal microbiome pre- or post-infection when compared with healthy calves, with age having the greatest impact on the development of the microbiome. This study and our previous shotgun metagenomic work lead us to speculate that the changes observed in other studies may be a result of direct interactions with the parasite during infection and not a consequence of pre-existing microbiome differences.