Associations between Escherichia coli O157 shedding and the faecal microbiota of dairy cows

AimsDairy cattle shed pathogenic Escherichia coli O157 (O157) in faeces, playing a role in human exposure. We aimed to measure faecal microbial communities in early lactation dairy cattle, and model outcomes with O157 shedding metrics. Methods and ResultsDaily faecal samples were collected from 40 cattle on two Colorado dairies for five consecutive days, and characterized for O157. 16S rRNA gene sequencing was used to measure sample-level microbial communities. Alpha-diversity metrics were associated with O157 outcomes via regression modelling, adjusting for confounders. Differential abundance of taxa were identified between O157(+) and O157(-) samples and between shedding days of individuals, using matched Wilcoxon rank-sum tests, zero-inflated Gaussian (ZIG) regression and negative binomial regression. After removing an outlier, multi-day and intermittently shedding cows had lower average richness compared to those that never shed. ZIG modelling revealed Bacillus coagulans to be more abundant in O157(-) samples, while Moryella were more abundant in O157(+) samples. Negative binomial models and Wilcoxon tests revealed no differentially abundant taxa between O157(+) vs O157(-) samples, or between shedding days of individuals. ConclusionsMicrobial diversity and some taxa may be influenced by or affect O157 shedding by dairy cattle. Significance and Impact of the StudyIf future work corroborates these findings, dairy cow microbial community changes may be used to guide on-farm strategies that mitigate O157 dissemination, protecting the human food chain.