Metagenomic analysis of the fecal microbiomes from Escherichia coli O157:H7-shedding and non-shedding cows on a single dairy farm

Escherichia coli O157:H7 (O157:H7) is a major zoonotic pathogen responsible for severe and sometimes fatal infections in humans. Cattle are the primary reservoir of O157:H7, although other animal species are also known carriers. Fecal shedding of this pathogen can potentially lead to contamination of pre-pasteurized milk, meat, water, produce, wildlife, and the environment. Understanding the relationships between O157:H7 carriage and the structure of the ruminant intestinal microbiome may inform development of mitigation strategies. To assess the compositional differences in the fecal microbiota of O157:H7-shedding and non-shedding cows, 14 fecal samples from lactating cows in the same dairy herd were analyzed using shotgun metagenomic sequencing. Results indicated that the microbial community, resistome, and virulome structures did not differ based on shedding status, but several unique taxa were identified in the fecal metagenomes in at-least 50% of the samples from the O157:H7-shedding cows. Further, differential relative abundance of 20 taxa belonging to the phyla Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Spirochaetes, Cyanobacteria, and Verrucomicrobia, were observed in the fecal samples between the two groups. The results of this study indicate that subtle differences in the fecal metagenomes of lactating dairy cows may be associated with E. coli O157:H7 shedding.