Simple SummaryJohne’s disease is a global economic burden. The disease contributes to reduced milk yield, reduced fertility, higher rates of susceptibility to other diseases and eventual death. Unhealthy animals are less efficient, producing higher kg of greenhouse gases per kg of output (milk and meat). Therefore, prognosis and diagnosis are important in terms of animal welfare and future climate change policies by reducing the impact of livestock on climate change. In the past decade, our knowledge around the microbiome in health and disease has increased. Next generation sequencing technologies have provided a new understanding of the interactions between the host microbiome and pathogens. The microbiome is a target for treatment, prevention of disease and a source of novel biomarkers of disease risk. The potential to improve animal health is highly dependent on our ever growing knowledge of the gut microbiome and their interactions with the host. With the aim to gain knowledge in the early months of exposure to MAP in calves, we investigated the dynamics of the gut microbiome (using faecal sample) of calves 3, 6 and 9 months post inoculation with MAP relative to unexposed controls.AbstractMycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne’s disease in ruminants, a chronic enteritis which results in emaciation and eventual loss of the animal. Recent advances in metagenomics have allowed a more in-depth study of complex microbiomes, including that of gastrointestinal tracts, and have the potential to provide insights into consequences of the exposure of an animal to MAP or other pathogens. This study aimed to investigate taxonomic diversity and compositional changes of the faecal microbiome of cattle experimentally challenged with MAP compared to an unexposed control group. Faecal swab samples were collected from a total of 55 animals [exposed group (n= 35) and a control group (n= 20)], across three time points (months 3, 6 and 9 post-inoculation). The composition and functional potential of the faecal microbiota differed across time and between the groups (p< 0.05), with the primary differences, from both a taxonomic and functional perspective, occurring at 3 months post inoculation. These included significant differences in the relative abundance of the genera Methanobrevibacter and Bifidobacterium and also of 11 other species (4 at a higher relative abundance in the exposed group and 7 at a higher relative abundance in the control group). Correlations were made between microbiome data and immunopathology measurements and it was noted that changes in the microbial composition correlated with miRNA-155, miR-146b and IFN-ɣ. In summary, this study illustrates the impact of exposure to MAP on the ruminant faecal microbiome with a number of species that may have relevance in veterinary medicine for tracking exposure to MAP.