The microbiome of the footrot lesion in Merino sheep is characterized by a persistent bacterial dysbiosis.

•This is the first study to characterise the microbiome of the Merino foot.•Different bacterial communities were present on healthy and footrot-affected feet.•Fifteen bacterial genera were preferentially abundant in footrot lesions.•The bacterial communities were similar at the active margin of mild and severe lesions.•The bacterial communities in footrot lesions were stable across the 10-month trial.