Fungi are a known cause of mastitis in cattle. Despite this, fungal milk communities associated with development of intramammary infections are under researched. Mastitis is one of the most common and costly diseases in dairying. Commonly, broad-spectrum antibiotics are used in treatment and may lead to an unbalanced milk microbial community (microbiome), potentially allowing for overgrowth of mastitis-causing fungi. This research aimed to explore the microbiome associated with healthy and mastitic (clinical and subclinical) milk, with a focus on fungi and bacterial-fungi interactions, and implications of repeated antibiotic usage.

This project assessed the association between the milk microbiome and mastitis, by sampling milk from healthy (H, n = 10), subclinical mastitis (S, n = 10), clinical mastitis (C, n = 12), and repeated clinical mastitis cases (R, n = 10) in lactating Holstein Friesian cattle. Samples were cultured and DNA metagenomic shotgun sequenced.