Investigating the role of bacterial raw milk community members in chlorate reduction

Chlorine-based detergents, used in the dairy industry for cleaning, often degrade into chlorate, contaminating milk and dairy products. Consumption of chlorate has been linked to thyroid dysfunction in adults and impaired neurological development in infants. Despite the ban on chlorine-based detergents in Ireland since 2021, chlorate contamination remains a problem in the dairy supply chain. A recent study found chlorate-reducing bacteria naturally present in raw milk, highlighting their potential for chlorate mitigation. In this study, shotgun metagenomic sequencing was applied to determine the effects of chlorate concentration and incubation conditions on the raw milk microbiome, specifically focusing on chlorate-reducing bacteria within the community. Chlorate-spiked milk samples from different farms showed reductions in chlorate levels over time, from day 10 onwards when stored at 4°C and after 24 hours when incubated at 25°C. Pseudomonas and Lactococcus were observed as the most dominant taxa in raw milk samples stored at 4°C and 25°C, respectively. High abundances of ydeP and narG genes were observed for 4°C samples and were attributed to Pseudomonas and various low abundance genera, respectively. High abundances of the napA gene were noted in 25°C samples and were attributed to the Lactococcus genus. Overall, this study highlights the presence of naturally occurring chlorate-reducing bacteria as part of the raw milk microbiome and identifies multiple genes linked to various pathways potentially involved in chlorate reduction. Furthermore, incomplete pathways potentially involved in chlorate reduction were found, suggesting metabolic cross-feeding and underscoring the community roles bacteria play in chlorate reduction in raw milk. Additionally, a few previously uncharacterised genes, such as ydeP, belonging to the dimethyl sulfoxide (DMSO) reductase gene family were identified at high abundances in samples that showed chlorate reduction, emphasising the need for further biochemical characterisation of these genes to better understand the pathways involved in chlorate reduction in milk.