The microbial content of raw and pasteurised cow’s milk as determined by molecular approaches including sequencing

The microbial composition of raw and pasteurised milk is assessed by industry on a daily basis. However, many such tests are culture-dependent and thus bacteria that are present at sub-dominant levels and/or that cannot be easily grown in the laboratory may be overlooked. To address this potential bias, we have employed a number of culture-independent techniques, including flow cytometry, real-time qPCR and high throughput sequencing, to assess the microbial population of milk from a selection of commercial milk producers, pre- and post-pasteurisation. The combination of techniques employed reveals the presence of a previously unrecognised and diverse bacterial population in unpasteurised cow’s milk. Most notably, the use of high throughput sequencing resulted in a number of bacterial genera being identified in milk samples for the first time. These included Bacteroides, Faecalibacterium, Prevotella and Catenibacterium. Our culture-independent analyses also indicate that the bacterial population of pasteurised milk is more diverse than previously appreciated but that non-thermoduric bacteria within these populations are likely to be in a damaged, non-culturable form. It is thus apparent that the application of state-of-the-art approaches can provide a detailed insight into the bacterial composition of milk and could potentially be employed in the future to investigate the factors that influence the composition of these populations.