The microbiota of dairy milk: a review

Abstract The number of studies using high throughput sequencing (HTS) methods for the characterisation of microbial communities of milk and dairy products has increased markedly in the last decade. Besides confirming what was previously known from low sensitivity and throughput cultivation based and cultivation independent techniques, HTS studies have provided deeper insights into the structure and function of microbial communities. While the comparison of raw data from different studies is still difficult due the lack of standard operating procedures, the availability of well-structured databases with raw and processed sequences has boosted our ability to get quantitative insights into the factors that shape the microbial communities of milk and dairy products. Here we critically review metataxonomic and metagenomic studies on milk from cows and other dairy species, and discuss potential sources and dynamics of microbiota during storage, transport and processing in liquid pasteurised milk, using the FoodMicrobionet database to carry out meta-analyses.