Culturomics as a tool to better understand the human milk microbiota and host–microbiota interactions

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For almost a century, it has been accepted that human milk contains viable microbial cells. However, for a considerable amount of this period, it was believed that they were the result of exogenous contamination, primarily from the skin or non-sterile handling. Early work using culture-dependent methods, supported by molecular profiling, however, identified the presence of lactic acid bacteria from an endogenous origin. This provided evidence that the human milk microbiota consisted of microorganisms that were not found solely on the skin surface and therefore could not result from contamination. Through the advent of next-generation sequencing, the field of microbiota research has caused a paradigm shift away from a typical focus on the presence of pathogenic microorganisms in human milk. This had led to a broad appreciation that the human milk microbiota consists of several hundred species of non-pathogenic commensal microbes – with many anaerobic microbial taxons being found only in the gastrointestinal tract outside of human milk. Nevertheless, as our appreciation of the complexity and diversity of the human milk microbiota has improved, many questions relating to the functional basis of host–microbiota interactions in the newborn infant’s gastrointestinal tract remain outstanding. To address these, mechanistic studies will be required in which the utilisation of isolated microorganisms will be essential. As such, a return to culture-dependent methods in the new paradigm of culturomics will be required. In this review, we bring together the current understanding of the human milk microbiota and how culturomics could play a fundamental role in furthering our understanding.