Emerging frontiers in human milk microbiome research and suggested primers for 16S rRNA gene analysis

Abstract

Human milk is the ideal food for infants due to its unique nutritional and immune properties, and more recently human milk has also been recognized as an important source of bacteria for infants. However, a substantial amount of fundamental human milk microbiome information remains unclear, such as the origin, composition and function of the community and its members. There is emerging evidence to suggest that the diversity and composition of the milk microbiome might differ between lactation stages, due to maternal factors and diet, agrarian and urban lifestyles, and geographical location. The evolution of the methods used for studying milk microbiota, transitioning from culture dependent-approaches to include culture-independent approaches, has had an impact on findings and, in particular, primer selection within 16S rRNA gene barcoding studies have led to discrepancies in observed microbiota communities. Here, the current state-of-the-art is reviewed and emerging frontiers essential to improving our understanding of the human milk microbiome are considered.

Keywords: 16S rRNA gene; Human Milk; Microbial barcoding; Microbiome; Microbiota; PCR primers.

Graphical abstract

Fig. 1

Sources of milk microbiota Two potential sources of bacteria which could contribute to the breast milk microbiome: retrograde flow and the entero-mammary pathway , , , . The retrograde flow pathway suggests that the during suckling, infant oral microbiota and breast skin microbiota can reach the breast milk microbiota. The entero-mammary pathway suggests that dendritic cells in the maternal gut that cross the intestinal epithelium can take up bacteria from the intestinal lumen which are then taken to the mammary gland through the blood and lymphatic systems.

Fig. 2

16S rRNA gene primers pair coverage of major breast milk microbiome genera Common 16S rRNA gene primer pairs 515F-806R, 27F-338R, 27F-533R and 784F-1061R were tested in silico against all sequences within major breast milk microbiome genera in the SILVA database using the TestPrime tool (set to allow 1 mismatch outside the 3′ first 5 nucleotides; https://www.arb-silva.de/search/testprime/) . Percentage of sequences (coverage) within each genus is reported. High and low coverage primer pairs are illustrated in green and red, respectively. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article.)

Fig. 3

Geographical distribution of breast milk microbiome studies Fifty-seven studies into the breast milk microbiome and factors that influence its composition grouped by geographical region. Thirty-two studies were conducted in Europe , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , 11 studies in Asia , , , , , , , , , , , 11 studies in North America , , , , , , , , , , , 6 study in Africa , , , , , and 5 studies in Latin-America , , , , . Five multi-country studies included: Germany and Austria , China, Finland, South Africa and Spain , , China and Taiwan, , and Ethiopia, Gambia, Ghana, Kenya, Peru, US and Sweden . Studies have most frequently been conducted in Spain (15 studies) , , , , , , , , , , , , , ,