Characterization of the diversity and temporal stability of bacterial communities in human milk

Abstract

Recent investigations have demonstrated that human milk contains a variety of bacterial genera; however, as of yet very little work has been done to characterize the full diversity of these milk bacterial communities and their relative stability over time. To more thoroughly investigate the human milk microbiome, we utilized microbial identification techniques based on pyrosequencing of the 16S ribosomal RNA gene. Specifically, we characterized the bacterial communities present in milk samples collected from 16 women at three time-points over four weeks. Results indicated that milk bacterial communities were generally complex; several genera represented greater than 5% of the relative community abundance, and the community was often, yet not always, stable over time within an individual. These results support the conclusion that human milk, which is recommended as the optimal nutrition source for almost all healthy infants, contains a collection of bacteria more diverse than previously reported. This finding begs the question as to what role this community plays in colonization of the infant gastrointestinal tract and maintaining mammary health.

Figure 1. The community composition of the 15 most abundant bacterial genera in each of 3 milk samples from 16 subjects was diverse.

The communities observed were found to be reasonably complex, and while consistent in composition over time for some subjects, a great deal of variation was observed over time in the samples of others.

Figure 2. A small proportion of the total richness was persistent within subject and represented the majority of the community present.

A. The number of OTUs (as defined by 97% sequence similarity) observed across all samples for each woman ranged from 100 to 600; however, only a small proportion of those OTUs were present in every sample from an individual subject-representing the individual core milk microbiome. B. The individual core milk microbiome for each woman was composed of the OTUs present in each of her samples. This relatively small number of OTUs represented the majority of the relative abundance of the community observed over time.

Figure 3. The community structure of bacterial OTUs in a milk sample often aligned by subject.

The complete linkage clustering of the samples based on the Bray-Curtis similarity metric demonstrated that, with several exceptions, samples from the same woman were often most similar to other samples from that same subject. Colored boxes represent samples from the same subject that clustered together.