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Human Breast Milk Microbiome Affected by Mode of Feeding

NEW YORK (GenomeWeb) – The bacterial makeup of human milk is influenced by mode of breastfeeding, according to a new study.

Until recently, breast milk was thought to be sterile, but it has since been found to harbor a low level of bacteria that may help establish the infant gut microbiome and possibly influence the development of conditions like asthma and obesity.

While it's unclear how the breast milk microbiome develops, there are two theories describing its origins. One theory posits that it originates in the maternal mammary gland, while the other theory suggests it is due to retrograde inoculation by the infant's oral microbiome.

A team led by University of Manitoba investigators examined the milk microbiome of nearly 400 mother-child pairs from the Canadian Healthy Infant Longitudinal Development (CHILD) birth cohort. As they reported in Cell Host & Microbe today, the researchers found that the human milk microbiome commonly contained Proteobacteria and Firmicutes. Additionally, they noted that mode of breastfeeding — direct breastfeeding or indirect using a breast pump — appears to affect the composition of the milk microbiome.

"This study considerably expands our understanding of the human milk microbiota and the factors that might influence it," senior author Meghan Azad of Children's Hospital Research Institute of Manitoba said in a statement. "The results will inspire new research about breastfeeding and human milk, especially related to pumping."

The researchers conducted 16S rRNA sequencing on genomic DNA extracted from breast milk samples obtained from 393 mothers three to four months after giving birth. The mothers provided samples that were hand expressed or pumped. For each of these samples, the researchers generated a mean 47,710 sequencing reads.

After filtering, the researchers uncovered 1,972 amplicon sequence variants (ASVs) representing 18 unique phyla. Two-thirds of the taxa they uncovered belong to the Proteobacteria and about a quarter belong to Firmicutes. Other taxa represented include the Actinobacteria and Bacteroides. The researchers identified a core set of 12 ASVs that were present in 95 percent of samples.

Through hierarchical clustering of the samples, the researchers identified four groups that largely differed based on their abundance of certain bacterial species like Moraxellaceae, Oxalobacteraceae, or Comamonadaceae. The clusters did  have varying levels of alpha diversity and their heterogeneity correlated with degree of breast pump-based feeding, the researchers noted.

They further delved into factors that could influence milk microbial diversity, exploring the influence of mode of feeding, number of siblings, sex, and other factors. Indirect breastfeeding — such as using a breast pump — was associated with both lower bacterial richness and diversity. The other factors had no associations with alpha diversity.

Similarly, when they examined relative abundance at a species and genus level, the researchers again found mode of breastfeeding to be associated with differences in taxa abundance. The researchers found Enterobacteriaceae and Enterococcaceae to be more abundant with indirect breastfeeding, while Gemellaceae and Vogesella were enriched with direct breastfeeding.

Direct breastfeeding samples were also enriched for members of the Actinobacteria phylum and Veillonellaceae, which are oral bacteria.

This suggested to the researchers that indirect breastfeeding might enable the enrichment of environmental bacteria, such as from the breast pump itself, while direct breastfeeding may enrich the presence of oral bacteria. Additionally, they noted that potential opportunistic pathogens like Stenotrophomonas and Pseudomonadaceae were enriched among indirect breastfeeding samples.

The researchers argued their study supports the theory that the breast milk microbiome is due to retrograde inoculation. Their findings indicate that the act of pumping and contact with the infant oral microbiome influences the milk microbiome, though they noted more research is needed.