Mothers and microbes, Part 2: The placental, breast milk, and breast tissue microbiomes

December 27th, 2015 by Amy Proal

While the vaginal microbiome has received a great deal of attention from the research community, recent research also indicates that microbes persist in the womb, where they come in contact with a fetus before it is born. Studies demonstrating the presence of microbes in the amniotic fluid have now been bolstered by the discovery of a placental microbiome. Dysregulation of this placental microbiome by pathogens has also been associated with preterm birth and low infant birth weight.

Consistent with the presence of a placental microbiome, naturally-born infants often harbor microbes not commonly found in the vagina. For example, while vaginal communities are often composed of up to 80 percent Lactobacillus, the microbiomes of newborn infants contain high levels of other taxa, such as Actinobacteria, Proteobacteria, and Bacteroides. Infants appear to have acquired these microbes in the womb, and not during the birthing process.

The most complete study of the placental microbiome to date was performed in 2014 by Aagaard and team at Baylor College of Medicine. After analyzing a number of earlier studies showing the presence of intracellular microbes in the placenta, the team conducted a large-scale metagenomic analysis of placental samples obtained immediately after birth from 320 women. The study found that the placenta harbored a low-abundance but metabolically rich microbiome. In other words, microbes detected in the placenta were often present in low numbers, but still influenced important bodily processes. This microbiome was characterized by the presence of microbes from the Firmicutes, Terenicutes, Proteobacteria, Bacteroidetes, and Fusobacteria phyla. Aaagard and team describe these particular microbes as nonpathogenic.

The placental microbiome has a taxonomic profile that is similar to the oral microbiome. The thicker the connecting line, the greater the similarity of the taxonomic profile. Source: Aagaard.

The placental microbiome has a taxonomic profile that is similar to the oral microbiome. The thicker the connecting line, the greater the similarity of the taxonomic profile. Source: Aagaard.

Placental microbiome populations identified by the team only minimally resembled the same mother’s vaginal or stool microbiome populations. If anything, they most mirrored her oral microbiome. Indeed, several species of the oral microbiome were detected in the placenta, including Prevotella tannerae (gingival crevices) and species of Neisseria (mucosal surfaces). This and similar data led Aagaard and team to conclude that the placental microbiome is likely established by the spread of the oral microbiome via the blood.

Although the species of microbes identified in the placenta varied considerably among subjects, the most abundant species found in most samples was E. coli. Aagaard and team note that pathogenic strains of E. coli can establish occult intracellular reservoirs within tissue of the urinary tract. E.coli is also a strong contributor to early-onset sepsis among extremely low birth weight neonates, causing the researchers to speculate that in these cases, “the placenta is a likely source.”

The team also looked at placental microbiome samples from women with a history of antepartum infections (primarily urinary tract infections in the first or second trimester). These women harbored higher levels of bacteria such as Streptococcus, Acinetobacter, Thioalkalivibrio, and Pseudoalteromonas. Some of these same microbes contribute to the development of vaginosis, causing Aagaard and team to hypothesize that inflammatorion generated in response to vaginosis or related infections might better allow certain pathogens to colonize the placenta in a manner that promotes UTIs.

The study also demonstrated variations in the placental microbiome communities of women who underwent a spontaneous preterm delivery before 37 weeks. Several taxa, such as Burkholderia, were found in greater number among subjects who delivered preterm. The relative abundance of Actinomycetales and Alphaproteobacteria were also increased in the preterm placenta. In contrast, Paenibacillus was enriched in the placental specimens of women who carried their babies to term.

A different study by researchers in China also found that placental microbiome populations of women who delivered low birth weight infants (LBW) were significantly less diverse than those of mothers who delivered normal weight infants (NBW). Differences in the composition of the placental microbiome between the LBW and NBW infants was demonstrated at both the phylum and genus level. For example, the relative abundance of Firmicutes was decreased in placentas corresponding to the LBW group, while Proteobacteria and Actinobacteria were detected in higher numbers. In addition, Lactobacillus percentage was positively associated with birth weight.

The breast milk microbiome

After birth, an infant’s health is further shaped by microbes it continually acquires from its mother’s breast milk. While just a few years ago breast milk was believed to be sterile, it is now understood to deliver a robust microbiome that varies among women. An enteric-breast circulation allows microbes from a mother’s gut to reach her mammary glands and vice versa via the blood. The intensity of this circulatory pathway appears to increase during the end stages of pregnancy and during breastfeeding. Microbes originating in a mother’s intestines may subsequently be present in her breast milk. These microbes may in turn play a large role in forming her infant’s early gut communities.

A significant number of microbes are transferred in this fashion. According to Spanish researcher Juan-Manuel Rodriguez, if a baby consumes 800 milliliters of milk a day, it acquires between 100,000 to ten million microbes. Breast milk also contains oligosacchiarides, or sugars used by Lactobacillus, Bifidobacteria and other bacteria to remain alive in the intestine. Differences in the intestinal microbiome have been documented between breast fed infants and formula fed infants. Rodriguez believes that the absence of breast milk microbes and oligosacchiarides in formula is the greatest factor driving these discrepancies.

Relatedness between milk bacteria and the rest of the human microbiome. Source: Cabrera-Rubio.

Relatedness between milk bacteria and the rest of the human microbiome. Source: Cabrera-Rubio.

Even conservative estimates point to several hundred microbial species in breast milk, with colostrum having a higher diversity than mature milk. The composition of the breast milk microbiome has also been shown to vary based on a number of factors. Cabrera-Rubio and team found that the composition of the breast milk microbiome significantly changed over the course of at least the first six months of lactation. Additionally, the weight of the mother affected the composition of her breast milk microbiome. Milk from obese mothers tended to contain a different and less diverse bacterial community than that obtained from healthy subjects. Excessive weight gain during pregnancy was also associated with higher amounts of Staphylococcus and Staphylococcus aureus in one-month samples, and higher amounts of Lactobacillus and lower amounts of Bifidobacterium in six-month samples.

In addition, mothers who underwent elective Cesarean delivery displayed “strikingly different” bacterial communities in their milk samples than those who gave birth by vaginal delivery. These differences were already present in colostrum and were maintained in breast milk at one and six months.

Diversity of the Spanish mature milk microbiome, C-section vs. vaginal. Source: Cabrera- Rubio.

Diversity of the Spanish mature milk microbiome, C-section vs. vaginal. Source: Cabrera- Rubio.

A second study by Cabrera-Rubio and team expanded on this last finding. The researchers analyzed the microbiome composition of breast milk taken from mothers after one month of exclusive breastfeeding. Higher bacterial diversity and richness was found in the milk samples of mothers who had delivered vaginally than from those who had delivered by C-section. The abundance of various microbial species also differed between the two groups – for example, higher levels of Bifidobacterium were related significantly to lower levels of Staphylococcus.

Returning to the first study, mothers who gave birth by nonelective C-section displayed a milk microbiome composition more similar to that of mothers who gave birth by vaginal delivery. This caused the research team to suggest that physiological changes produced in the mother during labor may influence the microbial composition of her milk. These changes include significant hormonal alterations associated with labor that do not occur in women who give birth by elective C-section.

The breast milk microbiome has also been shown to shift in women who suffer from mastitis, a condition in which breast tissue becomes painful and swollen. For example, Jiménez and team studied breast milk microbiome samples collected from ten healthy women and ten women with symptoms of lactational mastitis. While healthy subjects harbored a diverse array of different microbes, the milk microbiomes of women with mastitis reflected a significant loss of bacterial diversity. In fact, the milk microbiomes of women with acute mastitis were dominated by the single bacterium Staphylococcus aureus. Fungal, protozoan, and viral species were also identified in most of the samples obtained from these women, whereas single-celled microbes from the domain Archaea were absent in samples from the women with mastitis.

Staphylococcal/streptococcal counts in milk samples from women in the mastitis study.

Staphylococcal/streptococcal counts in milk samples from women in the mastitis study.

Because the enteric-breast circulation connects the intestines to the breast, some studies have found that specific probiotics may help women manage mastitis. For example, Fernandez and team in Spain administered women Lactobacillus salivarius PS2 orally during late pregnancy. The percentage of women who developed mastitis was significantly lower in this probiotic group than in control subjects.

The breast tissue microbiome

The discovery that human breast milk harbors a microbiome prompted Urbaniak and team in Canada to search for the presence of a breast tissue microbiome. Human breast tissue contains high levels of nutrient-rich fatty acids, which serve as an energy source for microbes. Furthermore, breast tissue is strongly perfused by blood vessels, which in turn flow into a widespread lymphatic system. This allows microbes to easily reach the area via the circulatory system.

In the first analysis of its kind, the team obtained tissue from 43 women. Samples were taken from various locations within the breast, from close to the nipple to as far back as the chest wall. A variety of bacteria were detected in all breast tissue samples. Some of these species, such as Lactobacillus and Bifidobacterium, are considered to be commensal, while taxa detected at other sites, including Enterobacteriaceae, Pseudomonas and Streptococcus agalactiae, are regarded as pathogens.

The most most abundant phylum detected in the breast tissue were Proteobacteria. This stands in contrast to the vagina, oral cavity, bladder, skin, and gut, where the phylum comprises only a small proportion of the overall bacterial community. The team subsequently concluded that “breast tissue may have a unique microbiota, distinct from that found at other body sites.” Proteobacteria is also the principal phylum found in human milk, as were many of the other bacterial species detected in the breast tissue. This naturally raises the possibility that many of the microbes an infant acquires in breast milk are derived from the breast tissue microbiome.

I should note that in this study some of the breast tissue samples were taken from women with breast cancer. These samples were collected outside of the “marginal zone” associated with cancer. In my opinion, however, it would be optimal for even more data to be obtained from completely healthy subjects.

Bacterial phyla detected in tumor tissue vs. paired normal tissue in the same patient.

Bacterial phyla detected in tumor tissue vs. paired normal tissue in the same patient.

In the meantime, other research teams are studying the breast tissue microbiome in cancer. In one study, samples were taken directly from breast tumor tissue samples. Xuan and team in California used molecular tools to compare microbial populations in these tissue samples to those detected in normal adjacent tissue from the same patient. Many differences in breast tissue microbiome composition were detected. For example, the bacterium Methylobacterium radiotolerans was relatively enriched in tumor tissue, while the bacterium Sphingomonas yanoikuyae was relatively enriched in paired normal tissue. Furthermore, breast tumor tissue contained significantly reduced amounts of bacteria, the proportion of which decreased with advanced disease. These lower levels of microbes were also accompanied by a reduction in the expression of antibacterial response genes that are normally active in breast tissue.


While the microbes an infant acquires during vaginal or C-section birth clearly influence its development, exposure to such populations is relatively brief. On the other hand, microbes in the womb or in breast milk may “seed” an infant over the course of months or even years. It appears that exposure to these microbes can promote wellness but also disease. We must consider then that continued exposure to these microbes during the most formative stages of development may shape a child’s health for years to come.

The microbiome populations discussed in this article must be studied in much greater depth. Still, mothers, their spouses, and the physicians they work with, should be well-informed about current research. Few mothers I know have been told that the placental microbiome, breast tissue microbiome, and breast milk microbiome exist. In my opinion, providing mothers with this knowledge will not alarm them, but instead empower them to make the most informed choices about how and when to conceive.

For example, I have seen cases in which mothers breastfeed their infants in the hospital after chemotherapy, and after removal of their second breast due to a tumor. I have incredible respect for these mothers and the resilience they demonstrate in the face of duress. Yet I can’t help thinking that they are not aware of the maternal microbiome. Their physicians may also not be aware of the latest research on the topic, which strongly suggests that the dysregulated breast tissue and breast milk microbiomes associated with cancer might allow more pathogens to be passed to the infant. Hopefully then, if more awareness is directed towards the maternal microbiome in health and disease, information about these communities can be included in reproductive counselling. That way every family can benefit in a proactive fashion from the most current scientific data.

2 thoughts on “Mothers and microbes, Part 2: The placental, breast milk, and breast tissue microbiomes

  1. Amy Proal Post author

    Hi Helen,

    Always good to hear from you!

    That’s true. Over the past century there has been some recognition that single pathogens can infect the womb. However, these infections were/are only believed to happen under certain circumstances.

    In contrast, the data in my post shows that ALL wombs are likely not sterile. Also, communities of microbes, rather than single pathogens, appear to impact fetal development in the womb. These differences are increasingly important as we better understand the the ability of the microbiome to impact health and disease processes.


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