The human milk microbiome: composition and perturbations

How do human microbiomes interact with the immune system?

Half of the cells in the human body are microbial, with each niche’s microbiome as unique to individuals as fingerprints. Microbiomes contribute many more genes than the human genome does to our human body. The microbiome is composed of the microbiota, its genes, and its products, which includes microbial structural products as well as microbial metabolites. Microbiomes are the second genome of our body. Microbiomes shape phenotypic traits of the host, including nutritional and metabolic traits.

Within the human immune system, microbiomes use chemical and metabolic signals to regulate the abundance and activities of immune cells, including lymphocytes. As lymphocytes respond to encounters with antigens, they regulate the constantly changing genetic sequences produced in immunoglobulins.

The complex cross talk between a microbiome and the body’s adaptive immune system determines whether the body

Recognizes a specific molecular pattern as non-self, or as a sign of endogenous cell and tissue damage, and
How vigorously the immune system responds.1

What is the composition of the human milk microbiome?

The human milk microbiome comprises organised networks of bacteria, viruses, fungi, archaea, and protozoa.

The median bacterial load of healthy human milk is 10 6 cells/ml, and something like 800 different species of bacteria have been identified, including a high load of bacteria which have been previously labelled as pathogenic (Staphylococcus aureus, Esherishia coli, Group B streptococci).
- It’s generally agreed that the core bacterial genera of the milk microbiome, universal across lactating women, are Staphylococcus, Streptococcus and Propionibacterium. Much smaller and more variable populations of Lactobacillus and Bifidobacterium may occur, but not in all breastfeeding women.2-6
- Non-viable bacteria are thought to be a significant part of the breast immune system, acting as antigens which interact with host immune cells, much like inactivated vaccines.
The viral fraction of human milk, the virome, is dominated by bacteriophages, which comprise 95% of human milk viruses. Bacteriophages modulate bacterial ecology by killing certain species.
The fungal fraction of human milk, the mycobiome, interacts with and stabilises the microbial domain in protective association networks, which together strengthen host health and immunity and resist overgrowth of any particular bacterial species (previously referred to as pathogen colonisation).
- Candida albicans is the most common fungal commensal in the human body, and Candida spp including C. albicans occur commonly in human milk, having a beneficial, probiotic effect, interacting with and containing bacteria.2, 7-12
- The mechanisms by which bacteria and fungi co-regulate in commensal communities are complex and diverse. In the gut, bacteria are known to limit fungal colonisation because bacterial metabolites activate mucosal immunity to fungi.

Methods of human milk microbiome sampling are not yet standardised

Neither culture nor PCR is yet able to determine the true composition of a human milk microbiome inside a lactating woman’s breast. It is not clear if findings from milk analysed in vitro can be extrapolated back to apply to milk which is still in the alveoli and ducts.

Culture-based methods select out bacteria from expressed breast milk on specific growth media, identifying species and numbers of colony forming units.
Molecular polymerase chain reaction (PCR) methods of analysing expressed breast milk identify DNA, which may be from viable or non-viable bacteria, non-cultivable bacteria, and bacterial fragments. Non-viable bacteria are thought to be a significant component of the mammary gland immune system, acting as antigens which interact with host immune cells, much like inactivated vaccines.

Human milk microbiomes are highly variable between mothers and in the one mother over time

The milk microbiome participates in the activation of myriad immune feedback loops within multiple complex systems. Micro-organisms interact together, with the milk metabolome, with milk oligosaccharides, with milk leukocytes, and many other factors to maintain physiological integrity and health of the lactating breast.4

The bacterial communities in human milk are highly dynamic. Antimicrobial-induced disturbance of milk microbiota is quickly reversed.

Human milk microbiome composition differs between colostrum, transitional and mature milk.2 Researchers agree that the composition of the human milk microbiome is also impacted by

Genetic predisposition
Ethnicity
Geographical location
Circadian rhythm
Age
Body mass index
Maternal nutrient intake, including of fatty acids, carbohydrates or proteins
Some studies have found differences in the milk microbiome depending on the infant’s mode of delivery, others haven’t.

Selected references

Dombrowska-Pali A, Wiktorczyk-Kapischke N, Chrustek A. Human milk microbiome - a review of scientific reports. Nutrients. 2024;16:1420.

Douglas P. Re-thinking benign inflammation of the lactating breast: a mechanobiological model. Women's Health. 2022;18:17455065221075907.

Douglas PS. Re-thinking benign inflammation of the lactating breast: classification, prevention, and management. Women's Health. 2022;18:17455057221091349.

Douglas PS. Does the Academy of Breastfeeding Medicine Clinical Protocol #36 'The Mastitis Spectrum' promote overtreatment and risk worsened outcomes for breastfeeding families? Commentary. International Breastfeeding Journal. 2023;18:Article no. 51 https://doi.org/10.1186/s13006-13023-00588-13008.

Groër M., Morgan K., Louis‐Jacques A., & Miller E.. A scoping review of research on the human milk microbiome. Journal of Human Lactation 2020;36(4):628-643. https://doi.org/10.1177/0890334420942768

Laba O. and Pyrohova V.. Study of the state of the vaginal microbiota in women with risk and threat of preterm birth. Reproductive Health of Woman 2022(5):39-44. https://doi.org/10.30841/2708-8731.5.2022.265477