Untapped microbiome magic
What are we finally learning about breastmilk and how can we make sure everyone benefits?
Article #4 of Raising our voices, even louder! A women's health long-read content series. Read all the articles here.
Nose to nipple. That was what I took from my breastfeeding antenatal class. It sounded easy. Scoop them up, line them up, and off they go.
But the reality for most of us is very different: sore nipples, swollen boobs and cries from everyone. Breastfeeding was the hardest 'easy' thing I've ever done.
Somewhere along the way, breastfeeding became political. On the one hand, we get ostracised for 'giving in' to formula and, on the other hand, we're criticised if forcing the 'breast is best' message.
Research suggests, likely due to the bioactive components in breast milk, that exclusively breastfed infants have a health advantage over formula-fed infants. Large-scale studies have demonstrated the long-term benefits of breastfeeding.
But, for many, breastfeeding is not an option.
Public health campaigners have been trying for years to address breastfeeding rates, often by pushing guilt-laden messages that help no one.
What if, instead of adding more pressure to already exhausted parents, we looked at alternative ways to provide some of the breastmilk’s goodness?
Thanks to startup, Booby Biome, we're moving closer to that solution. Founded in 2019 by a team of three female scientists, Dr Lydia Mapstone is the company's CEO.
The milky magic
The science says breastmilk is truly magic stuff. It contains all the macronutrients an infant needs to grow in the first six months. Like vitamin B12 for forming a baby's blood cells, vitamin D to help build strong bones and preventing rickets, and vitamin K to aid in blood clotting.
But it's more than simply a source of growth and nutrition. Research in recent years suggests it's far more complex than that.
"The liquid is rich in special sugars called Human Milk Oligosaccharides (HMOs), which make up 20% of its carbohydrate content. What's remarkable about HMOs is that babies can't digest them—humans don't have the necessary enzymes to break them down. This led scientists to a puzzling question: Why would breast milk contain large amounts of sugars that infants can't use for energy?” explains Dr Lydia Mapstone.
The answer, it seems, lies in the infant gut microbiome—the community of bacteria living in a baby's digestive system. It turns out that some bacteria, particularly those from the genus Bifidobacteria, can digest HMOs. These bacteria thrive in the infant gut and mammary glands, breaking down HMOs and outcompete harmful microbes.
But, the next question is, where do the bacteria within the infant microbiome come from, especially given that babies arrive from sterile environments?
Research suggests that 30% of an infant's gut bacteria come from birth, 20 to 40 percent from breastfeeding, and the remainder from the environment and other caregivers.
It's the 20 to 40 percent that interests BoobyBiome the most as they are the bacteria that successfully establish themselves in the infant gut microbiome.
"This community is known as the breast milk microbiome. Unlike the infant gut microbiome however, Bifidobacteria are less dominant, with this community also containing a mix of microbes from the oral and skin microbiome. Only a select group of bacteria are reliably found in both breast milk and infant stool, suggesting they are the most relevant for establishing the infant gut."
Over the past fifty years, there has been a concerning rise in childhood diseases and conditions like asthma and Type 1 diabetes.1,2 While various factors likely trigger these illnesses, one common thread among affected children is a disruption in their gut microbiomes.
"This connection is significant because we know that gut microbes play a vital role in developing the immune system. When children miss out on this microbial exposure, their immune systems may skip a crucial training window," explains Dr. Lydia.
Therefore, aside from helping babies develop, the milk microbiome provides a foundation for their future health.
Bringing breast benefits to all
The science tells us how important these microbes are, but, globally, only 48 percent of children are exclusively breastfed.
The reasons behind these stats are complex. But demonising formula and criticising already exhausted mothers is not helping.
Here's where BoobyBiome brings its own magic: "Our ambition is to provide these essential microbes to every baby, with the hope of one day reducing the rates of autoimmune disease onset."
How's the future looking?
A major research initiative, the $250 million Human Microbiome Project, which ran from 2007 to 2015 notably excluded breast milk microbiome. This oversight inspired BoobyBiome to create its own 'breast milk discovery platform'. Thanks to receiving hundreds of donated samples since 2019, the company has developed a comprehensive database cataloging all the bacterial species in the breast milk microbiome.
"By pairing breast milk samples with infant stool samples, we can track which bacteria successfully establish themselves in the infant gut. Our generous donors have also provided detailed questionnaires about their lifestyle and their baby's health, allowing us to explore how environmental factors influence the microbiome," outlines Dr Lydia.
A biobank of breast milk bacterial strains has also been built. These are explored and investigated in three ways:
Bioinformatics: analysis of the bacteria's genomes to predict their potential benefits for the infant gut.
Gut model: testing whether these bioinformatic predictions hold true in a laboratory setting.
Metabolomics: examination of the metabolites these bacteria produce to understand how they improve gut barrier integrity and support immune system development.
An interesting part of this research is the variation in microbiome across different donors.
Some mothers produce milk rich in beneficial bacteria with probiotic qualities, while others have up to ten times fewer microbes.
"We refer to those with particularly microbiome-rich milk as 'super donors' and often revisit them to collect additional samples. This allows us to track how their breast milk microbiome changes and better understand the factors contributing to their high microbial diversity," explains Dr Lydia.
The cause of these super donors is currently unknown, but similar to gut microbiome diversity, things like diet, antibiotic use and even cleaning products will likely have an impact.
"This variation in breast milk microbiomes could have important health implications. Studies suggest that infants who consume breast milk with lower microbial richness may be at a higher risk of developing allergies (Dzidic et al., 2020; Munblit et al., 2016)."
The long-term aim is to have things in place that will enable women to know in advance how 'super' their milk is.
Imagine the implications this knowledge will have on public health policy. The pre-conception period is a growing area of research. How long before our baby planning starts years, not months, in advance? Will we see breast milk microbiome-friendly stickers appear on products in years to come?
For those reading this who are planning for a baby and wondering what they can do now to improve things, BoobyBiome's advice focuses on supporting your overall health: "As we learn more, discussions about how to optimise the breast milk microbiome could become just as common as conversations around gut health today, shaping future recommendations for maternal and infant well-being."
Research is coming
Up until fairly recently, we didn’t know much about breast milk. While researchers initially overlooked it, recent studies have made significant discoveries.
The INSPIRE study by the University of Idaho sequenced breast milk samples globally, revealing differences between developed and developing countries' milk microbiomes. This suggests the potential need for geographically tailored supplements, though more research is needed to understand their impact on gut integrity and immune system development.
The Canadian CHILD cohort study found that infant feeding methods, such as expressed versus directly breastfed milk, influence the breast milk microbiome.
Additionally, the UK-based Baby Biome Study identified three distinct microbiome types in early infant stool samples. Building on this, the C-GULL study in Liverpool, which began in April 2023, reviews breast milk and stool samples from 10,000 mothers and infants.
"These studies, along with our ongoing research, are crucial for uncovering the complex interactions between breast milk and the infant gut microbiome, ultimately guiding the development of effective interventions to support infant health," explains Dr Lydia.
Why breast milk and oxygen don't mix
One such complex discovery happened within BoobyBiome's own research.
The team's investigations found that exposure to oxygen during storage destroys many of the beneficial members of the breast milk microbiome.
"We soon realised that creating technology that could fix this would be incredibly valuable—not just in research, but for parents expressing milk at home and hospitals storing donor milk. That's why our first product is a device designed to preserve the breast milk microbiome."
The company is working on a device that will attach to bottles to help preserve the beneficial bacteria.
What's next?
While BoobyBiome's immediate plans focus on milk storage, its long-term ambitions go further than that: "We hope to develop ways to predict which mothers may have milk that lacks key bacterial strains. If we can identify these cases early, we could provide a targeted bacterial supplement to help replenish the breast milk microbiome and ensure all infants receive the microbial benefits of breast milk, regardless of natural variation."
It's safe to say that this supplement will not be your average 'off-the-shelf' pill. The current probiotics market is problematic. Claims are unchecked and under-regulated, profit margins are high thanks to low-quality ingredients, and more is spent on marketing than product innovation. In reality, many brands only contain one strain of bacteria that does not survive the journey to the gut.
BoobyBiome is doing things differently, looking to transform the category: "We're using rigorous research, ensuring that our strains are sourced from breast milk, contain a representative mix of beneficial bacteria, and are paired with prebiotics to support colonisation. In addition, we intend to conduct food intervention studies and clinical trials to prove our solution's efficaciousness against rising infant disease."
Alongside supporting those who choose to breastfeed, the company is also working on a product to support formula-fed babies.
"Our next product is a live bacterial microbiome supplement for formula-fed infants. This supplement will contain a carefully selected blend of the highest-scoring bacteria we've isolated from breast milk, helping to support healthy gut development in babies who do not receive breast milk," explains Dr Lydia.
Spreading the magic
It's extraordinary to think that a readily available but overlooked resource could help us transform infant health.
However, while we wait for these products, whichever way you feed your baby is right for you.
Your mental health as a parent matters, too.
Breastfeeding is hard. Some of us cannot and do not want to do it. That's ok.
Feed is best.
Top three breast milk microbiome facts according to BoobyBiome:
1. Up to 40% of the pioneering bacteria in a baby's gut can come directly from the breast milk microbiome. These microbes help establish a healthy microbiome for digestion, immune development, and long-term health.
2. We still don't fully understand where these microbes that make up this community come from. There are two leading theories:
Retrograde flow from the infant's mouth: This theory suggests that bacteria from the infant's oral cavity are transferred back into the mammary ducts during breastfeeding, with specific species being enriched due to the presence of HMOs and thereby contributing to the breast milk microbiome (Moossavi & Azad, 2019)
Entero-mammary translocation: This hypothesis proposes that maternal gut bacteria are transported to the mammary glands via immune cells, a process known as bacterial translocation, seeding the breast milk microbiome (Rodríguez, 2014).
It is possible that both mechanisms play a role in establishing the breast milk microbiome, but further research is needed to elucidate their relative contributions.
3. The breast milk microbiome is a recent discovery. Until the 21st century, it was widely believed that breast milk was sterile! The discovery of live bacteria in breast milk has completely transformed our understanding of its role—not just as a source of nutrition but as a key contributor to infant gut and immune system development.
About BoobyBiome
BoobyBiome is a UK-based company dedicated to enhancing infant health by harnessing the beneficial bacteria found in breast milk. Founded in 2019 by Dr. Lydia Mapstone, Dr. Sioned Fon Jones, and Tara O'Driscoll, the team combines microbiology, chemistry, and neuroscience expertise to develop innovative products replicating the breast milk microbiome.
References
Zhou H, Sun L, Zhang S, Zhao X, Gang X, Wang G. Evaluating the causal role of gut microbiota in type 1 diabetes and its possible pathogenic mechanisms. Front Endocrinol (Lausanne). 2020 Mar 24;11:125. doi: 10.3389/fendo.2020.00125
Aldriwesh, M.G., Al-Mutairi, A.M., Alharbi, A.S., Aljohani, H.Y., Alzahrani, N.A., Ajina, R., Alanazi, A.M., 2023. Paediatric Asthma and the Microbiome: A Systematic Review. Microorganisms, 11(4), pp.939. Available at: https://doi.org/10.3390/microorganisms11040939 [Accessed 21 March 2025].