Old assumptions about human breast milk are giving way to new thinking about microbes in milk and their role in children’s health and our immune systems.


It happened again, most recently at a conference in Prague. After she gave her talk, a scientist came up to Shelley McGuire, a pioneer exploring the microbial communities found in human breast milk, and told her, You don’t know how to take a sample. Your samples must have been contaminated. Human milk is sterile.

McGuire, a professor of human nutrition at Washington State University, knows differently: She’s seen the microbes with her own eyes. But she understands the shock some feel when long-held assumptions are challenged. The realization that our health and well-being depend on vast communities of microbes hanging out in our most intimate areas has been something of an eye opener for a lot of researchers.

“It’s like a whole new world,” McGuire says.

Microbial communities—microbiomes—are everywhere. They are in our mouths, eyes, gastrointestinal tracts, and sex organs. Microbes cover our skin, swarm through air and water, and invest our soils with life-giving properties that feed the plants that feed us. Our gut microbes help us extract nutrients from our food, protect us from disease, and probably affect our moods and immune systems. Microbial communities in soil are plants’ metabolic partners and, as well, are able to sequester toxic metals and other materials, keeping them out of our food supply. Microbiota in air and water, meanwhile, perform critical environmental services that researchers are only now beginning to understand.

The names of bacteria found in the breast milk and other micro-biomes scroll forth like the personae dramatis from some ancient Greek play: Streptococcus, Staphylococcus, Pseudomonas, Serratia, Corynebacterium. One figure that gets bandied about is that human cells are outnumbered ten to one by our microbial partners. While that figure is almost certainly too high—it’s probably more like one to one—it hardly matters. We are not so much individuals as supraorganisms or, as microbial ecologist Larry Forney argues, we are each an ecosystem. “We’ve coevolved with these organisms,” he says.

Forney, a professor at the University of Idaho who works closely with colleagues at WSU, says that our rapidly increasing awareness of the importance of microbial communities to our health is due in part to technological advances. Before the advent of fast, cheap genome sequencing, we simply didn’t have a way to tell which microbes were doing what.

Another issue, in Forney’s view, is that we’ve been studying microorganisms one at a time. When Forney consulted with Proctor and Gamble on toxic shock syndrome and the role tampons play in creating a pathogenic environment, he first asked, “What bacteria are normally found in the vagina?” Proctor and Gamble scientists, he says, “like many others, were focusing on a specific pathogen that causes disease—and they were studying the hell out of it. But if you don’t know what healthy is, you’re going to have a hard time understanding what not healthy is.

“One way to think about these bacteria is that they really represent part of your innate immune system,” Forney says. Inoculation with that extended immune system begins, if not before, then certainly with the passage through the birth canal, where infants are blessed with their mothers’ microbes.



Some scientists, such as Forney’s New York University colleague, Martin Blaser, have argued that the increase in the number of C-section deliveries has resulted in a vast uptick in autoimmune diseases, such as diabetes, as well as other chronic conditions, such as obesity and asthma. While cautiously agreeing with Blaser, the author of Missing Microbes, Forney takes a broader view of the development of the human immune system.

“We talk about the natural progression of exposure, both at birth and throughout the early years when the immune system is maturing,” he explains. “There are a lot of things in the hygiene hypothesis—the use of antibacterial soaps and disinfectants, the use of antibiotics, C-sections—that are changing the way the process of community assembly takes place. If you think of it as an ecosystem that is very highly evolved and is repeated with billions of women, then anything you do to change things is like playing with fire.”

While we don’t know for sure when babies’ microbiomes first start to develop, there is some evidence of a microbial community in amniotic fluid and possibly the placenta. But one place a baby can for sure get a good dose of microbes is at a lactating breast.

Together with her husband, University of Idaho lactation biologist Mark McGuire, and WSU anthropologist Courtney Meehan, Shelley McGuire has formed an international team to study what Meehan calls the anthropology of child rearing.

Working in the Congo Basin with hunter-gatherers, Meehan’s work focuses on the early childhood environment, childcare, and nursing. Meehan and the McGuires’ first collaboration took place there, where they sought to understand how the physical and social environment in an Aka village affected the milk microbiome.

“Like a lot of cultures,” Meehan says, “the Aka capture childcare from many people in the community. Social networks are influencing the milk microbiome” as infants are passed around, cuddled, and played with.

The McGuires, Meehan, and their colleagues were among the first to use molecular techniques to show that there are bacteria in human milk.

“But here’s the real paradigm shift,” McGuire says. “When the baby nurses, whatever is in the baby’s mouth actually backwashes into the mammary gland with every suckle.” The suckling baby’s tiny mouth creates a vacuum around the mother’s nipple and when that pressure is released, the outward flow of milk reverses and baby spit gets into the breast. “This has been shown with ultrasound,” McGuire says, adding, “There’s reason to think that maybe the mom and the baby are a sort of supraorganism and that there is cross-talk between their microbiomes.”

Which sounds gross, and maybe even dangerous, except, as McGuire explains, “The big hypothesis is that the baby is playing in and exposed to the environment,” picking up whatever microbes are out there, “so all of those microbes go into the breast. The mammary gland has a very developed immune system, and the immune factors there can be customized to those bacteria [backwashing from the baby, the newly customized immune factors] then go back to the infant via milk.” The infant’s immune system is thus bolstered in ways that tailor it to the local environment.

It’s that supraorganism idea again, says Meehan. There’s you and your “multiple microbial communities,” all working together, “so you are a supraorganism. But we go one step further and put the mom and the baby together. Their bacterial communities are completely related.”

So related are the mother and child’s microbiomes that the one can be used therapeutically to treat the other. For instance, Spanish researchers cultured some of the bacteria in milk, turned it into supplements that were given to breastfeeding women—and cured their mastitis.

Although no one is yet exactly sure how bacteria end up in breast tissue and milk, Shelley and Mark McGuire in a recent paper suggest that there is likely an entero-mammary pathway from the mother’s gastrointestinal tract to her breasts, as well as bacterial exposure through nursing. However it gets there, one thing is sure: lactic acid bacteria—LAB—abound. LAB are also very common in fermented foods, including yogurt, that confer health benefits on their hosts. Human milk is, in other words, probiotic.



Late in the nineteenth century, Élie Metchnikoff noticed that Bulgarian peasants lived longer than average. Already a famous immunologist, and fascinated by microbiology, Metchnikoff figured that deleterious bacteria in the stomach caused aging—but that they could be controlled by lactic acid. The Russian scientist figured it must be the LAB-rich yogurt the Bulgarians were regularly eating that kept them healthy beyond their years. Metchnikoff himself religiously drank sour milk, and published his theory in The Prolongation of Life: Optimistic Studies in 1908—the same year he won a Nobel Prize for his work on immunity.

Ünlü Gülhan, an associate professor in the WSU/UI Bi-state School of Food Science, has studied lactic acid bacteria for years and, in the past few, has turned her attention to a popular fermented food from her native Turkey: kefir, “the champagne of the Caucasus,” as the late, great biologist Lynn Margulis called it.

Kefir is one of many fermented milk products popular all over the world. Traditional Turkish kefir is started with kefir grains, an admixture of 30 or more species of bacteria and yeast bound up in a matrix of sugars called kefiran. Kefir grains look like cottage cheese, like something bubbling and boiling, which may be the source of the word kefir which, in ancient North Caucasian, means “foam.” Before drinking, the grains are strained out of the fermented cow, sheep, or goat milk and, like mother of vinegar or sourdough starter, used again in the next fermentation.

But how do probiotics work? While still an area of intense study, at least one of the basic premises is simple. LAB “colonize the same space as pathogens and compete for the same nutrients,” Gülhan says. The good lactic acid bacteria simply outcompete pathogenic species.

LAB do much more, say Gülhan and her colleagues. LAB produce natural antimicrobials which, among other things, kill competitors like H. pylori, which can cause ulcers and gastric cancer; are anticarcinogenic (LAB kill cancer cells in vitro, and slow cancer cell growth in vivo); reduce cholesterol by various mechanisms; and bolster the immune system by increasing concentrations of immunoglobulin E, which binds allergens, thus deactivating them.

Kefir’s microbial content varies enormously across geographic space as well as by production method. The kefir we can buy in the United States is probably not nearly as diverse in microbes as the homemade kefir Gülhan grew up with—but that doesn’t mean kefir, yogurt, and other probiotic foods are less effective. Gülhan does point out that to get the benefit of lactic acid bacteria in our GI tracts, we need to consume probiotic foods several times a week, at least.

As with the diversity of probiotic foods, the mammary microbiome also shows considerable variation in the composition of communities in individual women. This brings to mind Larry Forney’s question: How do you know what unhealthy is if you haven’t yet been able to determine what health looks like? The McGuires “urge the clinical and public health communities to be patient…in order to allow human milk and lactation researchers to first understand what constitutes ‘normal’ in terms of the milk microbiome (as well as factors that impact microbial community structure) prior to jumping the gun to investigate if and how this important source of microbes impacts maternal and infant health.”

In short, says Mark McGuire, the milk microbiome is “very personalized.”



What, then, is a healthy microbiome? Is there a “normal” environment in the breast, the gut, the vagina? Is it simply the average of a given population’s condition? For WSU population geneticist Omar Cornejo, these are not just philosophical questions.

“The way I came to the world of microbes is that I was working on basic population genetics questions but I wanted my work to be applicable to something that could help society,” the Venezuelan scientist says. He’s worked on malaria as well as bacteria found in a watery environment: the human mouth.

Streptococcus mutans causes cavities in human teeth, but it hasn’t always done so. Dental caries caused by S. mutans only appeared about 10,000 years ago, Cornejo says, when humans developed agriculture.

“The adaptation to the new environment, which was influenced by diet, was not by single nucleotide substitutions, which is what we are used to seeing, but by the acquisition of new genes,” says Cornejo. “Of the new genes that were horizontally transferred [shared without mating] to S. mutans, about 70 percent were involved in carbohydrate metabolism, low pH resistance, oxidative stress”—all the issues S. mutans had to deal with after the change in human diet.

Cornejo and his colleagues figured this out with sophisticated statistical techniques and huge genomic and demographic data sets. So, for instance, the differences between two populations—of people or of microbes—can be determined by looking at allele frequencies. An allele is a variant form of a gene, a region of DNA that controls a specific trait. By analyzing the interplay of alleles, Cornejo can generate results that reveal the range of variation and relatedness between populations, as well as locate the point in time when certain traits changed.

What Cornejo wants to know is, “How much variation should we expect to see? What is healthy? What is normal?” He’s collaborating with University of Idaho microbiologist Forney to try to answer those questions. “We tend to define ‘healthy’ by what we perceive as the norm,” Cornejo says. But the norm can be misleading. “We know we have a very high proportion of overweight individuals in the population.” If we took the average weight of Americans as normal, and thus healthy, “we would be in trouble!”

Forney and Cornejo are investigating how microbial communities provide protection from disease. “We’d like to understand how different community compositions impact getting an STD, for example,” Cornejo says. Some compositions are more protective than others, and the composition of the community is very sensitive to changes in the local environment.

“What we are seeing,” Cornejo says, “is that whatever a single pathogen was doing, especially with bacteria, it is very relevant to who else is there, because what they are doing is going to change in the context” of the entire microbial community.

Cornejo says there are two primary contexts that affect the constitution of a microbial community. “One,” he says, “is the context created by other bacteria.” The other is the host—us, bacteria’s human partners.

Humans are “very similar but there are important differences among populations and regions. We respond differently to drugs. We have differences in our ability to respond to parasites.”

Most Europeans, for instance, don’t have the antigen receptor that blocks one of the parasites that causes malaria, whereas many African populations, because of a variation in an allele called duffy, do have that immunity.

Once we start to get a grip on those two components of contextualized health, “we start putting all these pieces together. We can put together the genetic composition of the host, the microbiome composition,” and all its genetic variation, “and the presence or absence of pathogens and start to ask, ‘How does that all add up to what we call disease?’”

Cornejo and Forney are launching themselves into what one writer called the invisible universe of microbial “dark matter.” What they find likely will, as Shelley McGuire says, “change everything.”

It’s an exciting time to be a biologist, a nutritionist, or a medical researcher, she says. “Now that we know nothing is sterile, we have to redo decades of work and relook at it with a microbiome lens on.”

Web extras

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