Press coverage by Derek Davis for earth.com
Every human body carries more bacteria than there are stars in the Milky Way. They coat our skin, line our noses, and swarm through our guts. Scientists who study them say almost no biological process runs without them. Yet most of these microbes have never been named, let alone understood.
That gap is now shrinking. The change comes in part from a decade-long effort to sample and store human microbiomes before industrialized life erases them. The New York Times recently profiled the two biologists behind that project, Mathilde Poyet and Mathieu Groussin. Their globe-spanning quest aims to map biology’s dark matter. The work points to a quieter story underneath the wellness hype. Our internal ecosystems appear to be thinning out, and no one is certain what we lose as they go.
A bank for living microbes
Poyet and Groussin met as postdoctoral fellows at the Massachusetts Institute of Technology. Both kept running into the same wall. Nearly every microbiome sample available to study came from wealthy, Western populations. That meant roughly 90 percent of human diversity was not included.
So they built the Global Microbiome Conservancy. Since 2016, the pair and their collaborators have traveled to Nepal, Iraq, Rwanda, Tanzania, and beyond. They reached some communities on foot and others by boat. By 2024, their lab at Kiel University in Germany held one of the world’s largest and most diverse collections of live gut bacteria.
Storing living microbes is far harder than storing their DNA. Oxygen kills many gut species within minutes of leaving the body, so samples must be processed and frozen fast. But the effort is worthwhile. Live bacteria allow researchers to ask what a microbe eats, what compounds it produces, and how it behaves alongside its neighbors. A strand of DNA alone cannot answer those questions.
Industrial life rewrites the gut
One of the conservancy’s central findings concerns how bacteria trade genes. Microbes are famously loose with their DNA. They pass it not only to their offspring but also to random neighbors, a process called horizontal gene transfer.
In a 2021 study, the team reported a clear pattern. Gut bacteria in industrialized populations swap genes at much higher rates than those in nonindustrialized ones. The genes being exchanged also track with local conditions. In fiber-rich communities, bacteria trade more genes for breaking down fiber. Where antibiotic use is heavy, they swap more resistance genes. In dense cities, they exchange more genes that help them spread between people.
The pattern extends to the whole ecosystem. In communities without indoor plumbing, heavy antibiotic use, or processed food, gut microbiomes tend to be diverse and stable. In industrialized settings, they look more agitated, with faster gene swapping, stronger stress signals, and more inflammation. Fewer species take up residence with each generation.
The thinning runs deep. In Western societies, the gut community of a healthy person can resemble that of someone who is chronically ill.
Healthy is not universal
The easy assumption is that a “good” microbiome looks the same everywhere. The conservancy’s samples suggest otherwise. A statistical model can predict health from gut bacteria in the United States, Canada, or Western Europe. Apply that same model elsewhere, and it falls apart.
Individual species resist tidy labels, too. An abundance of Treponema is normal in some lower-income populations and a warning sign in wealthier ones. Bifidobacterium, associated with better digestion in Western guts, is linked to higher body mass index in Paraguay. Even bacteria linked to optimal health can vary. Akkermansia muciniphila and Faecalibacterium prausnitzii, both known for anti-inflammatory effects, appear at different rates across populations. Groussin’s team suspects the microbiome may be adapting in real time to its surroundings. That would help explain findings that otherwise seem to contradict one another.
That context dependence is a caution for the booming market in gut testing, probiotics, and specialty diets. Many of these products have not been shown to work, and a few fad regimens have made people seriously ill.
What the microbes might do
Even so, specific microbes are yielding real leads. In the lab, Poyet’s team identified a gut microbe that consumes cholesterol before it can build up in the blood. The microbe converts it into coprostanol, a sterol the body poorly absorbs and passes in feces.
The idea has a long history. Researchers described cholesterol-eating gut bacteria as far back as the early 1900s. The species and genes responsible stayed hidden for a century. Work published in 2020 finally tied a family of microbial genes, known as ismA, to coprostanol production. People carrying these microbes had lower cholesterol in both stool and blood. Whether that link can be leveraged for therapy remains uncertain. In the Hadza people of Tanzania, where such microbes are present, heart disease is rare. Untangling that correlation will take years of further study.
Other scientists are mining the same biobank. One team studied children at high risk of obesity. They often lack a gut bacterium thought to help produce GLP-1, the hormone now famous as the target of a new class of weight-loss drugs. The findings echo a wider body of research linking gut bacteria to metabolism, appetite, and disease risk.
Promise, hype, and honest limits
Microbiome medicine remains a mixed record. Fecal transplants are now a standard treatment for stubborn Clostridium difficile infections. Probiotics can help head off the gut upsets that antibiotics sometimes cause. But other much-hyped ideas have fizzled. Vaginal seeding of babies born by cesarean does not significantly reshape the infant microbiome. Nearly two decades of research have failed to produce a bacteria-based weight-loss cure.
Asked what science can say for certain, one researcher offered a modest answer: fiber is probably good for you. It is a fitting summary of a field long on possibility and short on proven fixes.
A shrinking archive
The implications extend beyond any single drug. By 2050, the United Nations projects that about 70 percent of people will live in cities. Urban diets carry more calories and less fiber. As fiber intake falls, microbiomes tend to depopulate and grow more fragile. That is why some researchers now compare preserving them to running a seed bank for an entire microscopic ecosystem.
Poyet and Groussin are careful not to romanticize the communities they visit or to treat microbial loss as inevitable. There is no pure or primitive human state, they note. Assuming these ecosystems are doomed risks repeating old mistakes. They aim not to hoard microbes or chase miracle cures. They want to understand the strange, intimate partnership between humans and the trillions of organisms we carry before that partnership changes beyond recognition.
The 2021 research on gene transfer in industrialized microbiomes was published in the journal Cell.
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