What if some of the microorganisms that lived inside our ancestors for thousands of years are gradually disappearing from the human gut?

It's a fascinating possibility, and one that is becoming increasingly difficult to ignore. As our diets, lifestyles and environments have changed, so too have the enormous microbial communities living inside our intestines. Researchers are now discovering that certain microorganisms commonly found in populations following less industrialised lifestyles are remarkably rare, or even undetectable, in many people living in modern industrialised societies.

A new study published in Nature in October 2026 has provided some extraordinary insights into this phenomenon. By examining the gut microbiomes of two geographically distant Indigenous populations, researchers discovered that hundreds of microbial species appear to have accompanied humans through ancient migrations, surviving for tens of thousands of years.

Yet many of these organisms are now disappearing from industrialised populations.

The question is whether this represents a meaningful loss of biological function, or simply a natural consequence of our changing lifestyles.

The Remarkable Microbes That Travelled With Our Ancestors

The researchers examined the intestinal microbiomes of the Hadza, a hunter-gatherer population in Tanzania, and the Tsimane, an Indigenous population in Bolivia whose livelihoods include horticulture, foraging and fishing.

These populations live thousands of miles apart, and their ancestors have been geographically separated for many thousands of years. Yet when scientists examined their intestinal microorganisms using deep genetic sequencing, they discovered something remarkable.

The two populations shared 1,231 microbial species. Approximately 60% of the species identified in the Tsimane samples were rare or absent in the microbiomes of people living in industrialised societies.

The researchers then examined genetic differences between strains of these microorganisms. By analysing patterns of microbial evolution, they found evidence that many of the shared organisms had been associated with humans since prehistoric migrations out of Africa and into other parts of the world.

In other words, some of the microorganisms living inside these populations today may be descendants of microbes that travelled alongside our ancestors tens of thousands of years ago.

This is an important distinction. The researchers were not simply showing that two populations happen to harbour similar bacteria. They identified genetic patterns consistent with ancient microbial lineages being maintained and transmitted across human generations.

It suggests that our relationship with certain intestinal microorganisms may be far older and more enduring than previously appreciated.

How Modern Life Changes Our Microbial Ecosystem

Our intestinal microbiome is influenced by an extraordinary range of factors, including diet, medication, environmental exposure, sanitation, infections and contact with other people.

One particularly important influence is the availability of nutrients that microorganisms can use for growth.

Many intestinal bacteria possess enzymes that allow them to break down complex carbohydrates which our own digestive enzymes cannot process. These include certain dietary fibres and resistant starches found in vegetables, legumes, whole grains and other plant foods.

When these carbohydrates reach the large intestine, microorganisms can ferment them, producing compounds such as acetate, propionate and butyrate.

These short-chain fatty acids perform several important physiological functions. Butyrate provides energy for cells lining the colon and can influence intestinal barrier integrity, while short-chain fatty acids also interact with receptors involved in metabolic and immune signalling.

Different microorganisms specialise in processing different substrates. Consequently, the variety of plant compounds entering the intestine can influence which microbial populations are able to thrive.

In many industrialised societies, dietary patterns have shifted towards lower intakes of diverse plant fibres, alongside changes in food processing and eating habits. These changes may reduce the availability of substrates needed by particular microbial species.

However, diet is only part of the story.

Antibiotics can substantially alter microbial communities, sometimes reducing populations that take considerable time to recover. Improved sanitation and reduced exposure to certain environmental microorganisms may also influence which species are acquired and transmitted.

Even changes in social structure, household composition and contact with animals can potentially affect microbial transmission.

This means that the disappearance of particular gut microorganisms cannot simply be blamed on one food group or dietary habit. It is more likely to reflect a combination of changes associated with modern living.

Can We Actually Lose Gut Bacteria Across Generations?

One of the most interesting questions is whether microbial losses occurring within one generation could affect the next.

A study published in Nature in 2016 explored this possibility using mice colonised with human intestinal microorganisms.

Researchers fed the animals diets containing either plentiful microbiota-accessible carbohydrates or very low quantities of these fermentable substrates.

The low-fibre diet reduced microbial diversity, with certain bacterial populations becoming particularly depleted.

When fibre was reintroduced, some of these changes were reversible. However, when the low-fibre dietary pattern continued across several generations, the researchers observed progressive losses of microbial species that could no longer be restored simply by increasing fibre intake.

Restoring the original microbial community required both the missing microorganisms and the dietary substrates needed to support them.

This was an animal experiment, so it does not establish that the same process is occurring across human generations. Nevertheless, it illustrates an important ecological principle.

If a microorganism becomes extremely rare within a population, it may be less likely to pass successfully between generations. Over time, that organism could disappear from the community altogether.

Once a species has been lost, providing its preferred nutrients may not be enough to bring it back. The microorganism must also be available to recolonise the intestine.

This raises an intriguing possibility: some changes in the human microbiome may reflect not only what we are eating today, but the cumulative effects of environmental and dietary changes experienced by previous generations.

Does Losing Microbial Diversity Mean Losing Health?

This is where the science becomes considerably more complicated.

It is tempting to assume that a microbiome containing more species must automatically be healthier. However, microbial diversity is only one measure of an ecosystem, and it does not tell us everything about how that ecosystem functions.

Different microorganisms possess different metabolic capabilities. Some contribute to the breakdown of dietary fibres, others participate in bile-acid metabolism, while others produce compounds that influence immune signalling or the intestinal environment.

Two people may have similar levels of microbial diversity but very different microbial functions.

Likewise, a microbiome containing fewer species is not necessarily dysfunctional. Some healthy microbial communities are naturally dominated by particular organisms, and the significance of individual species depends upon the wider ecological context.

The crucial question is whether disappearing microorganisms perform functions that are beneficial to human health and cannot easily be replaced by other species.

For example, if a lost microorganism possesses unusual enzymes capable of processing particular plant compounds, its disappearance might reduce the range of metabolites produced within the intestine.

Alternatively, other organisms may be able to perform similar functions, meaning that the overall physiological consequences are relatively small.

The new Nature study provides compelling evidence of ancient microbial associations and substantial differences between industrialised and non-industrialised populations. However, it does not demonstrate that the missing species directly cause chronic disease or that restoring them would improve health.

Those questions remain unanswered.

Could We Restore Our Lost Microbes?

The possibility of restoring disappearing microorganisms is attracting considerable scientific interest, particularly as researchers develop more sophisticated approaches to identifying and cultivating previously unfamiliar bacterial species.

But restoring a microbial ecosystem is considerably more complicated than introducing a few bacterial strains.

Microorganisms exist within complex communities, competing for nutrients, exchanging metabolic products and interacting with their surrounding environment.

A newly introduced species may struggle to establish itself if the conditions required for its survival are absent, or if existing microorganisms occupy the same ecological niche.

This is why researchers are increasingly interested in combining microbial interventions with dietary strategies that provide the necessary substrates for those organisms to thrive.

It also explains why commercially available probiotics should not be viewed as a simple solution to the disappearance of ancestral microbial species. Most probiotic products contain a relatively small number of well-characterised strains, which may have little relationship to the organisms identified in these new studies.

For now, there is no established clinical method for recreating an ancestral human microbiome, nor is there convincing evidence that doing so would necessarily improve health.

What Can We Learn From This for Everyday Nutrition?

Although we cannot currently restore specific ancient microbial communities, there are practical lessons we can draw from the wider research.

One is the importance of dietary variety.

Different plant foods contain different combinations of fermentable carbohydrates, fibres and phytochemicals. Providing a broad range of these compounds may help support a more functionally varied intestinal ecosystem.

Legumes, vegetables, fruits, whole grains, nuts and seeds all contribute different substrates for microbial metabolism.

It is also worth remembering that microbial communities respond to habitual dietary patterns rather than isolated meals. Consistently providing fermentable substrates may be more meaningful than occasionally consuming a particularly high-fibre food.

However, this does not mean everyone should dramatically increase their fibre intake overnight. People with certain gastrointestinal conditions may need to adjust the types and quantities of fermentable carbohydrates they consume, and changes are often better introduced gradually.

Perhaps most importantly, we should resist the temptation to romanticise traditional lifestyles. Non-industrialised populations experience their own health challenges, environmental exposures and infectious disease burdens. Their microbiomes are different, but difference alone does not establish superiority.

What these populations provide is something scientifically invaluable: a window into the range of microbial diversity that humans have historically carried.

The Bigger Picture

For much of human history, we have thought about evolution primarily in terms of changes to our own genes.

Yet humans have never evolved in isolation. We have always existed alongside enormous communities of microorganisms, many of which have travelled with us, adapted to our environments and interacted with our physiology.

The discovery that hundreds of intestinal microbial species appear to have accompanied human populations through prehistoric migrations adds a remarkable dimension to this relationship.

It suggests that some of the microorganisms now disappearing from industrialised societies may represent ancient biological partnerships rather than temporary inhabitants of the gut.

We do not yet know whether their disappearance has meaningful consequences for long-term health. Nor do we know whether restoring them would be beneficial.

But the research raises an important question for nutritional medicine: as our lifestyles have changed, have we altered not only the foods entering our bodies, but also the microbial ecosystems that help determine what those foods become?

Understanding that relationship may prove to be one of the most interesting developments in the future of nutrition and human health.

References

Carter, M.M. et al. (2023) ‘Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes’, Cell, 186(14), pp. 3111–3124.e13. https://doi.org/10.1016/j.cell.2023.05.046

Carter, M.M. et al. (2026) ‘Prehistoric global migration of vanishing gut microbes with humans’, Nature. https://doi.org/10.1038/s41586-026-11106-1

Sonnenburg, E.D., Smits, S.A., Tikhonov, M., Higginbottom, S.K., Wingreen, N.S. and Sonnenburg, J.L. (2016) ‘Diet-induced extinctions in the gut microbiota compound over generations’, Nature, 529, pp. 212–215. https://doi.org/10.1038/nature16504

Sonnenburg, J.L. and Bäckhed, F. (2016) ‘Diet–microbiota interactions as moderators of human metabolism’, Nature, 535, pp. 56–64. https://doi.org/10.1038/nature18846