Disappearing Microbes: Species Your Grandparents Had That You Don’t
Somewhere in the last hundred years, the Western gut lost something it had carried for hundreds of thousands of years. Ancient bacteria.
Entire species that co-evolved with humans across millennia. They are gone – and the chronic disease epidemic that has grown in their absence may not be a coincidence.
In a series of rock shelters carved into the canyon walls of northern Mexico and the American Southwest, archaeologists found something extraordinary: preserved human faeces, sealed by a layer of adobe, undisturbed for between one thousand and two thousand years.
The scientists who extracted DNA from these coprolites were not expecting to find what they found. In just eight samples from a relatively confined geography and time period, researchers found 38% novel species – genomes that existed in these ancient human guts but had never been recorded in any modern microbiome database.
One species in particular appeared again and again in the ancient samples, as it appears in every traditional human population studied to date on every continent. It is found in the guts of the Hadza hunter-gatherers of Tanzania. In Amazonian communities. In Congolese Pygmies. In Bedouin populations. In the ancient peoples of Rio Zape.
It is almost completely absent from the gut of any person living in a modern Western city.
Treponema succinifaciens was completely absent from Californian samples. Data from Nepali microbiomes showed only partial presence for this microbe, a result suggesting gradual disappearance with increasing industrialisation.
Treponema bacteria are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialised societies.
Symbionts. The word carries weight. Not parasites. Not opportunistic colonisers. Symbionts – organisms that co-evolved with the human host over an evolutionary timescale so long it predates our species, providing functions we have not yet fully characterised, and whose absence we have not yet fully accounted for.
They are gone. And we don’t entirely know what they were doing.
This is the disappearing microbes story. It is, in some ways, the story that all the other gut health stories are about. The probiotic industry, the kombucha market, the personalised microbiome testing sector, the supplement economy worth tens of billions – all of it exists in the shadow of a depletion that none of it can adequately address. Because you cannot buy back what evolution built and industrialisation erased. Not yet. And possibly not ever.
The Numbers That Should Stop You Cold
Begin with the comparison that makes everything else legible.
The Hadza had an average of 730 species of gut microbe per person. The average Californian gut microbiome contained just 277 species, and the Nepali microbiomes fell in between. People with a farming-based lifestyle had an average of 436 microbe species, whereas those who live by foraging had an average of 317.
730 species against 277. The average Western gut carries less than 40% of the microbial diversity of a Hadza hunter-gatherer. Not different diversity – less. A contracted, simplified, impoverished ecosystem, operating on a fraction of the biological complexity with which it was designed.
These are not outliers. The Hadza comparison has been replicated across every non-industrialised population studied. The finding is consistent across continents, cultures, dietary traditions, and methodologies: the more industrialised the lifestyle, the lower the gut microbial diversity. And the lower the gut microbial diversity, the higher the burden of the diseases that define modern Western medicine.
Researchers at Stanford who led the Hadza sequencing study identified 124 gut-resident species vanishing in industrialised populations. Industrialised gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes.
Read that last sentence carefully. The bacteria that have replaced our ancient microbiome partners are not neutral substitutes. They carry genes for oxidative stress adaptation. The Western gut is not simply depleted – it has been colonised by organisms adapted to living in a chronically inflamed environment. The inflammation is not just a consequence of dysbiosis. It may be a condition the new microbial community is adapted to perpetuate.
What the Ancient Record Tells Us
The Hadza comparison is powerful. But it is a cross-sectional observation – a snapshot of two very different populations living very different lives. It is possible, in principle, to argue that the differences reflect genetics, environment, or any number of confounding variables rather than industrialisation per se.
The ancient DNA record makes that argument considerably harder.
The coprolites of Rio Zape – 1,400-year-old preserved human faeces from northern Mexico – contained microbial communities that more closely resembled those of non-industrial societies today than those of modern urban populations. Ancient microbiomes stood apart from their modern counterparts, for example lacking markers for antibiotic resistance. They were notably more diverse, including dozens of unknown species. Treponema bacteria, virtually unknown in the industrialised gut microbiome, were present.
The lead author of the research, Harvard microbiologist Aleksandar Kostic, described the findings with striking directness: the large proportion of novel bacterial genomes in these coprolites suggests that, sometime over the last thousand or so years, there was an “extinction event” in the human gut that eliminated dozens of bacterial species. “These are things we don’t get back.”
An extinction event. The language of ecology, applied to the interior of the human body. Species that co-evolved with our ancestors over hundreds of thousands of years – through every climate shift, every migration, every dietary transition the human story encompasses – eliminated in the blink of an evolutionary eye by the specific conditions of industrial modernity: processed food, antibiotics, sanitised environments, caesarean delivery, formula feeding, reduced physical contact with soil and animals and the microbial complexity of the natural world.
The Hinds Cave coprolites – 8,000 years old, from the American Southwest – showed microbial diversity consistent with what we see in traditional communities today. Diversity that took hundreds of thousands of years to assemble. Diversity that took less than a century of industrial living to dismantle.
The Immigration Experiment: Watching It Happen in Real Time
The archaeological evidence shows us the endpoint. A series of landmark immigration studies shows us the process – the mechanism of loss playing out in real human lives across a single generation.
Researchers at the University of Minnesota studied 514 Hmong and Karen individuals living in Thailand and the United States, including people who had recently migrated and their US-born children. The findings were striking in both their clarity and their speed.
Migration from a non-Western country to the United States is associated with immediate loss of gut microbiome diversity and function, in which US-associated strains and functions displace native strains and functions. These effects increase with duration of US residence and are compounded by obesity and across generations.
Immediate. Not gradual. Not a slow drift over decades. Arriving in the United States was sufficient to begin displacing the ancestral microbial community within months. “We found that immigrants begin losing their native microbes almost immediately after arriving in the US and then acquire alien microbes that are more common in European-American people,” said the study’s senior author Dan Knights.
The children of immigrants had even fewer species of gut microbes than their parents, suggesting the modern US lifestyle was causing each generation to lose more of their ancestral microbial heritage.
This is the multigenerational ratchet. Each generation begins from a depleted baseline. Each generation loses more. The diversity that took hundreds of thousands of years to accumulate cannot be rebuilt by adding a probiotic capsule to a Western diet. It cannot be rebuilt in a generation, or perhaps in several generations, even if the dietary and environmental conditions that allowed it to develop were somehow restored.
The microbiome that your grandparents’ grandparents carried – the one that co-evolved with the human immune system across the entire span of human history – is not available for restoration at £3.99 from the pharmacy shelf.
The Species We’ve Lost and the Functions We Don’t Understand
Treponema succinifaciens is the most documented of the vanished species, but it is far from the only one. The Stanford Hadza study identified 124 species in the process of disappearing from industrialised guts. 44% of the genomes recovered from Hadza microbiomes were absent from existing unified human gut microbiome datasets – organisms so rare in industrialised populations that they had never been systematically catalogued.
We do not fully know what these organisms were doing. That is the most uncomfortable scientific truth at the heart of this story. We know they were there, persistently, across all traditional human populations, across hundreds of thousands of years of human evolution. We know they are gone from the Western gut. We cannot yet specify, for most of them, exactly what functions they performed.
Some researchers hypothesise that Treponema may help rural people digest their high-cellulose diet and protect them from inflammatory diseases of the colon that are common among modern urban populations.
High-cellulose digestion. Protection from colonic inflammatory disease. These are two of the most significant functional gaps in the modern Western gut – insufficient fibre fermentation capacity and elevated rates of inflammatory bowel disease. Both associated with a species that is absent from essentially every Western gut microbiome.
The causal arrow is not fully established. What is established is that Treponema succinifaciens is present in all traditional populations studied, absent from all modern urban ones, and that its disappearance correlates with the emergence of exactly the conditions it may have protected against.
Beyond Treponema, the vanishing microbiome includes species from the genus Prevotella butyrate producers and fibre fermenters that dominate traditional gut microbiomes and are dramatically depleted in Western ones. It includes Succinivibrio, found in hunter-gatherer guts and the intestinal tracts of ruminants, apparently lost entirely from urbanised populations. It includes organisms so novel that they have no named genera, recovered from ancient coprolites and Hadza samples and found nowhere in the catalogued Western microbiome.
The gut microbiome of Western industrial populations is typically characterised by the loss of Treponema and the acquisition of Bifidobacterium as an abundant inhabitant of the adult gut. The factors that favoured this exchange and its health implications remain to be fully defined.
An exchange. The ancient symbionts, lost. A different community, adapted to industrial conditions, taking their place. We have spent enormous resources cataloguing and supplementing Bifidobacterium – the organism that arrived in the Western gut as Treponema departed. The irony is considerable: the probiotic industry has built billions in revenue around a genus whose prominence in the Western gut may be, in part, a symptom of the ecological disruption we should be trying to reverse.
The “Disappearing Microbiota Hypothesis”: The Framework That Changes Everything
In 2012, microbiologist Martin Blaser introduced what he called the “disappearing microbiota hypothesis” – a framework proposing that the chronic disease epidemic of the industrialised world is not primarily caused by what has been added to modern life, but by what has been removed from it.
The disappearing microbiota hypothesis rationalises the emergence of non-communicable diseases by pointing to the depletion of microbial contact in the modern industrialised world, resulting from changes in hygiene, antibiotic use, diet, lifestyle, and living conditions. The strong association between early nutrition and the compositional development of the gut microbiota, both impacting the individual’s later health, invites the idea of next-generation personalised diets based on individual risk circumstances. The NCD epidemic, particularly allergy and obesity, represents a fast-moving target and microbiota modulation may offer an innovative solution to halt it from the outset.
The implications of this hypothesis are profound and uncomfortable. If the chronic disease epidemic is substantially driven by microbial depletion – by the loss of organisms that calibrated immune function, metabolic regulation, and inflammatory response over hundreds of thousands of years of co-evolution – then the medical model built around treating those diseases after they develop is addressing the consequences while leaving the cause untouched.
While gut microbial diversity is decreasing, the prevalence of chronic inflammatory diseases such as inflammatory bowel disease, diabetes, obesity, allergies and asthma is on the rise in Westernised societies. Since the immune system development is influenced by microbial components, early microbial colonisation may be a key factor in determining disease susceptibility patterns later in life.
The diseases are not coincidental. They are not simply the product of poor diet, sedentary behaviour, and genetic predisposition. They are, the hypothesis proposes, the predictable consequences of an immune system calibrated over evolutionary time by a microbial community that is no longer there – a system shaped by relationships with organisms that are now absent, trying to function in an ecological context for which they were not designed.
The epidemiology supports this reading with uncomfortable consistency. Autoimmune diseases are rare in traditional populations and epidemic in industrialised ones. Allergies and asthma follow the same gradient. Inflammatory bowel disease is a disease of industrialisation – virtually absent before the twentieth century, now affecting millions. Type 1 diabetes, multiple sclerosis, rheumatoid arthritis: all rising, all correlated with microbial depletion, all concentrated in the populations with the lowest gut microbial diversity.
What Industrialisation Did, Step by Step
The depletion did not happen overnight. It accumulated across multiple stages, each stripping another layer from the microbial ecosystem:
Dietary transition. The shift from diverse, fibre-rich whole-food diets to ultra-processed, low-fibre industrial food starved the microbiome of the substrates – diverse plant fibres, resistant starches, polyphenols – that butyrate producers, fibre fermenters, and the full ecological guild of ancient gut bacteria depended upon. The dramatic shrinkage of individual gut microbiome diversity in Western urban populations depicts a maladaptive microbiome state that has been supposed to contribute to the rising incidence of chronic non-communicable diseases, such as obesity, diabetes, asthma and inflammatory bowel disease. The reduction in quantity and diversity of Microbiota-Accessible Carbohydrates in the diet has been considered one of the leading causes of the disappearing microbiome in Western urban populations.
Antibiotics. As documented in a previous article in this series, broad-spectrum antibiotics eliminate entire microbial guilds, reshape the gut ecosystem, and – with each successive course – push the microbiome further from its ancestral configuration. Tens of millions of courses prescribed in the UK annually. The cumulative disruption, transmitted across generations, has no parallel in evolutionary history.
Sanitisation. The removal of soil, animals, and environmental microbial complexity from Western lives – through sanitised water, indoor environments, reduced contact with nature – eliminated the continuous microbial inputs that replenished and diversified the gut ecosystem throughout human evolutionary history. The elimination of essentially all complex eukaryotic symbionts, including helminths and protists, from the human gut ecosystem in Western countries through sanitation technology has had a significant impact on microbiota community composition. Whether by sanitation or by antibiotics, elimination of species from the gut ecosystem induces a change in niche space utilisation by remaining species.
Birth and infancy. Caesarean section rates above 35% in the UK deprive infants of the maternal vaginal microbiome that constitutes their founding microbial community. Formula feeding eliminates the prebiotic oligosaccharides in breast milk that specifically nourish Bifidobacterium and other key early colonisers. Early antibiotic exposure shapes the infant microbiome during its most critical developmental window. Each of these insults, individually modest, accumulates into a profoundly altered starting point.
Each generation beginning lower. The Hmong and Karen immigration data makes this visible in a single lifetime: diversity lost from parents is not recovered by children. It is compounded. Each generation of Western children begins from a more depleted baseline than their parents, inheriting not just a genome but a diminished microbial ecosystem passed through the maternal microbiome, through birth, through early feeding.
The Ecological Analogy That Makes It Legible
The most useful way to understand what has happened to the Western gut microbiome is through the lens of macro-ecology – the science of ecosystems, not the science of medicine.
A healthy forest ecosystem is characterised by diversity: multiple species occupying distinct ecological niches, performing distinct functions, checking each other’s population dynamics, maintaining resilience through redundancy. Remove the apex predators and the prey species explode. Remove the decomposers and the nutrient cycle breaks. Remove enough species and the ecosystem shifts to a new, degraded equilibrium from which recovery is extremely difficult.
Loss of microbiota diversity appears as the most constant finding of intestinal dysbiosis. By analogy with macro ecosystems, this may be related to the loss of bacterial predators associated with our modern Western lifestyle. This hypothesis suggests that the reintroduction of bacterial predators in our digestive ecosystem may be an option for improving or restoring gut microbiota diversity.
The Western gut is not a healthy forest. It is a degraded ecosystem – its apex species gone, its ecological niches occupied by organisms adapted to the degraded conditions rather than the conditions for which the system was designed. The inflammatory signals that characterise Western dysbiosis are not simply the absence of protection. They are the positive presence of a microbial community adapted to chronic inflammation, shaped by the conditions of industrialised life, producing the outputs of a disturbed ecology rather than a balanced one.
Can It Be Reversed?
Here is where the science reaches its most honest – and most humbling – limit.
The short answer is: we don’t know. We do not know whether the species lost from the Western gut can be restored, because we have not yet developed the tools to restore them. The organisms that have disappeared are, in many cases, so oxygen-sensitive that they cannot be cultured in conventional laboratory conditions. Faecalibacterium prausnitzii – the most important butyrate producer in the human gut – dies within minutes of exposure to atmospheric oxygen. The organisms in the vanishing Treponema guild have never been successfully cultured from human gut samples at all.
You cannot supplement what you cannot culture. You cannot restore an ecosystem from an organism you cannot grow.
FMT – faecal microbiota transplantation – represents the most direct available approach to ecosystem-level microbiome restoration. The evidence for FMT in C. difficile infection is exceptional. The evidence for its use in broader dysbiosis-related conditions is accumulating but not yet conclusive. And FMT from industrialised donors transplants an industrialised microbiome – it does not restore the ancestral community. FMT from non-industrialised donors is theoretically more relevant but practically, ethically, and logistically complex.
What is achievable – what the evidence does support – is a meaningful movement in the right direction. Not restoration of the ancestral microbiome. But significant improvement in diversity, function, and the abundance of key species, through interventions that are available now:
Dramatic increase in dietary plant diversity – the most consistent predictor of gut microbial diversity in every population studied. Not just fibre quantity, but diversity: different types of fibre from different plant sources feeding different microbial guilds. The Hadza eat 600 or more distinct plant species across a year; the average British adult eats fewer than 20.
Reduction in ultra-processed food – which directly suppresses microbial diversity through its combination of low fibre, high sugar, emulsifiers, and preservatives, several of which have documented disruptive effects on the gut microbial community.
Exposure to the natural environment – soil contact, time in nature, reduced sanitisation of the domestic environment – which provides the continuous microbial inputs from the external environment that evolved alongside human gut ecology.
Radical reconsideration of antibiotic prescribing – as explored elsewhere in this series – particularly in childhood, where the microbiome is still being assembled.
None of this rebuilds the lost species. But it slows the loss. It shifts the trajectory. And it creates the ecological conditions under which, if we ever develop the tools to restore the vanished organisms, there might be a gut ecosystem capable of sustaining them.
The Civilisational Stakes
Step back from the individual biology for a moment and consider the scale of what is being described.
Humanity has, in the span of a single century, dismantled a biological relationship that evolved over millions of years. The organisms that calibrated the immune systems of every human who ever lived before the twentieth century – that regulated inflammation, supported metabolic function, protected against the conditions that now kill most people in the developed world – are gone from the guts of their descendants. Not reduced. Not depleted. In many cases, functionally extinct from the Western human gut.
The chronic disease epidemic – obesity, type 2 diabetes, cardiovascular disease, autoimmune conditions, inflammatory bowel disease, the neurological and psychiatric conditions increasingly linked to gut-brain axis disruption — is not simply the product of bad individual choices. It is, in substantial part, the expression of an ecological catastrophe playing out inside the human body, below the threshold of visibility, beneath the level at which any standard medical investigation would think to look.
The gut health industry – probiotics, supplements, fermented foods, microbiome tests – exists at the edge of this catastrophe, selling products that address the symptom without touching the cause, generating billions from the space between what we have lost and what we are trying to replace it with.
We are not going to buy our way back to the Hadza microbiome. The probiotic will not restore Treponema succinifaciens. The £49 capsule will not reverse a multigenerational extinction event in the human gut.
What might begin to reverse it – or at least stop accelerating it – is understanding what has happened clearly enough to stop pretending that the gut health aisle is the solution to a problem that is orders of magnitude larger than anything it was designed to address.
The microbes are disappearing. Some are already gone. The question now is not whether we can have what our grandparents had. It is whether we will leave our grandchildren anything at all.
The Postbiotic Dispatch is published by AYA Biome / The Postbiotic Company. We sit within the gut health industry and we are honest about what that means. This article does not advance our commercial interests – it contextualises them. The postbiotic model addresses what microbial fermentation produces. It does not restore what industrialisation has erased. We think that distinction matters, and we think our audience deserves to understand it.
Key sources:
• Merrill, Carter, Olm et al. (2023). “Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes.” Cell 184.
• Schnorr et al. (2014). “Gut microbiome of the Hadza hunter-gatherers.” Nature Communications.
• Obregon-Tito et al. (2015). “Subsistence strategies in traditional societies distinguish gut microbiomes.” Nature Communications.
• Warinner, Herbig, Mann et al. (2021). “Ancient coprolites reveal extinction event in human gut bacteria.” Science.
• Vangay et al. (2018). “US Immigration Westernizes the Human Gut Microbiome.” Cell.
• Plovier & Cani (2017). “Gut microbiota diversity and human diseases: Should we reintroduce key predators?” Frontiers in Microbiology.
• Blaser MJ (2014). Missing Microbes. Henry Holt & Company.