Missing Microbes

Why do so many people in industrialized Western societies have unhealthy microbiomes that lack diversity?

Picture this: Trillions of microorganisms are actively swimming around inside your stomach, your intestine, your colon—your gut. Around 1,000 species of bacteria alone naturally live inside the human gut, and there are lots of other microorganisms as well. Together, these species make up our gut microbiome, communicating with our cells to help us digest food, modulate our immune system, and protect us from infection.

If you were to lose a handful of those species, you could expect significant consequences for your health and physiological functions. You might have a bad stomach ache, for instance, and over time be predisposed to developing inflammatory bowel disease (IBD) and stomach cancer. But what if you were to lose 50 or even 100 species? That would seem catastrophic. So what to do about the fact that at this very moment, 124 gut microbiome species are in the process of disappearing from the human gut? 

It turns out that our industrialized lifestyle is at the root of this loss. The last 50–100 years have been marked by major industrial advances and a shift towards urbanized living in our Western world. This new lifestyle is characterized by highly processed foods with excessive amounts of sugar and fat, an increased use of antibiotics, and a move from natural environments to polluted and stressful settings.

The result of this change is that our inner system is silently collapsing—our microbiome stock is dying out, causing a destructive chain reaction throughout our bodies.

How many more microbial martyrs will we lose to our Western ways? When will our bodies say, “Enough is enough,” unable to function in the face of this disappearing act? 

We’ve evolved to live in harmony with the microbes that inhabit our bodies. Indeed, considering the balance between microbial and human cells, our nature is as much microbial as it is human. Everything we eat, our microbes eat. 

However, this complex ecosystem that developed over tens of thousands of years of human evolution was subjected to the rapid changes posed by industrialization in the last two centuries. Antibiotics, processed foods, insufficient amounts of fiber, other elements of our industrialized diet, and our largely sedentary lifestyles are causing disruptions in this delicate ecosystem. 

The last of the hunter-gatherers

What happens when the intricate, long-standing partnership between microorganisms and human cells begins to unravel? 

Matthew Carter, a PhD candidate at Stanford University, conducted a study that identified the 124 gut microbiome species that are disappearing from the guts of people in industrialized societies. His research looked at the gut microbiomes of the Hadza in northern Tanzania, one of the world’s last remaining populations of pure hunter-gatherers, comparing their gut microbiomes to those of people in Nepal and California.

With approximately 1,300 tribe members, the Hadza have no domesticated livestock, and they do not grow or store their own food. This population survives by catching and gathering its own food with handmade bows and arrows and foraging for edible plants. The Hadza diet is primarily plant based, with additions of meat, fat, and honey, and completely free of processed foods.

The diversity of the gut microbiome found in the Hadza is thought to be the ancestral state for humans. The shift to a Westernized lifestyle has led to an altered gut microbiota in industrialized populations, with decreased diversity of distinct microbes. 

Two distinct sets of microbe classes have been linked to industrialized and non-industrialized populations. The VANISH (volatile and/or associated negatively with industrialized societies of humans) microbes include species from the families Prevotellaceae, Spirochaetaceae, and Succinivibrionaceae, which are highly prevalent in the gut microbiota in traditional populations, such as the Hadza. But these species are now absent in industrialized populations.

“There’s no way to get them back,” says Carter. That’s because our modern diets lack the necessary nutrients to reintroduce them into our guts and maintain them. While the VANISH microbes have disappeared from the Western gut, a second set of microbes has prospered, and they are more abundant than ever in the American gut. These microbes are fittingly called BloSSUM, for bloom or selected in societies of urbanization/modernization. 

But things are starting to change for the Hadza. Carter says that when the Hadza’s fecal samples for this study were collected, they were more independent. Their land is increasingly encroached upon, and as they are experiencing increased contact with outsiders, contemporary settlements, and modern farming practices, those exposures may influence the lifestyle of the Hadza. Could this lead to the permanent disappearance of these VANISH organisms in the human gut altogether? 

“We now have all these BloSSUM species and we’ve lost these VANISH ones,” says Carter. He says it’s hard to say whether these species are good or bad. For example, one of the BloSSUM species is the Akkermensia muciniphilia. It has been studied for its ability to modulate and interact with our immune system, potentially helping people with cancer better respond to treatment, for instance. And now some companies have begun to sell it as a probiotic. 

But why did we acquire this organism? Carter wonders if it’s truly a good thing that it has blossomed. “Who knows?” he says.

Thus, the dilemma of modern American life: Even as we are surrounded by every fast and modern high-tech convenience, we are seeing a progressive and irreversible reduction of healthy gut bacterial diversity. That’s coupled with a rise in harmful bacteria strains, increasing our vulnerability to inflammation and infections, and strains whose functions remain unknown. The low-fiber Western diet is one of the main drivers of this microbiome loss. The fiber we eat nourishes the microbes that live in our guts, but if we don’t feed them enough, they end up dying. 

What does this mean for our health, for our lives? 

A Hadza hunter in northern Tanzania. Arnold Tibaijuka, CC BY-SA 4.0

Groups around the world are studying the health implications of this shift in microbiome composition. While obesity, high cholesterol, and cardiovascular disease have long been major health concerns, far graver dangers lurk in the shadows. 

There is increasing evidence that this shift is directly associated with the rise in other chronic, non-communicable diseases. 

“We’re living through generations of rather large reduction of microbes compared to the populations where they’ve maintained a higher diversity of fiber in their diet,” says Edward Deehan, a researcher who specializes in microbiome studies at the University of Nebraska-Lincoln. He says our reduced fiber intake is preventing us from supporting our natural beneficial community of microbes and that if we don’t change the way we eat, things are going to get worse. Without fruits and vegetables and whole grains in our diets, we cannot support a healthy gut ecosystem, and the number of chronic diseases will continue to increase. 

Anthony Hannan, a brain researcher at the Florey Institute of Neuroscience and Mental Health in Melbourne, Australia, investigates gene-environment interactions in brain disorders such as Huntington’s disease, an inherited disorder that causes neurons in parts of the brain to gradually break down and die. He stresses the importance of the complex intercommunication between the gut and the brain, saying our altered guts help explain the brain changes we see in Huntington’s. 

Hannan insists that a new idea should never be dismissed out of hand. In the past, Huntington’s disease was believed to be 100 percent genetic, and while it is caused by a genetic mutation to a single gene (HTT or huntingtin), it’s also more complex than that. Researchers no longer view Huntington’s disease and many other neurodegenerative disorders as purely genetic and brain-related, but as complex conditions involving both the brain and the body. In 2000, Hannan’s team was the first to demonstrate the beneficial effects of an environment that is mentally and physically stimulating in a genetic brain disorder and how an enriched environment can delay the onset of Huntington’s.

The same goes for Alzheimer’s and Parkinson’s diseases, says Hannan. While there are genetic aspects of both these diseases, neither is considered purely genetic. Negative factors such as chronic stress and unhealthy diets can act on the brain, and even accelerate the onset of these diseases through gut dysbiosis, which is an imbalance of the microbiome. “Having something like a Western or junk food diet can push the microbiome in certain directions, with particular microbial species that are considered less healthy and diverse, as well as other negative impacts on the body and the brain,” he warns. “We’re completely maladapted to this modern environment of unlimited, highly processed food, as we still have similar bodies and brains to our hunter-gatherer ancestors.” 

Carter of Stanford University says that small differences in the development of the microbiota can lead to big differences into adulthood. “You’re set on this path of how your microbiome will develop over time.”

Hannan warns that a bad lifestyle and negative environmental experiences and exposures in our generation may not stop with us. The negative effects of poorly nurtured microbiomes will be passed on to our children and grandchildren. Recent studies demonstrate that parents’ experiences and changes may be directly transmitted to offspring, influencing them in various ways, potentially making them more susceptible to a range of disorders, particularly those affecting the brain. 

“We could be setting up their health for multiple generations to follow,” Hannan says.

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