The world is facing an extinction event. Hundreds of species are disappearing from their native habitat. This impending extinction is distinct from the plight of the polar bears or frog populations and is not a result of global warming or deforestation. It’s happening within our guts, which are home to the trillions of microorganisms called the microbiota and the 2 million genes they carry called the microbiome.

Humans are composite organisms — ecosystems made up of human cells together with about 3 pounds of bacteria, our forgotten organ. Over the last decade, science has uncovered just how profoundly our microbiota is wired into our immune system, our metabolism and even our central nervous system. When these connections malfunction, serious disease may ensue.

For the approximately 180,000 years that humans exclusively foraged for food ... their guts [had] up to 50% more bacterial species and twice as many bacterial genes than ours do.

The best evidence that our microbiota is facing an extinction event comes from recent studies of modern-day hunter-gatherers, who provide a window into what our microbiota was like for the approximately 180,000 years that humans exclusively foraged for food. Hunter-gatherers from Tanzania, Venezuela and Peru have a microbiota that is remarkably similar to one another and yet very different from ours in the West. Their guts harbor up to 50% more bacterial species and twice as many bacterial genes than ours do. In comparison, our guts resemble a landscape in decline. Antibiotic use, C-sections, formula feeding and an obsession with hand sanitizer have all been implicated in this decline. But there is one difference that really sticks out: diet.


Modern-day hunter-gatherers eat up to 10 times more dietary fiber than most Americans consume each day. The complex carbohydrates found in fiber are what feed your gut bacteria. Eat a diet rich in fiber — found in vegetables, nuts, whole grains and legumes — and the richness of your microbiome will increase. People with more diverse microbiomes tend to be leaner and have better metabolic function. Conversely, if your diet is poor in fiber, you are starving your microbial self. Even more upsetting: You may also be starving your children’s microbiomes.

Our laboratory recently set out to test whether a lack of dietary fiber could have contributed to the deteriorated microbiota observed in Western people relative to hunter-gatherers. We fed mice a low-fiber diet and “watched” — using DNA sequencing — what happened to their guts. As we had suspected, the number of bacterial species declined precipitously. But when we bred these mice, we were astonished to find that the decline worsened with each subsequent generation.

We should have seen this coming. Much of our microbiota is, in a way, inherited from our mothers as we pass through the birth canal. If a mother’s microbiota is missing species, it follows that her child’s microbiota is also at risk of missing species. Putting the mice back on a high-fiber diet in an attempt to regain these lost species was futile. The damage to the microbiota was irreversible.

Although this study was performed in mice, not humans, it does mirror what we see in humans. Namely, that Westerners with our low-fiber diets are missing bacterial species that the higher-fiber consuming hunter-gatherers have in abundance. Another difference between the study and real life is that the mice were housed in sterile bubbles, while Westerners of course live in an environment filled with microbes. But Westerners take antibiotics on a fairly regular basis and sterilize our environment for fear of exposing ourselves to pathogenic bacteria. These behaviors mean we are reducing the chances of acquiring new beneficial bacteria.


What is the consequence of losing a portion of our microbiota? Hunter-gatherer populations are relatively free from Western diseases. This difference cannot be easily dismissed by the argument that modern medicine, by extending our life span, has “unmasked” diseases that these traditional populations don’t live long enough to experience. Asthma, allergies, Type 2 diabetes and childhood Crohn’s disease are just a few examples of diseases for which the age of onset is creeping ever younger. Nor can longer life spans explain why the childhood obesity rate in the United States is approaching 20%. (Obesity among hunter-gatherer children is non-existent.) Something serious is going on and our microbes may be at the center of it.

Our gut ecosystem is malleable, able to adjust to impulsive dietary choices. However, it appears that this ecosystem is also fragile and that dietary decisions made by one generation could affect the microbial ecosystem that future generations carry around inside them. While we all accept that we pass our genome onto our children, we now must appreciate that we also bequeath our microbiome. How we have cared for this community is not only important for our health, but also that of future generations.

Erica and Justin Sonnenburg run the Sonnenburg Lab at Stanford University and are the authors of “The Good Gut: Taking Control of Your Weight, Your Mood and Your Long Term Health.”

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