We’ve Lost Half of Our Gut Bacteria. Let’s Talk About the (Inner) Climate Crisis

We tend to think of climate change as something happening out there—melting glaciers, rising seas, forests under threat. But there’s another ecosystem in crisis, and it’s much closer to home.

Your body is home to a microscopic, teeming world. Trillions of microbes. Thousands of species. An ecosystem as dynamic and essential as any rainforest. And right now, it’s under threat.

Over generations, modern life has reshaped our internal landscape, particularly in Western cultures. Our microbiome hosts just half of the bacterial diversity of our ancestors—and our health is paying the price.¹

So…what happened? And can we fix it? Let’s dive in.

What Happened To the Modern Microbiome?

Industrialization, changing food patterns, and decreased soil quality, to name a few things. Centuries ago, our ancestors ate seasonal, plant-rich diets. Fast-forward to today, and just five percent of adults in the United States are even consuming enough fiber. 

And we’re seeing that reflected in our microbial footprint. Consider how the US microbiome compares to other more rural populations around the world:

• In California, the average microbiome has just 277 microbial species.

• In Nepal, farmer populations have been documented to have 436 microbial species.

• In Tanzania, the Hadza Tribe are host to over 700 microbial species.²

These numbers illustrate just how much our inner biodiversity has been depleted over time—but it also speaks to the fact that in some areas of the world, microbial communities still thrive.

The Cost of Losing Our Inner Biodiversity

Our microbiome is the soil of our health—the bedrock of countless essential systems. It’s the training ground for our immune cells, and a command center for the neurotransmitters that regulate our mood. It fuels our digestion, and touches everything from our metabolic health to our skin.

It’s why these evolutionary shifts have evolved into an ecological disaster for our health:

• Roughly 40% of adults navigate chronic digestive issues. Some studies say that number is as high as two-thirds in the US.^3,4

• Colorectal disease rates are on the rise—increasing by 3% annually for those under the age of 50.⁵

• More than 1 in 10 Americans navigate irritable bowel syndrome, or IBS.⁶

Not All Ecosystems Are Struggling

In some populations across the world, microbial diversity continues to flourish. We call these communities Microbiome Hotspots.

• In Northern Tanzania, the Hadza Tribe eats a plant-rich diet that rotates with the seasons—consuming upwards of 100g of fiber daily. Studies have shown that there are 124 microbial species in the Hadza microbiome that have all but gone extinct in Western guts.⁷

• In Northern Brazil and Southern Venezuela, the Amazonian Yanomami have the most gut diversity ever recorded in humans: nearly double that of the average American.⁸

• In Okinawa, Japan, there’s a particularly large population of centenarians. Studies have found that elderly women there have high levels of Akkermansia: a gut microbe linked with resilience and longevity.⁹

• In Finland, researchers found that children who had daily interactions with soil and plants increased their microbial exposure by 8 times.¹⁰

These Microbiome Hotspots remind us of a simple truth: Like all ecosystems, our microbiome is resilient and adaptable. And these populations provide a blueprint for how we might recultivate the diversity that we lost.

How Do We Rebuild Our Inner Biodiversity?

Here’s the good news: You don’t have to cross an ocean to change your microbiome for the better. Here’s what we can learn from the Microbiome Hotspots:

1. Eat seasonally. Consider this your excuse to hit up your local farmer’s market every week. (Better yet, try your hand at growing something in your yard or even on your windowsill.)

2. Diversify your fiber. Different gut bacteria live in different areas of your gut, fuel different health benefits, and have different food preferences. In other words, getting a wide variety of different plant and grain types on your plate is a great way to feed that natural biodiversity. (A prebiotic fiber supplement can help tip the scales, too.)

3. Spend time in nature. Our microbiome isn’t just influenced by what we eat. Research shows that we can shift it by other habits, too—and that includes exposure to the great outdoors.¹¹

4. Be consistent. These changes don’t happen overnight. It’s the result of sustained habits and lifestyle shifts. When you consistently feed your microbiome, it adapts—and the health benefits start to grow.

The modern world has reshaped our inner ecosystems, quietly and gradually. And we’re left with an inner world that’s less resilient than it once was.

But it isn’t a lost cause. Because unlike many ecosystems in decline, this one lives within you. It responds to how we nurture it: more plants, more variety, and more consistency.

When we restore balance at the root, the effects ripple outward—into how we feel, how we function, and how we live.

REFERENCES:

1. Moeller A. H. (2017). The shrinking human gut microbiome. Current opinion in microbiology, 38, 30–35. https://doi.org/10.1016/j.mib.2017.04.002

2. Conroy, G., A7F2375E-BB3B-4896-8F706A83EEA765D7, /Author/Nature-Magazine/, 7Ek1B681o6mb6QOBg14RKO, magazine, N., Nature-Magazine, First published in 1869, N. is the world’s leading multidisciplinary science journal. N. publishes the finest peer-reviewed research that drives ground-breaking discovery, & Partner. (2024, February 20). Modern hunter-gatherers have thriving gut microbiome, compared with Californians. Scientific American.

3. Reed, C. (2026, April 13). New survey finds forty percent of Americans’ daily lives are disrupted by digestive troubles. American Gastroenterological Association. https://gastro.org/press-releases/new-survey-finds-forty-percent-of-americans-daily-lives-are-disrupted-by-digestive-troubles/ 

4. Almario, C. V., Ballal, M. L., Chey, W. D., Nordstrom, C., Khanna, D., & Spiegel, B. M. R. (2018). Burden of Gastrointestinal Symptoms in the United States: Results of a Nationally Representative Survey of Over 71,000 Americans. The American journal of gastroenterology, 113(11), 1701–1710. https://doi.org/10.1038/s41395-018-0256-8

5. Colorectal cancer facts & figures 2023-2025. (n.d.). Cancer.org 

6. Ali, A., Shah, A., Amina, A., Ruddock-Scott, Z. A., Shah, Z., Rios, V. L., Abid, N., Gul, N., Khan, K., & Faisal, S. (2025). Prevalence of Irritable Bowel Syndrome Symptoms and Associated Risk Factors Among Medical Students. Cureus, 17(4), e82900. https://doi.org/10.7759/cureus.82900

7. Carter, M. M., Olm, M. R., Merrill, B. D., Dahan, D., Tripathi, S., Spencer, S. P., Yu, F. B., Jain, S., Neff, N., Jha, A. R., Sonnenburg, E. D., & Sonnenburg, J. L. (2023). Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes. Cell, 186(14), 3111–3124.e13. https://doi.org/10.1016/j.cell.2023.05.046

8. Clemente, J. C., Pehrsson, E. C., Blaser, M. J., Sandhu, K., Gao, Z., Wang, B., Magris, M., Hidalgo, G., Contreras, M., Noya-Alarcón, Ó., Lander, O., McDonald, J., Cox, M., Walter, J., Oh, P. L., Ruiz, J. F., Rodriguez, S., Shen, N., Song, S. J., Metcalf, J., … Dominguez-Bello, M. G. (2015). The microbiome of uncontacted Amerindians. Science advances, 1(3), e1500183. https://doi.org/10.1126/sciadv.1500183

9. Morita, H., Ichishima, M., Tada, I., Shiroma, H., Miyagi, M., Nakamura, T., Tanaka, H., & Ikematsu, S. (2021). Gut microbial composition of elderly women born in the Japanese longevity village Ogimi. Bioscience of microbiota, food and health, 40(1), 75–79. https://doi.org/10.12938/bmfh.2019-055
   

10. Roslund, M. I., Puhakka, R., Grönroos, M., Nurminen, N., Oikarinen, S., Gazali, A. M., Cinek, O., Kramná, L., Siter, N., Vari, H. K., Soininen, L., Parajuli, A., Rajaniemi, J., Kinnunen, T., Laitinen, O. H., Hyöty, H., Sinkkonen, A., & ADELE research group (2020). Biodiversity intervention enhances immune regulation and health-associated commensal microbiota among daycare children. Science advances, 6(42), eaba2578. https://doi.org/10.1126/sciadv.aba2578

11.  Sobko T, Liang S, Cheng WHG, Tun HM. Impact of outdoor nature-related activities on gut microbiota, fecal serotonin, and perceived stress in preschool children: the Play&Grow randomized controlled trial. Sci Rep. 2020 Dec 15;10(1):21993. doi: 10.1038/s41598-020-78642-2. PMID: 33319792; PMCID: PMC7738543.