Humans Have Lost Many of Our Gut Bacteria

No human is ever truly alone — each of us carries a diverse wealth of bacterial species in our gut, which help digest food, destroy other invading microbes, and regulate the immune system. When these bacteria levels are out of balance, researchers speculate, it can lead to autoimmune disease like multiple sclerosis and Crohn’s disease, or metabolic disorders like obesity and diabetes.

Learn More About Multiple Sclerosis and Gut Bacteria »

Autoimmune disorders are on the rise in Western nations like the United States. One possible explanation is the so-called “hygiene hypothesis”: growing up in excessively clean surroundings makes the immune system hyperactive and indiscriminate, leading it to attack the body by mistake. However, there’s a rival explanation, championed by microbiome expert Dr. Martin Blaser, which says that a depleted gut microbiome is to blame.

You Are What You Eat

New research published in PNAS may shed light on how the microbiome has changed as humans evolved from apes, and changed further as humans split into different cultural groups.


A research team gathered gut bacteria samples from humans in cities in the United States, rural towns in Malawi, and pre-industrial villages in Venezuela, as well as from wild chimpanzees, bonobos, and gorillas.

They found that compared to apes, humans have substantially less diversity in their gut bacteria. Moreover, the amounts of each type of bacteria changed as the human diet shifted: a fivefold increase in the abundance of Bacteroides, which helps digest diets rich in animal protein and fat, and a fivefold decrease in Methanobrevibacter, which helps digest plant materials, for example. There was also a large reduction in Fibrobacter, another plant-digesting species.

“Our results suggest that the human microbiome changed substantially before the rise of modern lifestyles, perhaps even before the rise of agriculture,” said lead author Andy Moeller, a Ph.D. candidate at Yale University, in an interview with Healthline. “Human microbiomes are less diverse than those of our ancestors millions of years ago.”

Read About the Link Between Antibiotics and Obesity »

Greater Development, Fewer Gut Bacteria

Looking deeper into human populations, Moeller found that humans from the United States differ substantially from people from Malawi and Venezuela.

An analysis showed that, in terms of bacterial diversity, the difference between Americans and Malawians was greater than the difference between Malawians and bonobos, suggesting that microbiome divergence and diversity loss are accelerated in Western countries. 

“U.S. human gut microbiomes are unique among human and ape populations,” Moeller said. “Malawi and bonobo microbiomes are distinct, but U.S. human microbiomes are far more divergent.”

I think the proliferation and overuse of antibacterial products in Western societies, and increasingly so in developing countries, is taking its toll on microbial diversity.
Jose Clemente, Mount Sinai

Here’s where the hygiene hypothesis re-enters the game. Part of the reason microbial diversity has suffered in the West, researchers think, is because we use large amounts of bacteria-killing products, including antibacterial soaps and antibiotics.

“It is important to keep in mind that modern lifestyle is radically different to that of our ancestors,” said microbiome researcher Jose Clemente, Ph.D., an assistant professor at the Icahn School of Medicine at Mount Sinai, in an interview with Healthline. “We know diet can affect the types and abundance of different bacteria in the gut. Antibiotics are also powerful modulators of microbial content in the gut, and although they have saved millions of human lives by killing pathogens, their abuse can lead to a substantial depletion of diversity.

“I think the proliferation and overuse of antibacterial products in Western societies, and increasingly so in developing countries, is taking its toll on microbial diversity,” Clemente added.

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The answer is not as simple as taking all the bacteria from, say, a Malawian child and putting it into the gut of an American child. Scientists still don’t know what purpose many of the bacteria in the human gut serve, and whether transferring a particular bacterium to a new host could be harmful.

Clemente said, “We need to think better on how to translate these findings into practical use: can we manipulate the microbiome for therapeutic purposes? What is the most effective way of doing so? Can we change the microbiome permanently, and if so, what are the consequences?”