Microbiome, Modern Life and Hygiene Hypothesis

Microbiome Depletion

Two recent studies reveal that Western diets and hygiene have eradicated a dozens of potentially beneficial bacterial species from our microbiome. One microbe we now lack assisted in metabolizing carbohydrates, other bacteria acted  as prebiotics, while another helped communicate with our immune system.

Scientists believe we may be losing species critical to our microbiome and general health.

In 2009, a team traveled to Venezuela to study the Yanomami, a remote tribe living as hunter-gathers in the Amazon rainforest for over 11,000 years. The tribe previously never had and direct contact with modern life.

Samples were taken from the villager’s fecal matter. The samples were later sequenced to observe which species flourish in the guts of the previously uncontacted tribe.

The researchers were astounded when they discovered the ecological diversity of species found in the Yanomami microbiomes.

As we continue to overuse antibiotics in our daily lives, we lose bacterial species in our guts, which may increase the risk for chronic disease like irritable bowel diseases (IBD), autoimmune diseases, asthma and even cancer.

But, scientists wonder if these two are linked. It's currently not clear whether higher diversity correlates to better health. But, it's also possible that we've lost important bacterial species from our gut that might be contributing to common chronic diseases.

Diet, Antibiotics, and Hygiene

We know that diet plays a major role on the communities of bacteria living in our gut. Unlike Americans who eat large meals all at once, hunter-gathers eat smaller meals throughout the day.

Scientists think there are other reasons than diet that affect our gut microbes, too. For example, the tribe had never been exposed to antibiotics before the researchers studied them in 2009.

Antibiotics are indiscriminate when it comes to the bacteria they deplete, and some of the species will not grow back. Researchers have noticed this is especially true in children that have been prescribed antibiotics. Disruptions to the microbiome at young ages can have major life-long consequences.

Another study observed the microbiomes of Papua New Guinea, who unlike the hunter-gathers in the Amazon rainforest, regularly use antibiotics. However, they still found high levels of diversity within their microbiomes. Researchers found 47 species in the Papua New Guinean’s that were absent in the Americans studied. The Americans on the other hand, only had four species that were missing from the Papua New Guineans.

Antibiotics, hygiene and sophisticated sanitation may deplete the bacterial species living in our gut. However, less diversity in our guts may be a small price to pay for overall improved health. Despite being at lower risk for autoimmune diseases and allergies, Papua New Guineans are actually significantly less healthy than those living in Westernized societies.


Clemente, Jose C., et al. 2015. "The microbiome of uncontacted Amerindians." Science Advances. Vol. 1, no. 3, e1500183 DOI: 10.1126/sciadv.1500183

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