Humans are hosts to one of the greatest mass extinctions known to earth – and it’s happening inside our gut. Our gut is home to trillions of bacteria, collectively known as the microbiota. Microbes are responsible for many bodily functions, both good and bad. We’ve all heard of some bad microbes, namely E. coli and C. difficule. These microbes can wreak havoc on our intestinal tract and cause us to get sick. However, we also have good microbes that have important jobs like digesting fibrous foods, providing us with energy, and boosting our immune system.

Over the last decades, we have lost diversity in the types and species of microbes in our gut. Scientists have shown that loss in microbe diversity leads to major health issues: obesity, diabetes, cancer, and autoimmune diseases. What is causing microbes to go extinct inside us? There are many reasons why this is happening, including the use (or misuse) of antibiotics and our diet.

In the early 20th century, diseases caused by infectious bacteria were common (think: cholera, pneumonia, syphilis). Scientists and doctors knew they had to find a way to kill off bad bacteria to cure the disease.  In 1928, Alexander Fleming earned the Nobel Prize for discovering penicillin, which was coined as “the single greatest victory ever achieved over disease.” Since his discovery, there has been a revolution: the use of antibiotics in medicine has saved millions of lives. However, using antibiotics is a lot like “throwing the baby out with the bathwater.” Meaning, antibiotics kill the beneficial microbes as well as the harmful microbes.  

Scientists today are learning that antibiotics are being over-used and mis-used, which is destroying our gut microbes. Our gut is like a rainforest ecosystem – under normal conditions, organisms live, grow, and die in balance. Now imagine the same rainforest is burnt by a fire.  The fire kills off anything in its path, regardless of the plant species or type. Similarly, antibiotics  generally do not regard the types of microbes they are killing, which leads to greater destruction inside our gut ecosystem. 

Studies found that children exposed to antibiotics early in life had lower diversity in their gut and increased risk of asthma and other allergy-related problems later in life. Other studies showed that people with lower microbial diversity had higher risk of inflammatory bowel disease, obesity, colorectal cancer, and diabetes. While some microbes are resistant to antibiotics, and others can bounce back after antibiotics, studies found that even short-term and low-dose antibiotic use can cause some microbes to go completely extinct.

In our modern world, antibiotics are not the only cause for the mass extinction of our gut microbes. Our diet, specifically the Western diet, is causing us to lose diversity inside our gut. The Western diet is high in fat and sugar, low in fiber, and less diverse in fruits, vegetables, and grains. With the agricultural boom and shift to monoculture over the last few centuries, we are now more likely to eat the same staple foods (think: corn, wheat, potatoes, rice, soy). Our gut microbes are highly sensitive to changes in our diet and a decrease in diversity of what we eat causes a decrease in diversity of our gut microbes. In addition, the Westernized diet is low in fiber. Fiber is the fuel for our gut and a diet rich in fiber increases our gut microbial diversity. Highly processed foods (think: refined grains, packaged or canned foods, bacon/sausage, and soda) may also contribute to loss of gut microbes. Diets high in fat and sugar help to feed the bad microbes while pushing out the good microbes. Having a diverse population of microbes means we have many players in the game that can help us fight off any bad microbes that want to invade our gut.

Across the world, researchers are coming together to save our microbes from extinction. Dr. Maria Gloria Dominguez-Bello of Rutgers University and her colleagues are creating a type of microbe bank. Known as the “Microbiome Vault”, this project aims to conserve “the diverse microbiota to ensure long-term health for humanity.” The goals of this project are to foster collaboration between researchers, global non-profits, and non-governmental foundations, to build and maintain a vault of microbes important to humans, and to create working collections of microbes to be kept for future use. With the efforts of those like Dr. Dominguez-Bello, it may still be possible to save our microbes before they become extinct.

Peer edited by Aaztli Coria

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