Gut microbiome serves as a “second brain” regulating our bodies

Our digestive tract contains some 1.5 kilograms of bacteria. This gut microbiome, long overlooked by doctors, has been gaining attention in recent years as scientists discover that its role extends well beyond digestion: these bacteria can influence our immune system, metabolism and even mental health. Yet a lot remains to be learned about how they function.

The gut microbiome is made up of around 1,000 bacteria strains and is the densest and most diverse microbiome in our bodies. “These bacteria perform specific functions based on their metabolism,” says Camille Goemans, a microbiologist and assistant professor at EPFL’s Goemans Lab of Drug-microbiota Interactions, within the School of Life Sciences. In addition to helping us digest fiber, they also produce vitamins, train our immune system, protect our intestines, regulate our weight and metabolism, and keep us in good mental health.

A growing number of diseases seemingly unrelated to our gut – such as allergies, obesity, autism and autoimmune disorders – are now found to be influenced by the microbiome. “These diseases were rare a century ago,” says Goemans. “But allergies, for instance, are now relatively common, and the reason seems to be related directly to our intestinal flora.” She points to manufacturing industries, sedentary lifestyles and modern diets as factors that have likely changed the balance of bacteria in our intestines. But how does the gut microbiome play such an important role in our overall health?

Starting at birth

This microbiome starts to be formed when we’re born. Fetuses initially don’t have a microbiome, as the mother’s womb is a sterile environment. During vaginal delivery, babies acquire their first bacteria from their mother’s vaginal flora, and then pick up more bacteria from their mother’s skin flora during breastfeeding. “Babies delivered through a cesarean section or who aren’t breastfed have less diversity in their gut microbiome, which increases their risk of certain diseases,” says Goemans. Some maternity wards attempt to counter this by wrapping newborns in a cloth containing their mother’s vaginal flora.

The gut microbiome is fully formed by the age of three. It then changes throughout our lives as a result of diet, exercise, stress and illness, not to mention any antibiotics we take that reduce the diversity of the bacteria in our intestines. “The broader the range of bacteria, the better able our gut microbiome is to keep us healthy,” says Goemans.

The broader the range of bacteria, the better able our gut microbiome is to keep us healthy

Changes in our intestinal flora could lead to diseases such as allergies, autoimmune disorders and digestive disorders including Crohn’s disease and irritable bowel syndrome. “When it comes to digestive disorders, genetic factors also need to be taken into account,” says Goemans. “The gut microbiome serves to protect our intestine. If the biome is lacking in some way, this protection becomes less effective, potentially leading to inflammation which in turn makes the disease worse. It’s a vicious circle that makes treatment difficult.”

The gut microbiome, also known as the human body’s “second brain,” can affect mental-health conditions such as anxiety, depression and bipolar disorder as well as neurodegenerative diseases like Alzheimer’s and Parkinson’s. Some of these bacteria produce dopamine, serotonin and other neurotransmitters that interact directly with the brain and nervous system. “These neurotransmitters create feelings of happiness, contentment and well-being. If they aren’t produced properly, our mental health can suffer,” says Goemans. “Patients with mental-health conditions often also have problems with their digestive tract. That’s especially true for people with autism spectrum disorder.”

Medical solutions

Given how important the gut microbiome is to our physical and mental health, scientists are exploring two methods for restoring this microbiome after an illness: taking probiotics and undergoing a fecal microbiota transplant (FMT). “Probiotics are living bacteria found in fermented foods and available as supplements,” says Goemans. However, their efficacy hasn’t been scientifically proven and can vary depending on the bacteria strains and patient in question.

Goemans recommends eating a diet rich in fermented foods (yogurt, sauerkraut, kimchi, kombucha and kefir). The “good” bacteria in our microbiome also need fiber (found in fruit, vegetables and whole grains) to grow. She suggests avoiding sugary processed foods, which encourage the “bad” bacteria to proliferate.

The scientific community is working to define what a healthy gut microbiome is – we still don’t have all the answers.

The other method, FMT, involves collecting a sample of a donor’s healthy microbiome and transferring it to a patient. It’s only used to treat infections of Clostridioides difficile – an antibiotic-resistant bacteria that causes severe diarrhea, nausea and cramps. If left untreated, these infections can be fatal. “But with FMT, the recovery rate is close to 90%.”

However this raises the question of how doctors can identify a healthy microbiome and a suitable donor. “That’s still a mystery,” says Goemans. “The scientific community is working to define what a healthy gut microbiome is – we still don’t have all the answers. Research on this flora is still in the early stages. For example, there are currently no long-term data on how an implanted microbiome develops over time.”

Antibiotics are the microbiome’s worst enemy

At Goemans’ EPFL laboratory, researchers are studying how antibiotics and other drugs affect the various bacteria in our intestines and how these bacteria contribute to antibiotic resistance. “Antibiotics are compounds that kill bacteria to free the body of an infection,” says Goemans. “Those on the market today don’t differentiate between useful bacteria and pathogens. Oral antibiotics often destroy some of the intestinal flora.” In some people the flora is able to recover naturally, while in others, the disturbance tends to last.

Scientists hope to be able to develop targeted treatments that can eliminate an infection without damaging a patient’s entire microbiome. They’re also examining the precise function of each type of gut bacteria. “We need to figure out how the different components interact before we can improve the health of the human body as a whole,” says Goemans.

Goemans believes it’s important to view the human body as a complete ecosystem. A balanced diet and healthy lifestyle are the keys to a properly functioning gut microbiome – and therefore to good physical and mental health. A group of scientists ran an experiment with mice that lacked intestinal flora, to find out just how critical the gut microbiome is. The germ-free mice survived just three days in a normal environment.