Our digestive tract harbors approximately 1.5 kilograms of bacteria collectively known as the gut microbiome. Once overlooked by doctors this complex ecosystem has recently gained scientific attention for its far-reaching impact beyond digestion. Research shows that these bacteria influence the immune system metabolism and even mental health though much remains to be understood about their functions.

Comprising around 1,000 bacterial strains the gut microbiome is the densest and most diverse in the body. These bacteria perform specific roles based on their metabolism says Camille Goemans, a microbiologist and assistant professor at EPFL’s Goemans Lab of Drug-Microbiota Interactions. Beyond aiding fiber digestion they produce vitamins support immune function, protect the intestines regulate metabolism and contribute to mental well-being.

An increasing number of conditions once thought unrelated to the gut such as allergies, obesity, autism, and autoimmune disorders are now linked to the microbiome. A century ago these diseases were rare says Camille Goemans. Today, allergies, for example, are widespread, and the cause appears to be directly connected to our gut flora. She cites industrialization sedentary lifestyles and modern diets as key factors that have likely disrupted the bacterial balance in our intestines. But how exactly does the gut microbiome play such a crucial role in overall health?

Formation of the Gut Microbiome
The gut microbiome begins developing at birth. Since the womb is a sterile environment fetuses do not have a microbiome. During vaginal delivery, babies receive their first bacteria from their mother's vaginal flora and later acquire more from skin contact and breastfeeding. Babies born via cesarean section or who are not breastfed tend to have less microbial diversity increasing their risk of certain diseases says Camille Goemans. Some maternity wards address this by exposing newborns to their mother's vaginal flora using a cloth.

By age three the gut microbiome is fully established but continues to evolve throughout life influenced by diet, exercise, stress, illness, and antibiotic use, which can reduce bacterial diversity. A more diverse microbiome strengthens overall health Goemans explains.

Disruptions in the gut microbiome can contribute to diseases such as allergies autoimmune disorders and digestive conditions like Crohn’s disease and irritable bowel syndrome. Genetic factors also play a role in digestive disorders says Camille Goemans. The gut microbiome helps protect the intestine, but if it lacks diversity this protection weakens increasing inflammation and worsening the disease. It creates a vicious cycle that makes treatment more challenging.The gut microbiome often called the body's second brain influences mental health conditions like anxiety depression and neurodegenerative diseases. Certain gut bacteria produce neurotransmitters like serotonin and dopamine, directly impacting mood and well-being.

To restore the gut microbiome after illness scientists are exploring probiotics and fecal microbiota transplants (FMT). While probiotics from fermented foods and supplements contain beneficial bacteria their effectiveness varies. Goemans recommends a fiber-rich diet with fermented foods while limiting processed sugars to support a healthy microbiome.

Source: https://www.myscience.ch/news/wire/gut_microbiome_serves_as_a_second_brain_regulating_our_bodies-2025-epfl