The human microbiome, the collection of bacteria and other microbes that live in our gut (intestines) and other parts of our bodies. A healthy, balanced microbiome can discourage health problems — and that depends on what you eat.

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When it comes to disease risk, are your genes your destiny? Science is increasingly suggesting otherwise. As scientists look for explanations for the roots of chronic disease as well as the connections between nutrition and health, the answer may be in your gut.

“There’s a better understanding of the recipe that brings people from a state of health to a state of disease,” said Alessio Fasano, MD, professor of pediatric gastroenterology and nutrition at Massachusetts General Hospital for Children.

Much of that understanding is centered on the human microbiome, the collection of bacteria and other microbes that live in our gut (intestines) and other areas of the body. Your gut microbiome alone is home to about 100 trillion bacterial cells. This is important, because our genes and our environment interact constantly, and our gut is the largest meeting point.

At the Finding Common Ground conference in Boston last month, Fasano said we inherit two genomes (a complete set of genes and DNA). The human genome has about 30,000 genes and essentially remains unchanged in our lifetime. Our microbiome contains about 150 times as many genes, but changes significantly in response to our diet and lifestyle habits. Because of this changeability, our microbiome affects whether we inherit our genetic “destiny.”

The microbiome you inherit at birth is healthier if you were born vaginally than if you were born via C-section. From there, nutrition and lifestyle take over. Dr. Gary Wu, professor of gastroenterology at the University of Pennsylvania and co-director of the PennCHOP Microbiome Program, said that how our microbiome develops in childhood may affect our risk of obesity and chronic disease later in life — and inflammation is likely the common thread.

Inflammation is our immune system’s main weapon against foreign invaders, and one layer of cells is all that separates the immune system from the gut microbiome. This means that a healthy, balanced microbiome can discourage inflammation while an unbalanced microbiome can encourage inflammation. “The microbiome is in training for the first three years of life for how we unleash our weapons when under attack,” Fasano said.

Ideally, the immune system only unleashes inflammation when we are really under attack. When the immune system regularly unleashes inflammation unnecessarily, it can lead to allergies and autoimmune diseases like celiac disease, inflammatory bowel disease and type 1 diabetes. (An autoimmune disease is a malfunction of the body’s immune system that causes the body to attack its own tissues.) Increasingly, chronic inflammation is also thought to be a root cause of cardiovascular disease, type 2 diabetes and some forms of cancer.

Wu said our diets and our exposure to antibiotics and chemicals alter our microbiota — for better or for worse. The composition of our microbiome affects how food is broken down in our bodies and how many calories and nutrients we absorb. Recently published research suggests that antibiotic use in childhood can contribute to obesity, and that artificial sweeteners can increase the risk of type 2 diabetes.

The connection between what we eat and the health of our microbiome is very complex, but a plant-based diet with lots of fruits and vegetables and few highly processed foods provides an abundance of prebiotics, aka food for the beneficial bacteria you want to have living in your gut. Regularly eating fermented foods, which contain beneficial “probiotic” microbes, may also shift our gut microbiota in a healthier direction.

“Few people really understand what the microbiome is and how nutrition impinges on it,” Fasano said. “You eat three to four times a day. If you eat junk, you have a microbiome out of balance.”