Understanding the human microbiome

The saying, “You are what you eat” is typically a reminder to eat healthy foods to become a healthy person. However, modern research into the human microbiome is pointing to much bigger ideas: That what you eat becomes part of what you are.

If you’ve had an interest in dietary health in the last 15 years, you’ve heard words like “prebiotics” and “probiotics,” but you may not have a full understanding of the secret world inside our bodies.

The human microbiome is a complex system of cells that’s found throughout our bodies, especially in the gut, mouth, and skin. Its constituents are referred to as microorganisms, or microbiota – trillions of bacteria, parasites, viruses and fungi that interact with our bodies in many different ways. The microbiome accounts for nearly 3 percent of your body mass.

It may make you squirm a little to learn that there are trillions of microorganisms living in and on your body, but don’t worry! These microorganisms have been with us for a very long time, and if you treat them well, they’ll do the same for you. A healthy microbiome can help us digest food, synthesize useful metabolites and neurotransmitters, and regulate immune responses.

“In a person who is healthy, they live throughout the body and are existing with us side-by-side,” said Dr. Sachin Goyal, a gastroenterologist at Mercy Gastroenterology Clinic. “You can consider it as an organ system within the organ system.”

The diverse prevalence of gut bacteria across all animals suggests that our relationship with microbiota has been present since our earliest days of evolution. One theory is that microbiota allowed us to strike a healthy balance between carnivory and vegetarianism.

“The plant-based diet takes a lot of energy to digest,” said Dr. Ashutosh Mangalam, associate professor of pathology at the University of Iowa. “The biggest dinosaurs were herbivores. If you’re a carnivore, you have a fitter, smaller body because there’s not much to digest. Humans figured out how to utilize both.” This omnivorous diet was a necessity based on seasonal availability of plants and animals to eat. When we began foraging for raw foods, we took in the bacteria that lived in them. These bacteria started producing metabolites in our gut that gave us an evolutionary edge in processes like digestion and supporting our immune system. “We have outsourced lots of our jobs to these bacteria,” Mangalam said.

Each person’s microbiome is a unique collage of microorganisms which are collected and curated throughout their life. They are differentiated by factors like environment, diet, and hygiene.

“When we’re born, we don’t have any microbiota,” says Dr. Mangalam. “Then we acquire lactobacillus from milk. This liquid diet creates a very simple microbiome that helps us digest chemicals in the milk, to give us energy. All the fun begins when we move from a liquid diet to a solid diet. What happens is that when we start solid food, we need bacteria to digest plant-based materials.” As we continue to grow and vary our diet, location, and lifestyle, different microbiota join our microbiome and create different effects. Since the way we live outwardly can affect the way our microbiome grows inwardly, it’s important to listen to our bodies to find out what helps and hurts this relationship.

At this point, we generally know that having a healthy microbiome sets us up for better digestion and immune response. But what happens when our microbiome isn’t working well? The FDA has not established regulations for testing or treating the gut microbiome. However, the effects of dysbiosis, or an imbalance in the microbiome, are clear, Goyal said. “A good amount of research shows links between dysbiosis and colon cancer, inflammatory bowels, and ulcerative colitis. Mood-associated disorders may also have something to do with the microbiome. The research is not conclusive yet, but everything is pointing towards it.” Mangalam’s lab is studying the link between an unhealthy microbiome and multiple sclerosis.

So how do we make sure that our bodies are populated by healthy, effective microbiota? The composition of your microbiome can be improved by eating raw fruits and veggies, or “prebiotic” foods, such as yogurt, sauerkraut, and kimchi. Prebiotic foods can contain the good microorganisms that will find a home in your body. Once the microbiota are present, it’s important to maintain a diet that allows them to flourish, propagate and work symbiotically with you.

Good microorganisms do their best work when they can access the starches found in “probiotic” foods, which are high in dietary fiber and complex carbohydrates. These foods include fruits, vegetables, whole grains, legumes and nuts. They contain microbiome-accessible carbohydrates, or MACs. The microbiota break down starches that our bodies couldn’t otherwise metabolize and turn them into short-chain fatty acids which our body can use to keep us healthy.

Goyal recommends against indiscriminate use of antibiotics. While you should always follow your doctor’s orders to take them, don’t take antibiotics that were prescribed to someone else, or after your course has already run through. They’re unlikely to help your health, and can damage the ecosystem of your gut.

Research on the human microbiome is rather new, but the future microbiome-based medicine appears bright.

“The problem is that this is unregulated right now,” said Goyal. “Probiotics are considered food supplements rather than medicine.” The U.S. Food and Drug Administration has also not regulated or authorized any tests that could detect if your microbiome is at risk, he said. “When we lack that basic test, it becomes harder to focus recommendations. If we had that test, we could say, ‘You’re lacking in this organism that is good for you, so take this.”

Mangalam remains positive that medical regulations for microbiome health could evolve in the next three to five years.

The microbiome is a symbiotic relationship that all people carry with them throughout life. Like many topics in medicine and nutrition, while it is not yet fully understood, its passive benefits are clear and the ways we can influence it are known. Eating prebiotic foods and foods that are high in dietary fiber and complex carbohydrates, combined with regular exercise, can help keep you, and your microbiome, healthy.