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The Ecosystem Within

The Ecosystem Within

Human Microbiomes and How to Keep Them Happy

You may have heard of the “gut microbiome” and “gut health” in recent years, coupled with advertisements for kombucha and probiotic supplements. Nearly every grocery store hosts a shelf or more holding a rainbow of kombucha and a variety of probiotic capsules. In 2012, a survey from the CDC noted that 1.6% of American adults had taken probiotics in the last 30 days, but by May 2020 that percentage grew to 22%. But what is the gut microbiome?

The first common misconception around this key factor in our health is that the “gut” is in the stomach. However, when we speak about the gut, what we actually mean is our intestinal tract—the large and small intestines. The “microbiome” is the system of microorganisms (also referred to as “microbiota”) that grow and develop within that gut. I spoke with Dr. Maria Marco, Professor of Food Microbiology at the University of California Davis and Chair of their Food Science Graduate Group, for a deeper understanding of how it works.


The microbiome that lives in our gut contributes to the rest of our body’s health. This is because our intestines are home to 80% of our body’s immune-producing cells and provide the most nutrient-rich ground for bacteria to develop. The majority of the human body’s microbiota will grow and change within the intestines, which influences every other system in our bodies.

We are well aware, for example, that diet has a massive effect on the condition of our cardiovascular system, and this is largely involved with the bacterial balance of our intestines. A report from 2017 highlighted this link, indicating that the gut’s control over our metabolism can increase or decrease inflammation and cholesterol in the heart and bloodstream. The health of our intestines is a major factor in deciding our likelihood of developing conditions that lead to heart failure.

Not only will life here play into your digestive, cardiovascular, and immune system health, but over the last decade scientists have found connections to the central nervous system—including the brain. One analysis reported that gut health has a direct effect on conditions like epilepsy, depression, and even autism. This document served to report that ketogenic diets have been found to be extremely beneficial, reducing the rate of seizures in epileptic children by 50%. This diet reduces carbohydrate intake, moving the body into the state of ketosis, where it draws energy from a different form of compound. While scientists previously assumed the benefit of the diet in this resulting metabolic change, more recent findings link it to the gut microbiome and an increase in the microorganisms Akkermansia and Parabacteroides. The ketogenic diet is now being studied to help treat autism, Alzheimer’s, and Parkinsons. Whatever happens in your gut microbiome will affect the way the rest of your body operates. This is why many health conditions come with a specific, doctor-recommended diet.


“Each of us is unique in our microbial fingerprint,” Dr. Marco explains. The microorganisms living in a person are as diverse and changing as we are. Our “fingerprint” can be affected by plenty of factors out of our control— genetics, genotypes, health conditions, age, and environmental inputs to name some. It can be hard to outline what a standard microbiome looks like with all of these variables competing, but Marco also makes sure to emphasize the most well known variable of them all: diet.

Microbes live in every corner of our bodies. If someone loves sugar, bacteria that also love sugar will thrive inside them; likewise for someone who’s eating a lot of fiber. With microorganisms in our bodies outnumbering actual human cells at a ratio of ten to one, the “you are what you eat” mantra takes on a greater meaning. The good news is that unlike our genetics and age, we have a lot of control over our diets.


There have been studies that analyze associations between diet and the gut microbiome generally. One study analyzed the daily diet of thirty-four healthy people alongside measurements of various bacteria in their stool samples over the course of seventeen days. The results clarified three main points: 1) the reaction of each person’s microbiome to the same diet was different; 2) participants were affected by food choices, but not “conventional nutrients”; and 3) a change in the microbiome required at least two days of dietary change. This study clarifies for us that microbiomes are personal, our diet matters, and that it takes at least two days for that diet to affect our internal microbiota.

An interesting factor in this study was the inability to measure the relationship between specific nutrients with changes in bacteria found in stool samples. This is because a nutrient, such as potassium, can contain a range of microorganisms. Therefore, not all potassium is equal in its effect on the gut microbiota. More research is needed to deduce exactly what creates this variety in bacterial content across one specific nutrient.

The American Gut Project was formed to address the opening in the study of food microbiology created by the many factors involved. It is an open-source and open-access project in which anyone can submit their own samples and records for microbiologists to analyze. Using data from the project, one study attempted to draw out a relationship between Akkermansia, a common microbe found in the human gut, and the likelihood of obesity. While the study found that a relatively high abundance of the bacteria Akkermansia was correlated with a reduced risk of obesity, that correlation declined with age. This means that as the age range of subjects went up, the same large amounts of Akkermansia were less effective at preventing obesity. However, there are plenty of ways that any person can stay on top of their internal balance of bacteria regardless of their age.


“It may sound cliche, but sleep and taking care of yourself is the best way to ensure the health of your gut,” says Marco. “Taking care of yourself,” is an umbrella term that includes all of the usual suspects: sleep, water, fruit and vegetable fibers, and exercise will all contribute to a long-term healthy microbiome. Marco goes further to say that “it’s all connected to how microbes have evolved to live with us.” As long as humans have been alive, these little guys have been living in our bodies, and over millennia, have grown accustomed to a particular environment. That means the secret to a healthy gut is no secret at all—your great great great great great (and so on) grandparents have already set up the system. You only need to operate it.

Multiple studies have found, for example, that intake of dietary fiber will significantly reduce the risk of colon cancer. It really is as simple as “eat your fruits and veggies.” These fruits and veggies will push the rest of your food through your body, reducing the contact time that waste has with your insides and making room for your healthy microbes. Think of them as the “cleaning service” of your gut microbiome. As the bad bacteria in waste is moved away, the bacteria that you want to live in you is given room to grow. Different fruits and vegetables also will promote the growth of some of that beneficial bacteria naturally. Akkermansia, for example, loves the high concentration of polyphenols found in apples, beans, flaxseeds, berries, and nuts. Long-term health—barring surprises and uncontrollable variables—is largely about choice. As Marco states, “We can [promote health long-term] with decisions we can make for ourselves.”

If you’re looking for a short-term solution for your health, probiotics are popular for a reason. Plenty of studies have been conducted proving that beneficial probiotic intake can improve gastrointestinal health in a matter of weeks. Probiotic use has also been linked to the reduction of risk of diarrhea (infectious or caused by antibiotics) and the lessening of the length of respiratory illnesses. This metaanalysis of seventy-five studies focusing specifically on probiotics on respiratory illness found a great number that quantifiably proved their value in shortening the duration.

Marco herself was part of an expert panel in 2021 that formed an official consensus statement on the beneficial effects of fermented foods specifically. “The production of fermented foods and beverages with greater quality control will ensure the delivery of products that provide flavour, texture and health-related attributes,” it declares. The statement speaks on the safety and quality of various fermented foods, finding that there can be variation in nutritive value from different providers. Overall, however, these foods offer a number of benefits for the human microbiome.


There are things you can control, and things you can’t. Your health is largely affected by your dietary decisions, regardless of whatever else may affect it. Your genetics, environment, and age can give you trouble, but if you manage yourself to the best of your ability, it will be a great boon to your internal microbiome and therefore the rest of you. Try to keep a solid sleep schedule with enough hours of rest, drink your water, move your body, and eat your fruits and vegetables. I know, it sounds crazy. Incorporating naturally probiotic fermented foods into your diet sure could help as well. And if you find yourself with a bout of coughs and sniffles as the temperature drops, opt for some extra probiotics—it’s well documented that they’ll have you feeling better sooner.