What Is the Gut Microbiome?

The gut microbiome refers to all the microorganisms living in the digestive system. The microbiome is individual to each person and is important to digestive health as well as to overall health.

Studies of the gut microbiome are ongoing, but it’s becoming clear that certain types of bacteria, yeast, and other fungi are more or less beneficial for overall health. People may be able to affect their microbiome with diet and other lifestyle factors. 

This article will cover the microbiome in a broad sense, including how the diversity of microorganisms in it may affect overall health.

What’s Considered a “Healthy” Microbiome?

What is “healthy” in the gut microbiome is not yet well understood. For instance, there’s no master list of different types of bacteria and in what proportion everyone should have to be healthy.

What is known is that the composition and diversity in the gut microbiome do have an effect on health. Composition takes into consideration which microbes are in the gut and in what numbers. Diversity refers to the idea of having many different types of species of microbes.

Dysbiosis refers to a shift in the microbiome to less diverse or less favorable to overall health. Many things can lead to dysbiosis, including receiving antibiotics, having an infection, and dietary changes.

The gut microbiome protects the body in various ways. It’s not yet known exactly how the makeup of one person’s microbiome may affect their health. However, some broad generalizations can be made about how diet and other environmental factors may shift the microbiome in one direction or another.

Ways to Support Your Microbiome

Your microbiome is developed in the first years of life. It is relatively “set” by the time you are 3 years old. However, it can be shifted by certain factors. The most common way to have an effect on the microbiome is by making adjustments to diet.

Evaluate Your Diet

Diet, starting with that of the birthing person for an infant, is an important factor in the gut microbiome. In general, a diet that contains many different types of foods—especially plants, including fruits, nuts, and vegetables—supports a diverse gut microbiome.

One 2021 study showed that gut microbiome diversity was increased in people who ate certain foods. Not every possible food was included in the results of the study, however.

Foods associated with having a more diverse microbiome include:

• Eggs
• Plant-based foods (in the study the examples were spinach, seeds, tomatoes, and broccoli)
• Nuts
• Fish (white fish and oily fish)
  

Foods associated with a less diverse microbiome included:

• Bacon
• Desserts that included dairy
• Meat pies
• Ultra-processed foods (in the study, the examples were sauces and baked beans)

The authors point out that there’s room for nuance. The quality, source, and type of a food are all important in considering if it will promote a diverse gut microbiome. For instance, plant-based foods that are ultra-processed may not have the same benefit for the microbiome as a whole fruit or vegetable.

Research isn’t at the point in which all the parts of the human diet can be pinned down to how they affect the microbiome. Further, there’s not enough evidence to tell everyone exactly what they should eat to support their microbiome. Much of the research is still being done on mice, and that doesn’t always directly translate to what may happen in humans.

Any broad dietary advice needs to be viewed as being just that—not specific to any one person. That doesn’t mean it might not be helpful, but it may not provide all the information needed.

The best approach is to work with a healthcare provider to make a dietary plan that takes the whole person into account. This includes culture and food preferences since a diet plan is no good if a person isn’t going to follow it. 

Beneficial Foods

With all those caveats taken into account, there may be some items that, when added to the diet, can shift the microbiome in the direction of more diversity. This can include:

• Foods that contain prebiotics (specialized plant fibers that healthy gut bacteria like): Such as artichokes, asparagus, bananas, blueberries, garlic, leeks, and onions
• Fermented foods that contain probiotics (live microbes found in the gut microbiome): Such as kefir, kimchi, natto, refrigerated sauerkraut, and yogurt
• Foods containing polyphenols (antioxidant compounds found in plants): Such as fruits, seeds, vegetables, tea, cocoa products, and wine
  

Foods That May Be Detrimental

There is no single list of foods that are worsen the gut microbiome for everyone. However, a diet that includes higher amounts of these foods may decrease the number of bacteria in the microbiome and their diversity, such as:

• Artificial sweeteners (saccharin, sucralose, and aspartame)
• Beef (red meat)
• Saturated fats (milk, cheese, butter, pork, beef, lamb, poultry, coconut oil, palm oil)
  

In one study, a gluten-free diet (a diet containing no gluten, a protein found in certain grains like wheat, barley, and rye), a Western diet (a diet high in animal protein and fat and low in fiber), and a high protein/low carbohydrate diet were associated with a decrease in bacteria considered more helpful and an increase in bacteria considered less helpful.

Manage Stress

You may not think of stress as something that can affect the gut microbiome. However, it has been shown that psychological stress (as opposed to physical stress) may interfere with the microbiome. The research has mostly been done on animals (such as mice). This is called preclinical data because it has not yet been tested in many well-executed studies in humans.

The gut microbiome can be shifted, but it is also fairly elastic. It tends to go back to what it was before the disruption. Chronic stress, however, may change the microbiome long enough to lose some of that stability.

Chronic stress may also trigger the immune system. This could lead to dysbiosis, although what it means for overall health isn’t yet well understood. It’s possible that the disruption from stress could result in a long-term change that affects the risk of developing or worsening other illnesses.

For that reason, managing stress may help keep the gut microbiome in balance. "Stress reduction" is a broad term. There are many ways to reduce stress, and what is helpful will differ from person to person. 

The Importance of Gut Health

The study of the gut microbiome is still in the early stages. Much of the research is on animals or computer models rather than humans. That doesn’t mean nothing has been learned, but rather that it is not proven. Humans are complex. The gut microbiome (with its trillions of organisms) is intimately involved in health.

Diet, psychological stress, and environmental exposures can all affect the gut microbiome. They can shift it into helpful or unhelpful directions. It is not yet known how individuals can affect the microbiome to get the results they are looking for, such as a lowered risk of certain diseases.

However, it is known that the makeup of the gut microbiome may affect many disease processes. For example, certain microbiome “signatures” have been associated with the potential for the development of cirrhosis (liver scarring) and diabetes.

Therefore, it’s important to be mindful of your gut microbiome. Science is not yet at the level of personalized medicine in knowing how to make the most of your own microbiome or how to change it beneficially.

However, enough is known that you can gain some benefit from including more of certain foods in your diet (and less of others), reducing stress, and doing what you can to avoid infections or obvious environmental toxins like heavy metals. 

Immune Function

The drinks, foods, and medications that go into your mouth and through your digestive system have an effect on your body, including your immune system. The inside of digestive organs has a layer that serves as a buffer between what you take in and the rest of your body. This layer can be weakened by dysbiosis or by other disease processes.

The gut microbiome may “learn," over time, how to respond to the substances it comes into contact with. Not only foods and medicines but also other things that get into your body, like pollen or bacteria in the environment that may cause disease.

The immune system might react in a way that clears the things that may do harm. Or it may overreact, doing too much, such as mounting an allergic reaction to a food or other substance.

Researchers don’t yet understand how to shift the microbiome so that it helps the immune system to react appropriately in all cases. Keeping the gut microbiome in balance and supporting it in the ways identified may be helpful in keeping the immune system working well.

Gut-Brain Axis

The gut-brain axis is the connection between the gut microbiome and the brain (the central nervous system). It’s thought that the diversity and makeup of the gut microbiome may have an effect on the brain, including the development of neurological disorders.

It’s also thought to work in the other direction, with the brain having an effect on the gut microbiome. For this reason, some digestive conditions, such as irritable bowel syndrome (IBS), are now being thought of as disorders of the gut-brain interaction.

Summary

The gut microbiome is the community of bacteria, yeast, and fungi in the digestive system. There are many unanswered questions about the gut microbiome, but it is clear that it has a significant effect on overall health.

Keeping the microbiome in balance is a subject of study, but it is not yet well understood as to how to achieve a beneficial mix of microorganisms. Dietary changes, stress reduction, and avoidance of things that may disrupt the gut microbiome may be able to change the composition.