Trillions of microorganisms, also called microbes, make up your microbiome. In your gut, these microbes include bacteria, fungi, viruses and parasites. While the way you’re born plays a big role in shaping your unique microbiome, numerous other factors — such as what you eat, how much time you spend outdoors, and even travel — can affect it. The particular balance of microbes that you maintain in your gut microbiome can significantly impact your health.

What is the microbiome?

“Microbiome” is defined as the collective genomes of the microorganisms in a particular environment — whether that be the human body, the ocean, or a soil sample. In your body, most of your microbes are found in your stomach and large intestines, known as the gut microbiome; there, the tiny “bugs” (microbes) outnumber your human cells by 10 to one. That’s a good thing, because this personal population of microorganisms plays a pivotal role in your overall health. 

What do gut microbes have to do with your health?

Because the largest microbial communities are in our guts, a lot of research has focused on the role of gut microbes in health and disease. Although many microbes have neither beneficial nor negative effects on our health, there are several ways our gut microbes impact our health. 

Gut microbes:

• Fight off pathogens.
• Produce vitamins that our own cells can’t, such as vitamin K.
• Break down fiber from food.
• Produce many molecules, including short-chain fatty acids (SCFAs), that keep our intestines healthy and provide the necessary cues to the host to regulate and maintain metabolic and immune health.

But this is only the beginning. Since the first complete human microbiome profiles were published in 2012 (see here and here), hundreds of follow-up studies have helped elucidate the important and complex role of the microbiome in human health and disease. Some of the most well-studied topics include immunity, obesity, and metabolic function.

How to improve your gut microbiome 

You can bring new meaning to the phrase “food is medicine” by embracing nutritional and other health lifestyle practices that positively impact your gut microbiome — and in turn your health. While the science of the microbiome is still in its infancy, studies indicate that three simple steps can really benefit you:

• Eat plenty of fiber.
• Avoid processed foods with ingredients like artificial sweeteners or emulsifiers.
• Avoid unnecessary medications.

The gut microbiome’s role in regulating immunity

Researchers have concluded that your gut microbiome improves immunity — so you’re more easily able to fight off infections and less likely to get sick in the first place. 

• An intact gut microbiome is critical for training both the innate (i.e., barriers that form the immune system’s first line of defense) and the adaptive immune system (i.e., specialized cells that fight pathogens).
• Gut microbiome composition can impact whether your immune system overreacts to harmless microbes or food particles.
• Gut microbiome composition can promote or control gut inflammation. The less inflammation the better, from a disease perspective.

Learn more: The Link Between Blood Sugar and Your Immune System.

The microbiome and weight loss

Some of the earliest studies investigating the relationship between the gut microbiome and obesity were motivated by observations that antibiotics — which obliterate gut microbiome diversity — cause weight gain in animals and humans. To explore whether the microbiome could cause obesity and why, researchers from Washington University took microbiomes from lean and obese human twins and gave them to germ-free mice eating the same food and getting the same amount of exercise each day. They found that:

• The mice that received the microbiomes from the obese twins gained weight.
• The mice that received the microbiomes from the lean twins had no change in weight.
• The microbes from the obese twin were better at extracting energy from food.

Several microbiome differences have been observed between lean and obese humans, and functional studies will help determine whether the microbiome can be leveraged to prevent obesity. 

The key takeaway: Most research indicates that a diverse assortment of good gut bacteria — which can be improved by a diet low in processed foods and high in fiber — can help you stay slim. One study found that lean people have significantly more diverse gut bacteria than those who are obese.

The microbiome and diabetes

Research on the microbiome's effect on diabetes is growing, and recent findings show that it plays an important role. A 2019 study looked at the link between our gut bacteria and diabetes and found that when the gut has too many unhealthy microbes (a condition known as dysbiosis), it can aid in the progression of insulin resistance. This puts you at increased risk for diabetes because the body is no longer able to produce enough insulin or use the insulin it makes effectively. The end result: more sugar in your blood. While it’s unclear exactly what mechanisms are at play here, dysbiosis “may reshape intestinal barrier functions and host metabolic and signaling pathways, which are directly or indirectly related to the insulin resistance” in type 2 diabetes, according to the study’s findings.

A 2020 Lancet report dives deeper into gut bacteria’s role by reviewing findings of more than 40 human studies. They uncovered several ways that the gut microbiome may promote the development of diabetes, including findings that harmful types of bacteria can impair the digestion of sugars and the production of certain gut hormones that control this delicate system. Good bacteria, however, can have a protective effect; they produce increased anti-inflammatory chemicals that in turn help regulate appetite and blood sugar, decreasing the risk of diabetes. 

Learn more: The Link Between Blood Sugar and Your Immune System.

The microbiome and other diseases

Studies show that disease is associated with imbalanced (i.e., dysbiotic) microbiomes. While scientists are still trying to determine whether microbiome dysbiosis is a cause of disease or just another symptom of disease, altered microbial communities have been observed in a number of different conditions:

• Inflammatory bowel disease (IBD), including Crohn’s disease
• Psoriatic arthritis
• Type 1 diabetes
• Celiac disease
• Liver diseases (including NASH)
• Cancer (Colorectal; CRC)  

Additionally, alterations in microbiome composition have been observed in dozens of other conditions—including Alzheimer’s disease, multiple sclerosis, depression, autism spectrum disorder, and others.

Best foods for a healthier gut microbiome

Many research studies conclude that one of the most effective ways to impact your microbiome is by modifying what you eat. Studies point to several important takeaways:

Increased fiber intake can increase bacteria that produce gut-healthy SCFAs and other bioactives that promote metabolic and immune health. Examples of high-fiber foods:

• Vegetables, including: acorn and butternut squash; collard greens; kale; broccoli; carrots; spinach; Brussels sprouts; green beans; sweet potatoes; asparagus. 
• Fruits, including: avocado; raspberries and blackberries; pears; kiwi; pomegranate; citrus, such as oranges and tangerines.
• Beans and legumes, including: chickpeas, lentils; green peas; edamame; many kinds of beans, such as kidney, black, pinto and navy.
• Whole grains, including: bulgur; kamut; pearl barley; quinoa; buckwheat; whole oats.

In contrast, low fiber, high-fat diets — such as the common Western diet — are associated with microbiome dysbiosis and increased inflammation.

Artificial sweeteners and emulsifiers have been associated with microbiome dysbiosis and decreases in beneficial bacteria.

The gut microbiome has been named the link between diets high in processed foods (which are low in fiber and full of ingredients such as artificial sweeteners) and chronic disease.

The ins and outs of fiber

Not all fibers are created equal. Read more: The Many Sides of Fiber. Generally, it is best to obtain the fiber you need from your diet. However, fiber supplements might be necessary if you cannot access diverse, high-quality, fresh fruits and vegetables or if you have a disease condition that requires additional supplementation. 

Fiber is generally broken down into two classes—soluble and insoluble—although resistant starches are sometimes classified as fiber as well.

• Insoluble fiber: bulks up your stool and helps it pass through the GI tract faster. Types include lignin and cellulose. 
• Soluble fiber: reduces spikes in blood sugar and supports metabolic health. Types include gums, pectins, and fructans like inulin and oligofructose.
• Fiber can be a double-edged sword for people with digestive issues:
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Prebiotics and probiotics 

As just discussed, scientists classify dietary fibers as soluble or insoluble fibers. Some (but not all) dietary fibers are considered prebiotics. Read more: What You Need to Know About Prebiotics.

Prebiotics, which are generally non-digestible carbohydrates, are unique dietary fibers that act as a substrate for beneficial bacteria in the human gut. Since they are digested quickly by microbes, prebiotics produce beneficial molecules for humans, including the important and beneficial SCFAs (butyrate, acetate, and propionate)—which are believed to play a role in regulating appetite, blood sugar and immunity. 

Prebiotics are found in many fruits and vegetables (from artichokes to yams), especially those that contain complex carbohydrates, such as fiber and resistant starch. Prebiotics can also be synthesized via enzymatic digestion of complex polysaccharides.

Probiotics (such as yogurt) are different in that they contain live organisms, usually specific strains of bacteria that directly add to the population of healthy microbes in your gut. Unlike prebiotics, which interact with gut bacteria to boost the production of SCFA’s (the health-boosting molecules discussed above), probiotics appear to work differently, and the exact mechanisms are still being studied and determined. While certain reports question their general health efficacy, others state that probiotics appear to have some health benefits. In certain specific disease states, the efficacy of some probiotics is more transparent, including in:

• Antibiotic-induced diarrhea
• Sepsis in infants
• Necrotizing enterocolitis in preterm infants
• Upper respiratory tract infections

Like prebiotics, you can take probiotics through both food and supplements. In addition to  yogurt, other probiotics include bacteria-fermented foods such as sauerkraut, kombucha and kimchi. Probiotic supplements also contain live organisms. 

As one leading medical organization sums up, “a probiotic may show promise in treating a condition, [but] it's likely that the research is still in early stages.” Studies are complex just given the fact that there are literally hundreds if not thousands of different strains and combinations of bacteria in various probiotic supplements.

Medications can upset your microbiome

Certain prescription and over-the-counter medications can impact your microbiome — and not always in a positive way. 

• Antibiotics are major disruptors of gut microbial communities and can cause conditions such as diarrhea or C. diff (also known as Clostridioides difficile or C. difficile) infection. Although they are not effective against viruses, many people take antibiotics for diseases caused by viruses. Not only does this fail to cure the illness, but it also contributes to the conditions mentioned above as well as the antibiotic-resistance crisis.
• Proton pump inhibitors (a class of drugs used to treat GERD,  peptic ulcers, and H. pylori), such as Prilosec, Prevacid, and Aciphex, have been associated with altered microbiomes.

Your microbiome and the future of personalized medicine

As the delivery of healthcare advances, “precision health” or “personalized medicine” is coming into play more and more. Individual approaches to managing your microbiome will become increasingly advantageous to adopt. 

• Individual responses to fiber vary from individual to individual, and as discussed above, some types of fiber are actually harmful to people with IBS. 
• Groundbreaking research from Israel has also shown that the same exact food might spike one person’s blood sugar levels but not another person’s, and this difference appears to be related to the microbiome. 
• Responses to probiotics are also highly personalized. 

We’re rapidly acquiring the data we need to be able to create custom microbiome-based treatments for people based on their lifestyles, existing microbiomes, and health histories.

Key takeaways

Targeting your microbiome through nutritional modifications offers the promise of improved gut, metabolic and immune health — and ultimately increased longevity and a higher quality of life. As personalized nutritional interventions become more refined and accessible, their beneficial impact will become clear. Until then, the best course of action — for the health of your gut, and for you — is to eat plenty of fiber, cut back on processed foods, and avoid unnecessary medications. Be kind to your ”inner garden” microbes, and they’ll be kind to you.