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Microbiome - The Connection Between Diet, Disease, and Your Gut

Microbiome: The Connection Between Diet, Disease, and Your Gut

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Did you know there’s a direct connection between the bacteria that live in your gut, your lifestyle, and your risk of developing chronic diseases?

Lifestyle factors such as diet and exercise can change the makeup of your gut’s microbiome. Understanding the relationship between these variables and the bacterial composition of your intestines can help you support your overall gut health and reduce your risk of developing a chronic disease like cancer, heart disease or diabetes.

What is the Gut Microbiome?

Microbiome - The Connection Between Diet, Disease, and Your Gut
Microbiome – The Connection Between Diet, Disease, and Your Gut

The human gut microbiome, also known as the gut flora or gastrointestinal microbiota, is an intricate and intertwined community of microorganisms (such as bacteria) that live in your digestive tract.

Scientists first observed microbes under a microscope in the 17th century. More than 200 years later, scientists discovered that microbes are the cause of diseases like cholera and tuberculosis. For many years, we thought that because microbes were the cause of diseases, we should eradicate them.

Later, scientists realized that there are also “good bacteria,” and sweeping them all off from the mucous membranes of our bodies would do more harm than good.

In other words, bacteria can be beneficial. Modern science has proven that certain microbial strains fight off diseases and their symptoms.

In terms of gut health, that means that your body has to maintain a balance between good and bad bacteria.

What You Will Learn

In this article, you’ll learn why balancing the microbes that colonize your body is crucial for your health. We’ll review how the gut microbiome strongly influences the brain, the blood, and even our emotions. And we’ll look at how we can modulate (influence) these bacteria to our advantage.

I’ll also show you an easy way to test your gut flora at home to learn more about your intestinal microbiome composition. I did two of these tests and was fascinated by the results — and especially by the microbial diversity (which indicates how many different types of microbes live in my gut).

How to Support Your Gut

Supporting your gut follows the same three principals as maintaining a healthy lifestyle in general:

  1. Eat healthily
  2. Exercise regularly
  3. Get enough sleep

Both exercise and quality sleep relieve stress, which is a mechanism that can impact the composition and function of the bacteria in your intestines.

Maintain a Healthy Diet

A Healthy Diet Supports Your Gut
A Healthy Diet Supports Your Gut

The food you eat directly influences the array of microbes in your gut. Every type of bacteria thrives on certain kinds of food for fuel. Some like carbs, while others prefer fat, protein or fermented foods.

If you want to reduce the number of a particular type of microbe in your gut, starve them of the foods they like.

For example, according to the analysis of my gut microbiota, I have less gluten-digesting microbes than people who report no ailments and high level of wellness. While I don’t have celiac disease (as far as I know), my relatively low number of those bacteria is likely because I avoid grains in my diet. That deprives them of the fuel they need to expand their colony.

On the flip side, if you want your good bacteria to thrive and keep harmful bacteria at bay, you need to maintain a healthy dietary lifestyle. Eating a diet rich in sugars, processed carbs, grains and dairy will lead to a dysbiosis (a microbial imbalance or maladaptation), and ultimately to the development of chronic diseases.

In other words, a diet that feeds all the “wrong” bacteria while not providing enough food for the “good” ones may have significant negative long-term health implications.

Exercise Regularly

Regular Exercise Reduces Stress and Supports Your Gut
Regular Exercise Reduces Stress and Supports Your Gut

Based on scientific studies, regular exercise can increase the microflora diversity in your gut. The proliferation of bacteria can then modulate mucosal immunity and improve barrier functions, thus reducing the risk of obesity and metabolic diseases.

The mucosal immune system determines how well your body can protect itself against pathogens and environmental toxins. The better that immune system works, and the better it blocks such pathogens from getting into your bloodstream (barrier function), the less likely you get sick and develop systematic inflammation — the root cause of metabolic ailments.

Get Enough Sleep

The gut-brain axis connects the gut and the brain (see below). And you probably already know that the brain is responsible for managing sleep, via the release of certain hormones (such as melatonin) via the pineal gland.

However, the body has a backup plan for many critical functions, including the release of melatonin. If the pineal gland isn’t functioning adequately, the gut can jump in and assist by converting the amino acid tryptophan into serotonin.

The body can then further convert serotonin into melatonin, a sleep hormone that manages the body’s circadian rhythm. It’s another example of how your “second brain” (the gut) can influence chemical processes that are entirely unrelated to digestion.

Good Bacteria vs. Bad Bacteria

Good vs. Bad Bacteria - Help Your Body to Maintain The Balance
Good vs. Bad Bacteria – Help Your Body to Maintain The Balance

We are hosts to billions or even trillions of bacterial cells, most of which are located on the external and internal linings of the body. Microbes populate our skin and the mucosa of the gastrointestinal tract, the urinary tract, and many other surfaces of our body. Many of those microorganisms are so-called “commensal microbes,” which do not have any effect on our health (that we know of today).

Others are beneficial bacteria that provide extra nutrients, increase our body’s defenses, and modulate specific metabolic processes. Both beneficial bacteria and commensal microbes compete against harmful pathogens. They colonize the surface of the skin and mucosa, eliminating that space that virulent microbes would use to take root and subsequently cause disease.

In other words, the healthy bacteria on our skin and in our gut fill up the “empty space” and prevent harmful bacteria from colonizing and causing problems.

If you’re healthy, there is no “empty” space in your gut that’s not already populated by bacteria. That’s why supplementing with probiotics might not work if the bacterial strains in the supplement don’t have room to settle in. Adding bacteria to your gut’s microbiome is all about displacing and replacing what’s already there. That makes modulating the microbiota in your gut a long-term process that often requires changes in your lifestyle.

Moreover, recent scientific initiatives, such as the International Human Microbiome Consortium and the Human Microbiome Project, have been studying how specific changes in the balance of good bacteria have an impact on our health and the development of chronic diseases.

However, similarly to healthy bacteria, pathogens can colonize the gut and fill the available space. When that happens, healthy bacteria will find it difficult to set in — even if we try to add them through probiotics.

That’s why taking a prebiotic or probiotic supplement often “enhances” your gut flora only temporarily — or for as long as you take the supplement.

Gut and Health

Gut dysbiosis, which is the disruption of the healthy microbiome, causes gastrointestinal problems and increases the risk of both colon cancer and autoimmune diseases.

What you eat not only impacts the delicate balance of microbes in your gut, it also directly influences the risk of developing chronic diseases and many other health problems including:

  • Insulin resistance or insulin sensitivity (diabetes)
  • Crohn’s disease
  • Irritable bowel syndrome (IBS)
  • Diet-induced obesity
  • Small intestinal bacterial overgrowth (SIBO)

As a result of the latest research on gut microbiota, there has been a boom in the sale of prebiotics, probiotic foods and supplements. There are numerous lines of research currently exploring the link between bacterial strains and their health effects.

The Gut-Brain Axis

The Gut-Brain Axis Connects your Gut with Your Brain
The Gut-Brain Axis Connects your Gut with Your Brain

During its evolutionary formation, the gut was optimized as a means to absorb nutrients. However, it needed an integration center, as well as sensory and executive pathways that allowed our bodies to expel toxins and unwanted contents (and to fight off pathologic bacteria). The neuronal connection in the gut was essential for that process to work correctly, and it became an independent network from that of the brain.

This “gut brain” contains around 200 million neurons. That’s incredible, considering that the brain functions properly with “only” 86 billion neurons. In time, the human body integrated the two neuronal systems and started to share several functions that complement each other.

Even though the connection between the brain and the gut was evident for many years, recent studies have revealed a very complex system of interaction between the gastrointestinal tract and brain function. It appears that microbiota is capable of modulating the function of the brain by releasing neurotransmitters, chemical messengers, hormones, and even metabolites (as in the case of short-chain fatty acids).

For example, Bifidobacterium species in the human gut produce a neurotransmitter called gamma-aminobutyric acid (GABA), which is an inhibitory neurotransmitter that may have an analgesic effect and may even reduce abdominal pain from a neuronal perspective.

Another example is Lactobacillus rhamnosus, which is a common probiotic strain to control post-antibiotic diarrhea. These bacteria cause a change in the expression of GABA receptors in the brain and reduce psychiatric symptoms such as anxiety and depression.

On the other hand, pathogen species such as Streptococcus, Enterococcus, Escherichia, and Candida produce a neurotransmitter called serotonin, which scientists have linked to anxiety, depression, impulsive behavior and other mental health problems. Similarly, there are many other examples of how gut microbiota is capable of changing essential aspects of our health, such as the modulation of pain, changes in mood and certain mental diseases.

The gut is not only linked to the central nervous system, however. It is also profoundly related to the immune system through an extensive network of lymphoid tissue that’s associated with the mucosa of the gastrointestinal tract. This is why recent studies report that certain bacterial strains have a positive effect on autoimmune diseases such as inflammatory bowel disease (chronic inflammation), rheumatoid arthritis, asthma and others.

Bacterial Strains and Their Implications in Health and Disease

The Health Benefits of Probiotics
The Health Benefits of Probiotics

After putting all the evidence together, scientists have realized that the gut is more than just a digestive organ. It’s a valuable player for maintaining and promoting health, and can even contribute to the prevention of several chronic diseases. We now understand that the genes of our gut microbiota and their molecular activity directly influence the expression of genes in the rest of our body.

Thus, there is a great deal of current research about several bacterial strains which are beneficial for our health. These are just a few of the most important:

  • Lactobacillus acidophilus
  • Lactobacillus rhamnosus
  • Lactobacillus reuteri
  • Bifidobacterium species

Lactobacillus Acidophilus

Lactobacillus acidophilus is one of the members of a group called lactic acid bacteria. They are usually found in fermented foods like sauerkraut, tempeh, miso and yogurt.

This bacterial strain has been found to modulate the immune system and reduce the severity of several vaginal disorders such as vaginosis and candidiasis (yeast infection). It is capable of fighting off Helicobacter pylori and reduces the incidence of several other infections in the gastrointestinal system.

Lactobacillus acidophilus is also used to prevent allergic disorders such as allergic rhinitis and dermatitis. Additionally, it reduces antibiotic-induced diarrhea and may be helpful for treating inflammatory bowel disease and other bowel problems.

No wonder so many different brands use Lactobacillus acidophilus as an additive in yogurt and similar products. It’s also a common ingredient in probiotic supplements, often being combined with other strains like bifidobacteria and Streptococcus salivarius. There are many subtypes of lactobacilli within the acidophilus group, and we don’t yet fully understand the mechanisms by which they promote health.

Fermented Food, Such As Sauerkraut Feeds The Healthy Bacteria in Your Gut
Fermented Food, Such As Sauerkraut Feeds The Healthy Bacteria in Your Gut

Lactobacillus Rhamnosus

Lactobacillus rhamnosus is a bacterial strain that was discovered when scientists began their search for another lactobacillus strain that could survive stomach acid. They wanted to find a suitable candidate for a probiotic supplement. Lactobacillus rhamnosus has the structure of a rod, and it produces a compound called bacteriocin, which has potent antimicrobial activity against Pseudomonas, Escherichia coli, Salmonella, Staphylococcus, Streptococcus and other pathogens.

Thus, this bacterial strain is often used to prevent the colonization of pathogens, to kill them off, and to revert antibiotic-induced diarrhea.

An interesting finding is that people who receive Lactobacillus rhamnosus strains along with antibiotics would also benefit from the health effects of these bacteria. Studies report that this bacteria retains the ability to colonize the human gut during antibiotic treatment.

These bacteria adhere firmly to the epithelium of the intestine, which makes it even harder for other pathogens to colonize. Lactobacillus rhamnosus helps prevent and treat infectious diarrhea, reduces the incidence of allergic diseases in children, and has been used for atopic eczema treatments. Finally, this strain has a potential anti-obesity effect because it modulates obesity biomarkers such as fatty acid synthase.

Lactobacillus Reuteri

Lactobacillus reuteri is also known as strain F275 to avoid confusion with Lactobacillus fermentum in the scientific literature. One of the most critical properties of Lactobacillus reuteri is the synthesis of a molecule called reuterin, and another called reutericyclin. These molecules are capable of killing pathogen bacteria, protozoa and fungi.

Additionally, L. reuteri produces several vitamins, including folic acid, vitamin B12 and thiamine, making them available for absorption into the bloodstream. Similarly to many other bacterial strains in the gut microbiota, L. reuteri is capable of regulating immune function by suppressing proinflammatory cytokines and causing a local reduction of allergies in the gastrointestinal tract.

According to various studies, L. reuteri administration in infants reduces the crying time caused by infant colics. It’s helpful in necrotizing enterocolitis and in preventing several infectious and inflammatory diseases in the colon.

Bifidobacterium Species

There are many Bifidobacterium species, and the most important in the field of probiotics are bifidobacterium animalis spp lactis, Bifidobacterium bifidum, Bifidobacterium breve, and Bifidobacterium longum. In the case of B. animalis spp lactis, it survives the acidity of the stomach without a problem, has been shown to accelerate the bowel movements in people suffering from constipation, and reduces minor gastrointestinal symptoms such as bloating and distention in healthy patients.

This strain has anti-inflammatory properties and may reduce the severity of several inflammatory diseases, primarily when they are located in the gastrointestinal tract.

Bifidobacterium bifidum is another significant strain under these probiotic species. It reduces the incidence of eczema, is useful in managing radiation-related diarrhea and rotavirus-induced diarrhea, reduces the risk of infection of Clostridium difficile, and has been found to be beneficial for immune function in elderly patients.

On the other hand, Bifidobacterium longum exerts potential anti-inflammatory effects which are helpful in preventing diseases such as ulcerative colitis and may help normalize bowel function in elderly patients.

The studies on Bifidobacterium breve are usually focused on the immunomodulatory role in infants and children for preventing food allergies, atopic dermatitis, asthma and other immune-related diseases.

How Do You Test Your Gut Microbiome?

uBiome Explorer Kit
uBiome Explorer Kit

I’m not a fan of ads, but I have to admit that the ones I see when browsing through my Instagram feed are often relevant and useful.

A few months ago, I saw an ad from a company called uBiome. They enable regular consumers, like you and I, to take a stool sample at home and have your fecal microbiota analyzed in a professional lab.

It’s essential to differentiate between analyzing the bacteria in your stool, which is an incredibly reliable process, with an inherently unreliable food sensitivity test (often referred to as an IgG-4 antibody test). Stay tuned for an upcoming article on that topic.

uBiome offers a variety of different test kits, but the ones I tried are called Explorer and SmartGut.

For both tests, uBiome leverages the latest DNA sequencing technology and research from the NIH Human Microbiome Project to give you unprecedented access to all the information that lies in your gut microbiome.

Explore Your Microbiome

What Can You Learn From Your Microbiome?

My Microbial Diversity
My Microbial Diversity

In a nutshell, a lot! The amount of information you can derive from the microbes in your gut is almost overwhelming. Fortunately, uBiome Explorer presents the findings in an easy-to-understand and easy-to-consume manner.

On a high level, the uBiome report shows the following information:

  • Microbial diversity (unique microbes)
  • Weight-influencing microbes
  • Gluten-digesting microbes
  • Anti-inflammatory microbes
  • Lactose-digesting microbes
  • Impact of artificial sweeteners on your microbes
  • Probiotic (foods) microbes
  • Impact of alcohol on your microbes and alcohol metabolism
  • Sleep microbes
  • Vitamin-producing microbes
  • Nutrient metabolism
  • Trimethylamine (TMA)-producing microbes

What’s cool is that the report not only shows you the results, it also provides links to scientific research and suggests things you can do to improve your gut health as it relates to a specific type of microbe. Recommendations include:

  • Foods
  • Supplements
  • Lifestyle

What I recommend is implementing some of these suggestions, and then testing your gut again to see if and how you have improved.

What Did I Find Out About My Gut Microbiome?

As I mentioned above, the amount of information I got from that report was incredible, and it’s too much to share it all here. However, I wanted to share with you some of the findings that I thought were especially interesting.

I’m in the 81st percentile of microbial diversity, compared to thousands of others who have taken the test. That means I have a lot of different types of microorganisms in my gut. But there’s still room for improvement.

Gluten-Digesting Microbes in my Gut
Gluten-Digesting Microbes in my Gut

I have very few gluten-digesting bacteria in my gut. That shouldn’t come as a surprise, considering that I don’t eat grains. Remember, you can reduce the number of individual bacteria by not feeding them the food they need to thrive.

However, that means that every time I make an exception and have a pizza (which has both gluten and lactose), I can expect GI issues because I don’t have the enzymes to properly digest those foods — even though I don’t have celiac disease.

Additionally, I learned that my glass of red wine that I enjoy most evenings has not negatively impacted the abundance of bacteria that often appear in lesser amounts in people who regularly drink alcohol.

I Have An Abundance Of Sleep Microbes In My Gut
I Have An Abundance Of Sleep Microbes In My Gut

Additionally, I have an abundance of Serotonin-producing bacteria (sleep microbes). Maybe that’s because I have a strict bedtime routine and good sleep hygiene.

Where I’m lacking is in the following areas, which I plan to tackle by consuming more foods that feed the supporting bacteria:

  • Anti-inflammatory bacteria (eat more mushrooms and foods containing inulin)
  • Probiotic bacteria (eat more fermented foods)

Explorer vs. SmartGut

uBiome Explorer Specimen Collection Tube
uBiome Explorer Specimen Collection Tube

SmartGut is a product that your doctor would order if you have a chronic gut condition, such as IBD/IBS, or symptoms such as gas, bloating or diarrhea.

SmartGut detects beneficial and pathogenic microorganisms associated with specific infections, lifestyle choices, and gut conditions including inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS).

Explorer allows you to discover your microbiota without the help of a doctor. Even better, you can use Explorer to analyze the microbiome of not only your gut, but also your nose, mouth, skin or genitals.

Interactive online tools enable you to explore how your microbiome compares to others and to monitor yourself over time.

I took both tests and, unsurprisingly, got very similar results.

How Can You Modulate Your Gut Microbiome?

As we have reviewed in this article, the gut is one of the largest organs in the body. It’s linked to the central nervous system, immune function, and modulates several molecules and metabolic processes. However, improving the gut’s microbiome might be more complicated than you think.

It’s not only about buying and taking expensive probiotic supplements. We also need to reduce harmful bacteria to make room, and carefully choose bacterial strains with antibacterial activity to replace them.

That’s why I recommend making naturally prebiotic and probiotic food part of your diet. For example, you can eat sauerkraut several times a week as a side dish.

Supplements can certainly help if you’re making the transition from an unhealthy to a healthy diet, or if you’re on antibiotics due to an infection or other diseases. However, don’t think you can get away with using supplements while maintaining a lifestyle that’s not conducive to healthy gut flora.

Did You Know That Tea Can Help Improve Your Gut Microbiome?

Pique Tea Crystals have 12x the antioxidants or regular tea
Pique Tea Crystals have 12x the antioxidants or regular tea

I recently learned that the polyphenols (naturally-occurring plant compounds) in tea can also have a positive impact on your gut. You can learn more about that Pique Tea’s blog.

There’s emerging evidence that tea polyphenols can improve your gut microbiome by supporting the growth of probiotic strains like Lactobacillus and suppressing the growth of pathogenic bacteria like C. difficile!

Dr. Sarah Ballantyne, PhD – also known as the Paleo Mom

I prefer to have a cup of coffee in the morning, but recently stumbled across a tea brand called Pique Tea. Their tea crystals have 12x the antioxidants of regular tea and it tastes delicious. So if you like tea, I recommend you give them a try. It’s yet another simple method of supporting your gut!

Frequently Asked Questions (FAQ)

What is the Microbiome Diet?

The Microbiome Diet is a new diet that touts a restoration of gut health and claims to aid in weight loss.

Frankly, if you have a healthy dietary lifestyle — one that is characterized by eating fresh food that mimics what our ancestors ate for millions of years — you don’t need to do anything extra to support your gut.

What Bacteria Live in the Small Intestine?

The stomach and proximal small intestine contain relatively few microorganisms, mostly because of the presence of gastric acid, which makes those parts of your gastrointestinal tract an unpleasant home for bacteria.

However, there is a medical condition known as small intestinal bacterial overgrowth (SIBO) or small bowel bacterial overgrowth (SBBO), which is defined as an increase in the number of bacteria in the upper GI tract.

What Role Do Branched-Chain Amino Acids (BCAAs) Play in Gut Health?

As a Crossfit enthusiast, I knew about the vital role of BCAAs in muscle synthesis and recovery. However, research on piglets has shown that BCAAs are also involved in maintaining an intestinal barrier function. A study conducted by Japanese researchers has demonstrated “that dietary supplementation with BCAAs promotes intestinal development, enhances enterocyte proliferation, increases intestinal absorption of amino acids (AA) and glucose, and improves the immune defenses.”

What’s a Leaky Gut or Leaky Gut Syndrome?

Leaky gut (also known as intestinal permeability) is a condition in which the cells in the intestinal linings become permeable, thus allowing toxic nutrients into your bloodstream.

Research has shown that eating a diet high in grains, legumes and other foods containing antinutrients increases the risk of developing leaky gut.

What’s the Connection Between the Gut and Insulin Sensitivity?

Insulin sensitivity (diabetes) is a metabolic disease that is often caused by systematic inflammation. In the same way that your diet influences the microbiome in your gut, you can modulate those inflammatory pathways through the diet you eat.

An altered gut microbiome may contribute to obesity, which in turn can promote insulin resistance.

What Are Bile Acids?

Bile acids are organic compounds in bile that facilitate the digestion and absorption of lipids (fatty acids) in the small intestine.

Can a High-Fat Diet Negatively Impact My Gut Health?

Eating a diet that’s high in healthy fats can undoubtedly change the composition of your microbiota. Additionally, eating unhealthy fats, such as vegetable oils that are high in omega-6 fatty acids, can negatively impact your gut and your overall health by causing inflammation and intestinal permeability.

Should I Take Probiotic Supplements?

Performance Lab - Prebiotic Supplement
Performance Lab – Prebiotic Supplement

Some smart marketers claim that taking probiotic supplements can prevent or treat diseases like schizophrenia, autism and many others.

Scientific evidence strongly suggests that most chronic ailments, including mental diseases, are influenced or caused by lifestyle choices and diet in particular. However, it would be naive to think that taking a probiotic supplement can outweigh an otherwise crappy diet. That’s not how it works.

However, supplements are proven to help with conditions such as antibiotic-induced diarrhea and travelers’ diarrhea, and in some cases have been shown to help with ulcerative colitis, food allergies and vitamin deficiencies.

If you choose to use a supplement, I recommend a high-quality brand, such as Performance Lab. They offer an excellent prebiotic (fiber) product that contains inulin.

The probiotic brand I like is Garden of Life, which is also recommended by Dr. Perlmutter.


Besides increasing our consumption of fermented foods and probiotic supplements, there are a few other things we can do on a day-to-day basis to positively modulate our gut microbiota.

Reducing stress, sleeping properly, maintaining a diet with sufficient fiber, and engaging in moderate exercise may improve our overall health and promote the growth of healthy gut bacteria. These measures will not only modulate our microbiome but also contribute to our general health and improve our quality of life.

About the Author Michael Kummer

I was born and raised in Austria. I speak German, English, and Spanish. Since moving to the U.S., I have lived and worked in the greater Atlanta area. In my twenties, I was a professional 100m sprinter. These days I do mostly CrossFit. I'm a technologist and Apple fan. I love science and don't believe anything unless there is proof. I follow a Ketogenic Paleo diet and intermittently fast every day. I'm married and have two trilingual kids. My goal with this blog is to share what I learn so that you can spend time on something else. Check out my latest Diet, Fitness, and Technology articles.

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