The gut microbiome revealed+ gut health supplements, microbiome labs & more!

By Kim Crawford, M.D. Last updated: March 19, 2024
The gut microbiome revealed+ gut health supplements, microbiome labs & more!


If you follow medical news, you know the gut microbiome is largely responsible for your overall health. Amazing, isn’t it? Hippocrates was right! After reviewing the ins and outs of the gut microbiome, I’ll get into gut health supplements and recommend the best gut microbiome test. Here’s what I’ll cover.

  • What is the gut microbiome?.
  • Gut microbiome components
  • How the gut microbiome works
  • Functions of a healthy gut microbiome
  • Normal versus abnormal gut microbiome
  • Prebiotics
  • Benefits and specifics of Prebiotics
  • Prebiotic Fibers
  • Prebiotic Oligosaccharides
  • Galacto-oligosaccharides
  • Resistant Starch
  • Polyphenols
  • Flavonoid Polyphenols
  • Other Flavonoid Polyphenols
  • Hydroxycinnamic Acids
  • Probiotics
  • Synbiotics
  • Postbiotics=Paraprobiotics=Ghostbiotics
  • Beneficial gut microbiome byproducts
  • Short-chain Fatty Acids
  • SCFA production in commensal(host) and probiotic strains of bacteria
  • Butyrate and gut health
  • Butyrate and the gut-brain barrier
  • Butyrate and Aging
  • Propionic acid (Propionate)
  • Acetate
  • Acetate from Dietary Sources
  • What Shapes the Adult Microbiome?
  • Healthiest Microbiome Diet
  • Foods that promote inflammation= avoid
  • Anti-inflammatory foods
  • Best gut microbiome supplements
  • Best microbiome test=microbiome labs (Yes, there’s an app for it!)


What is the Gut Microbiome?

The gut microbiome is a complex ecosystem comprising trillions of microorganisms, including bacteria, fungi, and viruses (specifically bacteriophages). These microorganisms and their genes collectively make up the gut microbiome.

Bacteriophages, or the “virome,” are viruses that specifically infect and replicate within bacteria. Interestingly, they outnumber gut bacteria and help shape the composition of the gut bacterial communities.

On the other hand, Fungi make up a smaller portion of the gut microbiome, known as the “mycobiome.” Candida is a prevalent genus of fungi in this microbiome.

Understanding the composition and dynamics of the gut microbiome, including these various components, is an active area of research as it has implications for our overall health and well-being.

The gut microbiome’s organisms are categorized into various taxonomic levels, including phyla, classes, orders, families, genera, and species. These taxonomic classifications help researchers understand the diversity and structure of microbial communities in the gut.

The gut microbiota can vary among individuals, and differences in the abundance of specific phyla can significantly impact health. The four dominant phyla commonly found in the gut microbiome are Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. Firmicutes and Bacteroidetes comprise around 90% of the gut microbiota.

Within the Firmicutes phylum, the Clostridium genus is particularly abundant, representing a large percentage of this group. Other genera within Firmicutes, such as Lactobacillus, Bacillus, Enterococcus, and Ruminicoccus, also play essential roles in the gut microbiome.

Understanding the distribution and abundance of these different taxonomic groups within the gut microbiome is crucial for studying their functions and potential impacts on human health.

While the focus has often been on bacteria in the gut microbiome, research has shown that both the mycobiome and virome can also play important roles in gut health.

The mycobiome, or fungal community in the gut, can be influenced by various factors, including diet and environmental factors. Dysbiosis or imbalances in the mycobiome have been associated with some immunodeficiency states and inflammatory disorders, such as Inflammatory Bowel Disease (IBD).

For example, specific fungal cell wall epitopes, such as anti-Saccharomyces cerevisiae antibodies (ASCA), have been found to be a biomarker for Crohn’s disease and are cross-reactive with the fungus Candida albicans.

Antibiotic use can also affect the balance of the mycobiome and lead to the overgrowth of certain fungi in the gut. We’ll discuss this later on in this article.

Overall, the mycobiome is an essential component of the gut microbiome, and its contribution to gut health is an active area of research.

The virome, composed chiefly of bacteriophages, is a highly diverse biological system within the gut. Bacteriophages are viruses that specifically infect bacterial cells, and their presence and activity can directly impact the immune system.

Bacteriophages can influence the immune system by stimulating the production of specific immune molecules, such as interleukin-1b and tumor necrosis factor-alpha, by macrophages. These molecules are involved in immune responses and inflammation.

Additionally, the gut virome is responsive to changes in diet. Different dietary compositions can influence the abundance and activity of specific bacteriophages within the gut.

In the next section, we’ll discuss the “gut bugs” populations found in each section of the gastrointestinal (GI) tract.

Understanding the population dynamics and functions of gut bacteria in different sections of the GI tract is crucial for comprehending their roles in digestion, nutrient metabolism, immune function, and overall gut health.

Gut Microbiome Components

The microbiota composition varies along the length of the gastrointestinal tract, from the mouth to the colon.

The colon, specifically the large intestine, harbors the highest density and diversity of bacteria in the gut. This is primarily due to increased nutrient availability (such as undigested dietary fibers) and slower material transit time through the colon. The colon’s lower pH also favors certain bacterial species’ growth.

In contrast, the small intestine generally has a lower abundance and diversity of microbiota than the colon. Several reasons contribute to this difference. Firstly, the transit time in the small intestine is relatively faster, allowing less time for the bacteria to colonize and establish. Additionally, the small intestine is exposed to the influx of digestive enzymes and bile from the liver, which can impact the growth and survival of certain bacterial species. Lastly, food substrates are delivered intermittently to the small intestine, further limiting the availability of nutrients for bacterial growth.

It’s important to note that even though the small intestine has a lower bacterial population, it still plays a crucial role in the digestion and absorption of nutrients.

Understanding these regional differences in the composition and function of the gut microbiota is essential for unraveling their contributions to overall gastrointestinal health and metabolic processes.

The human oral cavity harbors a diverse and abundant microbial community known as the oral microbiome. This microbiome typically exists in the form of a biofilm, commonly called dental plaque.

The oral microbiome includes various bacteria, such as Streptococcus mutans, Porphyromonas gingivalis, Staphylococcus, and Lactobacillus. Streptococcus mutans is a prominent component of the oral microbiota and is strongly associated with the formation of dental plaque and tooth decay (caries). It can metabolize sugars, produce acid, and contribute to the demineralization of tooth enamel.

Lactobacillus is another bacterium in the oral microbiome that can ferment sugar and produce lactic acid. This acid can also contribute to the development of dental caries.

Beyond oral diseases like caries and periodontitis, the oral microbiome has been linked to several systemic diseases. Research has found associations between oral microbiota and conditions such as esophageal, colorectal, and pancreatic cancers, diabetes, Alzheimer’s disease, cardiovascular disease, cystic fibrosis, and rheumatoid arthritis.

However, it’s important to note that these associations do not necessarily imply causation, and further research is needed to fully understand the complex relationship between the oral microbiome and systemic diseases.

Interestingly, the oral microbiome can also be targeted for disease treatment. Probiotics, such as a particular strain of Streptococcus called Streptococcus A12, have been investigated for their ability to buffer the acidic pH within biofilms. This buffering effect may help prevent dental caries caused by acid-producing bacteria in the oral microbiome.

Understanding the composition, dynamics, and interactions within the oral microbiome is crucial for maintaining oral health, preventing oral diseases, and potentially influencing systemic health.

While the esophagus has its distinct microbiome, that is beyond the scope of this discussion. Moving on to the stomach, let’s discuss the basics.

The human stomach harbors a diverse array of microbes, with five major phyla dominating the microbial population: Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria, and Proteobacteria. At the genera level, certain microbial genera are particularly prevalent in the stomach microbiome. These include Prevotella, Streptococcus, Veillonella, Rothia, and Haemophilus, among the most common genera in the gastric environment.

Observing the intricate composition of the human stomach microbiome and the key players contributing to its microbial diversity is fascinating. Understanding the role of these significant phyla and genera in the stomach microbiota is crucial for unraveling the complexities of digestive health and disease susceptibility.

Several factors influence the composition and diversity of the gastric microbiota, including diet, medication usage, inflammation, and Helicobacter pylori infection.

Diet: Dietary patterns and nutrient composition can affect the microbial composition of the stomach. Studies have shown that diets high in fruits, vegetables, and fiber are associated with a more diverse and stable gastric microbiome. In contrast, diets high in fat and sugar can disrupt the microbial balance in the stomach and promote the growth of potentially harmful bacteria.

Medication Usage: Medications such as proton pump inhibitors (PPIs) and antibiotics can significantly affect the gastric microbiota. PPIs work by reducing stomach acid production, which can alter the stomach’s environment and affect the growth of certain bacteria. Antibiotics, conversely, can cause extensive changes in the gastric microbiota by eliminating harmful and beneficial bacteria and allowing opportunistic pathogens to colonize.

Inflammation and Gastric Mucosa: Inflammation of the gastric mucosa and atrophic gastritis can also impact the composition of the gastric microbiota. Chronic inflammation can decrease microbial diversity, promote the growth of pathogenic bacteria, and cause imbalances in the stomach microbial community.

Helicobacter pylori Infection: Helicobacter pylori infection is one of the most significant factors affecting the gastric microbiota. H. pylori is a Gram-negative bacterium that colonizes the stomach mucosa, and its presence can cause a range of gastric conditions, including gastritis, peptic ulcers, and gastric cancer. H. pylori has been shown to alter the gastric microbiota by reducing microbial diversity and increasing the numbers of certain bacterial species.

Understanding the factors influencing the gastric microbiota is essential for developing strategies to promote a healthy microbial community and prevent or treat gastric diseases.

The small intestine is the most extended section of the gastrointestinal (GI) tract and has its own microbiome. Its microbial composition differs from that of the stomach and colon. Some bacterial genera commonly found in the small intestine include Lactobacillus, Clostridium, Staphylococcus, Streptococcus, and Bacteroides.

The population of bacteria in the small intestine increases as you move from the duodenum (the first part of the small intestine) to the distal ileum (the last part before the large intestine). The bacterial counts in the duodenum range from around 104-105 colony-forming units (CFU) per milliliter, while in the distal ileum, where transit slows down, the counts increase to 107-108 CFU/mL.

The composition of the small intestinal microbiota also changes gradually along the length of the small intestine. There is an increase in the proportion of gram-positive bacteria compared to gram-negative bacteria, as well as a shift from facultative anaerobic (oxygen-tolerant) to strict anaerobic species.

Small Intestinal Bacterial Overgrowth (SIBO) is a condition characterized by excessive bacteria within the small intestine. This overgrowth can disrupt the normal digestion and absorption processes, causing abnormal fermentation of nutrients and leading to symptoms such as excessive gas, bloating, diarrhea, and malabsorption.

SIBO has been linked to various conditions, with up to 78% of irritable bowel syndrome (IBS) cases being associated with SIBO.

It’s interesting to note that hormonal deficiencies can contribute to the development of SIBO. Hormones play a crucial role in regulating gut motility and maintaining the balance of gut bacteria. Any disruption in hormonal levels can affect food movement through the GI tract and promote the growth of bacteria in the small intestine.

Indeed, the various aspects of our health, including gut health and hormonal balance, are interconnected, and disruptions in one area can impact others. Understanding the role of the small intestine microbiome and conditions like SIBO can help develop effective treatments and maintain overall health. Now, let’s talk about the section of the G.I. tract where much of the “action” is: the colon.

The colon, also known as the large intestine, houses the most diverse and abundant microbiome in the human gastrointestinal tract. This microbiome is composed mainly of obligate anaerobes, which thrive in the colon’s low-oxygen environment.

Among the most abundant bacteria in the colon are members of the genus Bacteroides and anaerobic gram-positive cocci like Peptostreptococcus, Eubacterium, Lactobacillus, and Clostridium.

The colonic microflora plays a vital role in various host digestive processes. One of its primary functions is the fermentation of non-digestible carbohydrates, including dietary fibers that escape digestion in the upper gastrointestinal tract.

The colonic bacteria break down these fibers through fermentation, producing several beneficial byproducts, such as short-chain fatty acids (SCFAs). SCFAs, mainly acetate, propionate, and butyrate, are important energy sources for the colonic epithelial cells and contribute to overall colon health.

The gut microbiome is also involved in other essential functions, including:

  1. Nutrient metabolism: The colonic bacteria metabolize certain compounds that the host cannot digest, such as complex polysaccharides, proteins, and bile acids. The microbiome can influence nutrient availability and absorption in the host through these metabolic processes.
  2. Vitamin synthesis: Some colon bacteria can produce vitamins, such as vitamin K and specific B vitamins. These microbial-synthesized vitamins can contribute to the host’s vitamin status and play essential roles in various physiological processes.
  3. Immune modulation: The gut microbiome interacts with the host immune system, helping to educate and shape its development. The microbial community in the colon can regulate immune responses, promote immune tolerance, and protect against potential pathogens.

Many studies on the gut microbiome rely on analyzing fecal samples to study the luminal “fecal” colonic microbiome. Fecal samples provide valuable insights into the overall composition and functions of the colonic microbiota.

However, it’s worth noting that there are also colonic-adherent microbiota that interact more directly with the host immune system. These adherent microbes require sampling through intestinal biopsies during procedures like colonoscopy to study their specific interactions with the host.

Understanding the functioning of the gut microbiome is a complex and evolving field of research. Ongoing studies uncover the intricate roles of the colonic microbiota in human health and disease.

How the gut microbiome works

Yes, it is true that approximately ten times as many microbial organisms inhabit our bodies as there are human cells. These microbes colonize various body parts, including the gut, digestive tract, genitals, mouth, and nose.

The health of someone’s microbiome is determined by the balance between “bad bacteria” and “good bacteria.” A healthy microbiome requires a higher ratio of beneficial to harmful bacteria to maintain resilience and stay symptom-free.

Unfortunately, factors such as a poor diet, high levels of stress, and exposure to environmental toxins can disrupt this balance, leading to an overabundance of potentially dangerous bacteria, fungi, yeast, and pathogens.

Although the human microbiome is home to various types of microorganisms, bacteria have been found to play a vital role in controlling immune function and inflammation. Researchers have identified over 10,000 different species of microbes in the human body, each with unique DNA and specific functions.

Maintaining a healthy balance of bacteria in the microbiome is crucial for overall health and well-being. Promoting diversity and abundance of beneficial bacteria through a balanced diet, reducing stress levels, and minimizing exposure to toxins can help support a healthy microbiome and its associated functions.

Indeed, researchers are still uncovering the many ways that different strains of bacteria affect various aspects of human health. Even so, some general characteristics of a healthy versus unhealthy microbiome have emerged in existing research.

A healthy microbiome is typically characterized by a high diversity of bacterial species, with a balance between “good” and “bad” bacteria. Additionally, it generally is more stable and resilient, able to resist changes in response to various factors such as diet, stress, and environmental toxins.

Conversely, an unhealthy microbiome is often characterized by a lower diversity of bacterial species and an overgrowth of pathogenic or “bad” bacteria. These imbalances in the microbiome have been associated with various health conditions, including obesity, autoimmune disorders, cognitive decline, and inflammation.

In summary, a healthy microbiome is diverse, balanced, and stable, while an unhealthy microbiome lacks these qualities. Ongoing research will likely uncover additional factors contributing to microbiome health and disease. Here are the basic functions of the microbiome.

Functions of a Healthy Gut Microbiome

As you know, the gut microbiome profoundly impacts our overall health and plays a vital role in various physiological processes. Here are some additional points to consider:

  1. Mucosal homeostasis and immune cell modulation: The gut microbiome helps maintain the balance and function of immune cells in the gut mucosa. It promotes immune cell development, regulates immune responses, and supports the integrity of the gut lining.
  2. Vitamin synthesis: Some beneficial bacteria in the gut can synthesize specific vitamins, such as vitamin K and many B vitamins. These vitamins are essential for various physiological processes in the body.
  3. Influence on gastrointestinal hormones: The gut microbiome can impact the production and response to gastrointestinal hormones, such as ghrelin and leptin, which are involved in appetite regulation and metabolism.
  4. Maintenance of intestinal homeostasis: The gut microbiome helps maintain a healthy environment in the intestines by regulating factors such as pH levels, bile acid metabolism, and nutrient absorption. This contributes to the overall balance and proper functioning of the digestive system.
  5. Regulation of epithelial cell proliferation and differentiation: The gut microbiome influences the growth, proliferation, and differentiation of epithelial cells that line the intestinal wall. This is crucial for maintaining a healthy gut barrier and proper nutrient absorption.
  6. Prevention of pathogenic colonization: Beneficial bacteria in the gut compete with and prevent the colonization of pathogenic microorganisms. They help maintain a balanced microbial community and reduce the risk of infections or overgrowth by harmful bacteria.

So, what is “normal?”

Normal Versus Abnormal Gut Microbiome

A healthy microbiome begins to form from birth and develops during early childhood. By age 3, a person’s microbiome closely resembles an adult’s. However, the microbiome continues to evolve throughout life, adapting to changes in diet, lifestyle, and other factors.

While the relative abundances of different microbial species can fluctuate, the overall community and function of the microbiome remain relatively stable and healthy. This stability allows the microbiome to perform important functions, such as synthesizing specific vitamins, aiding digestion, and supporting immune function.

On the other hand, an unhealthy microbiome can also be stable, leading to chronic disease. The concept of resilience is crucial in understanding the impact of disturbances on the microbiome. A resilient microbiome can withstand temporary disruptions, such as a single course of antibiotics, and return to its original state.

However, persistent interferences, like long-term changes in diet, recurrent antibiotic use, or disruptions during vulnerable periods (such as infancy or the peripartum period), can create a new, disease-promoting state in the microbiome.

It’s important to note that the relationship between the microbiome and specific diseases is still an active area of research, and more studies are needed to fully understand the complex interactions. However, maintaining a diverse and resilient microbiome through a balanced diet, healthy lifestyle choices and judicious (sparing) use of medications may support overall gut health.

There are specifically known indicators of a healthy gut microbiome. For example, gut microbiome alpha diversity (diversity in one sample) has been linked to positive human health, while lower levels of diversity are associated with several acute and chronic diseases. Another well-known marker is the Firmicutes to Bacteroidetes (F/B) ratio.

In addition, several particular bacterial species have been recognized for their benefits, such as Faecalibacterium prausnitzii. F. prausnitzii has been consistently reported as one of the primary butyrate producers in the gut, with the ability to reduce gut mucosal inflammation and protect against both colorectal cancer and inflammatory bowel disease. We’ll get “heavily” into the importance of butyrate and other vital fatty acids.

Another important bacterium is Akkermansia muciniphilaA. muciniphilia has been shown to contribute to the maintenance of a healthy gut barrier, regulate immunity, and modulate inflammation. Notably, a lower abundance of this organism has been associated with multiple diseases.

If you are reading this article, chances are you’ve read other articles about the gut microbiome. And perhaps you’ve been as confused as everyone else over the gut microbiome terminology. Let me clarify all of this terminology for you so you know what’s what moving forward. Let’s first discuss the terminology of the gut microbiome and gut health supplements.


Prebiotics are defined as “selectively fermented ingredients that result in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefit(s) upon host health.”

The original definition of prebiotics, established in 1995, described these compounds as non-digestible food ingredients that play a crucial role in influencing the growth and activity of specific bacteria in the colon. By selectively stimulating the proliferation of one or a limited number of beneficial bacterial species, prebiotics were believed to enhance host health through their interactions with the gut microbiota.

The updated definition of prebiotics in 2004 introduced three critical criteria to refine the classification further. According to this revised definition, prebiotics should meet the following requirements:

Resistant to Gastric Acidity and Hydrolysis: Prebiotics must demonstrate resistance to gastric acidity, enzymatic hydrolysis by mammalian enzymes, and absorption in the gastrointestinal tract to reach the colon.

Fermented by Intestinal Microbiota: Prebiotics should be fermentable by the intestinal microbiota, indicating their ability to undergo microbial metabolism in the gut environment.

Selective Stimulation of Beneficial Bacteria: Prebiotics must selectively stimulate intestinal bacteria’s growth and/or activity associated with health and well-being, emphasizing their role in promoting the proliferation of beneficial microbial species in the gut.

Now for the benefits and more specifics.

Benefits and specifics of Prebiotics

Prebiotics can modify the gastrointestinal microbiota through dietary strategies for potential health benefits. Studies have shown that increased intake of dietary fiber, particularly fermentable fiber, can promote the growth and diversity of beneficial gut bacteria, leading to improved gut health and reduced risk of chronic diseases.

Low fiber intake, prevalent in Western societies, has been linked to impaired gut microbiota with reduced diversity and an overgrowth of potentially harmful bacterial species. This may contribute to the development of chronic non-communicable diseases, including obesity, cardiovascular disease, type 2 diabetes, and colon cancer.

Intervention studies in humans have also demonstrated that increasing dietary fiber and whole grains intake can increase gut bacterial diversity, highlighting the importance of a high-fiber diet for maintaining a healthy gut microbiome.

Therefore, prebiotic-rich foods such as whole grains, fruits, vegetables, and legumes can be an effective dietary strategy to promote gut health and potentially prevent chronic diseases.

Prebiotic Fibers

According to the definition provided by the Codex Alimentarius Commission in 2009, dietary fibers are described as “carbohydrate polymers with ten or more monomeric units, which are neither digested nor absorbed in the human small intestine,” and they fall into three categories:

  1. Edible carbohydrate polymers naturally occurring in foods as consumed.
  2. Edible carbohydrate polymers obtained from food raw materials through physical, enzymatic, or chemical means have a beneficial physiological effect supported by generally accepted scientific evidence.
  3. Generally accepted scientific evidence supports Edible synthetic carbohydrate polymers with a demonstrated beneficial physiological effect.

This definition recognizes the diverse range of dietary fibers in natural foods and those obtained through various processing methods. It emphasizes that these carbohydrates should resist digestion and absorption in the small intestine and have scientifically demonstrated health benefits.

Indeed, plant-based fibers can be classified into various categories based on their origin, such as cereals and grains, fruits, vegetables, nuts, and legumes. It is important to note that different types of plants contain different fibers with distinct chemical compositions and physicochemical properties.

For example, bananas contain resistant starch and inulin-type fructans, which are prebiotic fibers that can promote the growth of beneficial gut bacteria. On the other hand, apples are a good source of pectin, another dietary fiber with health benefits.

Diets rich in various plant-based foods can provide a wide range of dietary fibers, thus supporting the diversification of the gut microbiota. The different types of fibers in these foods can selectively stimulate the growth of beneficial bacteria in the gastrointestinal tract, leading to a more diverse and balanced microbiota composition.

Therefore, consuming diverse plant-based foods can contribute to a healthier gut microbiome and overall gut health.

The microbial conversion of complex polysaccharides into monosaccharides involves a variety of biochemical pathways, which are facilitated by the enzymatic activities of bacteria in the gut.

When complex carbohydrates, such as dietary fibers, reach the colon, gut bacteria ferment them. The end products of this fermentation process include short-chain fatty acids (SCFAs) and gases such as hydrogen (H2) and carbon dioxide (CO2).

SCFAs, namely acetate, propionate, and butyrate, are the primary products of bacterial fermentation in the colon. These SCFAs are crucial in maintaining gut health and have several beneficial effects on the host.

SCFAs serve as an energy source for colonocytes, promote sodium and water absorption, and help regulate the colon’s pH. They also have immunomodulatory properties and can influence various body processes, including inflammation and metabolism.

The proportions of SCFAs produced during fermentation can vary based on the types of carbohydrates ingested and the gut microbiota composition. Different bacteria have different metabolic capabilities, which can result in variations in the production and ratios of SCFAs among individuals.

Therefore, measuring SCFAs in the colon can provide valuable information about bacterial fermentation and the health status of the gut microbiota.

Prebiotic Oligosaccharides

A regular diet typically contains various prebiotic oligosaccharide carbohydrates, including inulin-type fructans. Inulin-type fructans naturally occur in foods such as chicory root, Jerusalem artichoke, garlic, and certain cereals like wheat.

It is important to note that inulin-type fructans in foods can contribute to their prebiotic effects. Prebiotics are non-digestible dietary fibers that promote the growth and activity of beneficial bacteria in the gut, thus supporting gut health.

Inulin-type fructans, specifically, have been shown to selectively stimulate the growth of Bifidobacteria and Lactobacilli, which are considered beneficial bacteria in the gut microbiota. Remember that wheat grown in the U.S. may be problematic for many people, so watch out for GMOs and gluten.


These diary-derived prebiotics have potential immune-modulating effects. Beta-galacto-oligosaccharides are prebiotic dietary fiber that can benefit the gut microbiota and immune system.

In a well-done study conducted on elderly subjects, supplementation with β-GOS was shown to have several positive effects on immune function. Some key findings from the study include:

Increased levels of the immuno-regulatory cytokine interleukin-10 (IL-10) regulate the immune response and reduce inflammation.

Significant reduction in the expression of IL-1β, a pro-inflammatory cytokine associated with the inflammatory response.

Increased interleukin-8 (IL-8) blood levels are involved in immune cell recruitment and activation.

Improvement in Natural Killer (NK) cell activity is vital for the body’s defense against viruses and cancer cells. Next, let’s move on to something you probably have heard about called resistant starch.

Resistant Starch

Resistant starch (RS) is naturally present in cereal grains and other starch-containing foods. It refers to a type of starch that resists digestion in the small intestine and reaches the large intestine intact. The resistance to digestion can be influenced by factors such as granule morphology, amylose-amylopectin ratio, and interactions with other food components.

RS is classified into four classes based on its digestibility. These classes help categorize the different types of RS based on their resistance to digestion and their impact on gut health.

One interesting study demonstrated that RS has a bifidogenic effect, meaning it increases the concentration of beneficial bacteria such as Bifidobacteria.

It also increased the levels of other beneficial bacteria, including Bacteroidetes, Akkermansia, and Allobaculum species. These bacteria are essential in maintaining gut health and promoting a balanced gut microbiota.

Furthermore, studies conducted in vitro and on mice have shown that resistant starch increases the production of short-chain fatty acids (SCFAs).

SCFAs are beneficial compounds gut bacteria produce during dietary fiber fermentation, including RS. SCFAs have several health benefits, such as providing energy for colonocytes, promoting gut health, and influencing various physiological processes.

While there are limited studies on humans, some evidence suggests that high amylose maize starch (HAMS) administration, a type of resistant starch, may have prebiotic effects in adults.

Other examples of resistant starch include cooked and cooled pasta and rice, oats, green bananas, certain legumes, and raw potato starch. For my extensive practice of autoimmune patients eating strict AIP, the best choice is green bananas.


The primary sources of polyphenols are fruits such as berries, grapes, citrus fruits, apricots, apples, plums, cherries, peaches, and tropical fruits. Additionally, polyphenols can be found in popular beverages such as green and black tea, fruit juices, coffee, red wine, cocoa, and beer, as well as in various seeds, grains, and nuts.

Vegetables are also a good source of polyphenols, with onions, spinach, broccoli, cauliflower, artichoke, tomato, beans, soybeans, carrots, capers, and olives being some of the most common sources. Even spices and herbs such as clove bud, turmeric, celery, parsley, mint, rosemary, thyme, sage, dill, curry, and ginger contain high levels of polyphenols.

Polyphenols are a diverse group of compounds, and their concentration and type can vary widely depending on the food source. However, a diet rich in fruits, vegetables, nuts, and whole grains is generally associated with a high intake of polyphenols and other beneficial phytochemicals.

Polyphenols have numerous health benefits, including antioxidant and anti-inflammatory effects. Some studies have suggested they may protect against chronic diseases such as cardiovascular disease, type 2 diabetes, and certain cancers.

Flavonoid Polyphenols

Flavonoids are a major class of dietary polyphenols, constituting up to 60% of polyphenol intake. Due to their widespread presence in various foods and impressive biological functions and activities, flavonoids are continuously being studied for their potential as drugs or food supplements.

Some of the most common flavonoids include:

  1. Quercetin: This flavanol is abundant in foods such as onions, broccoli, tea, and apples. Quercetin is known for its antioxidant and anti-inflammatory properties.
  2. Catechin: A flavanol found in tea (mainly green tea) and various fruits, catechin is recognized for its potential health benefits, such as cardiovascular protection and anticancer properties.
  3. Naringenin: A flavanone present in citrus fruits like oranges, grapefruits, and lemons, naringenin has been studied for its antioxidant and anti-inflammatory effects.
  4. Cyanidin and Anthocyanin: These flavonoids give fruits and berries such as blackcurrants, raspberries, strawberries, blueberries, and grapes their vibrant red, purple, or blue color. Anthocyanins have various health benefits, including cardiovascular health and improved cognitive function.
  5. Daidzein and Genistein: These are the main isoflavones found in soybeans and soy products. Isoflavones have been studied for their potential role in hormonal balance and reducing the risk of certain chronic diseases.

Other Flavonoid Polyphenols


  • Naturally occurring phytochemicals of the flavonoid class.
  • Referred to as “phytoestrogens” due to their estrogen-like effects.
  • Predominant sources are legumes, particularly soy products.
  • Commonly found in fermented soy foods like soy paste and unfermented soy products like tofu and soy flour.


Phenolic acids:

  • Found in leguminous plants, vegetables (spinach, broccoli, kale), berry fruits, apples, coffee, tea, citrus juices, wine, beer, cereal brans, and olive oil.
  • Provide substantial antioxidative and anticancer activities.

Hydroxybenzoic acids:

  • Simple aromatic acids with substantial antioxidative and anticancer activities.
  • Main representatives are gallic and ellagic acid, abundant in fruits and nuts.


  • Naturally occur as glycosides named anthocyanins.
  • Responsible for the red, purple, and blue hues of various fruits, vegetables, cereal grains, and flowers.
  • Main sources include teas, honey, wines, fruits (apples, berries), vegetables (beets, onions), nuts, olive oil, cocoa, and certain cereals.


  • Another important class of naturally occurring flavonoids.
  • Metabolic precursors of certain flavonoids and isoflavonoids.
  • Abundant in hops and, therefore, in beer, as well as citruses, apples, certain vegetables (shallots, tomatoes, potatoes, bean sprouts), and various plants and spices (licorice, cardamom).

Ellagic acid:

  • Dimeric derivative of gallic acid.
  • Richest sources include blackberries, raspberries, strawberries, cranberries, pomegranates, walnuts, and pecans.
  • Possesses anti-carcinogenic, antioxidant, anti-inflammatory, anti-bacterial, anti-atherosclerosis, anti-hyperglycemic, anti-hypertensive, anti-fibrosis, and cardioprotective effects.

Hydroxycinnamic Acids 

Cinnamic acid:

  • Acts as the precursor of hydroxycinnamic acids, a diverse group of phenolic substances present in almost every plant.
  • Common hydroxycinnamic acids include caffeic acid and ferulic acid.

Caffeic acid:

  • Found in many fruits such as apples, plums, tomatoes, and grapes.

Ferulic acid:

  • Found in tomatoes and beer in an accessible form, making it efficiently absorbed.
  • Also found in an esterified form in grain cell walls (in cereals).

Chlorogenic acid:

  • Another essential phenolic acid with varying intake levels.
  • Coffee drinkers can consume up to 800 mg per day of chlorogenic acid.

Honorable mentions include rosmarinic acids, curcuminoids, and stilbenes, which will be discussed below in the “supplements” section. Now, let’s switch our focus from prebiotics to probiotics.



Probiotics are live microorganisms that provide health benefits when consumed or applied to the body. They can be found in several sources, such as yogurt and other fermented foods, dietary supplements, and beauty products. Probiotics often contain bacteria from groups like Lactobacillus and Bifidobacterium, which are commonly used. In addition to bacteria, some probiotics may also include yeasts like Saccharomyces boulardii.

Different types of probiotics may have other effects. For example, suppose a specific kind of Lactobacillus helps prevent an illness. That doesn’t necessarily mean another type of Lactobacillus or Bifidobacterium probiotics would do the same thing.

Probiotics work through various mechanisms to exert their beneficial effects on the host. Here are the three primary mechanisms:

  1. Synergistic Effects with Indigenous Microbiota: Probiotics interact with the existing beneficial bacteria in the gut. This interaction helps promote a healthy balance of the gut microbiota. Probiotics can influence the production of short-chain fatty acids (SCFAs), which are essential for gut health. SCFAs provide energy for the colon cells, support maintaining the intestinal barrier function, and have anti-inflammatory properties. I’ll go into this in much greater depth shortly.
  2. Enhancement of Epithelial Barrier Integrity: Probiotics can strengthen the integrity of the epithelial barrier, which is the gut’s protective lining. By enhancing the barrier function, probiotics help prevent the passage of harmful substances from the gut into the bloodstream, reducing the risk of inflammation and other adverse health outcomes.
  3. Modulation of the Host’s Immune System: Probiotics can influence the immune system in the gut. They can help regulate immune responses, promoting a balanced and appropriate immune reaction. This modulation of the immune system can be beneficial in preventing and managing certain inflammatory conditions in the gut.

Additionally, probiotics have been found to affect electrolyte absorption, gut motility, and even the perception of painful sensations. These actions can further contribute to their overall beneficial impact on digestive health.

It’s important to note that the specific mechanisms of action may vary depending on the strain and probiotic used and the individual’s unique microbiome and health condition.

Now, let’s clarify what synbiotics, paraprobiotics, ghostbiotics, and postbiotics are. Whew, right? Let’s start with simple synbiotics.



Synbiotics are mixtures that consist of live microorganisms (probiotics) and substrates selectively utilized by host microorganisms (prebiotics) that provide a health benefit to the host. A symbiotic blend, which is what is commonly found for sale, typically contains a proven probiotic and a proven prebiotic.

There are two types of synbiotics: complementary and synergistic. A complementary synbiotic contains a live microorganism (which may or may not be a proven probiotic) and a substrate (which may or may not be a proven prebiotic). These components work together to provide a health benefit.

On the other hand, a synergistic synbiotic consists of a live microbe (not necessarily a proven probiotic) and a substrate (not necessarily a proven prebiotic) that the microbe can utilize for its growth. The combination of these components has a synergistic effect in promoting health.

In practical terms, a product labeled as a symbiotic blend typically contains a well-researched and proven probiotic strain combined with a proven prebiotic ingredient. The prebiotic substrate is often a fiber or polyphenol blend, which can selectively support the growth and activity of the probiotic microorganisms in the gut.



The scientific community has proposed various terms for inanimate microorganisms and their components that can provide health benefits. Some commonly used terms for these substances include non-viable probiotics, paraprobiotics, ghostbiotics, heat-inactivated probiotics, and postbiotics.

In 2021, the International Scientific Association for Probiotics and Prebiotics (ISAPP) defined postbiotics as “a preparation of inanimate microorganisms and/or their components that confer a health benefit on the host.” This definition encompasses various substances derived from microorganisms that can positively affect human health.

Postbiotics can include various components such as cell components, cell fragments, and metabolic products of microorganisms. These substances can be derived from microbial sources, including bacteria, yeast, and fungi.

The health benefits of postbiotics are thought to arise from their interactions with the host’s body, including interactions with the immune system, promoting a healthy gut environment, and influencing various physiological processes.

It’s worth noting that the term postbiotics has gained significant recognition within the scientific community. However, it is important to continue researching and understanding the specific mechanisms of action and health benefits associated with these inanimate microorganisms and their components. Next, let’s identify the by-products we want produced by a healthy gut microbiome.

Beneficial gut microbiome byproducts

Intestinal microorganisms play a crucial role in various metabolic processes, including producing short-chain fatty acids (SCFAs). SCFAs, also known as volatile fatty acids, are an essential carbon flow from the diet to the host microbiome. They have several beneficial effects on the host’s health.

Maintaining a balanced intestinal microbiome promotes overall health and prevents diseases. Probiotic microorganisms have been found to positively impact the balance of the intestinal microbiome and the production of metabolites, including SCFAs.

Only a few of the approximately 60 known phyla of bacteria are commonly found in the human intestines. These include Firmicutes, Bacteroides, Actinobacteria, Fusobacteria, Proteobacteria, Verrucomicrobia, Cyanobacteria, and Spirochaetes. However, the two dominant bacterial phyla in the human gut are Gram-positive Firmicutes (such as Lactobacillus spp., Bacillus spp., and Clostridium spp.) and Gram-negative Bacteroidetes.

These phyla contain various bacterial species that contribute to the diversity and functionality of the gut microbiota. Imbalances in the relative abundance of these phyla have been associated with certain health conditions.

The gut microbiome has a remarkable ability to biotransform various chemical compounds. One of its essential roles is converting complex nutrients into simpler forms that the host can easily absorb and utilize.

Intestinal microorganisms break down complex nutrients, including plant cell wall components such as cellulose, pectin, hemicellulose, and lignin. These components are typically indigestible by the host’s enzymes alone. However, the gut microbiota contains specialized microorganisms with the necessary enzymes to degrade these complex carbohydrates. And when the fermentation starts- magic!

Short-chain Fatty Acids

Gut bacteria microbially ferment complex nutrients, producing short-chain fatty acids (SCFAs) as metabolic byproducts. The most common SCFAs produced in the gut are acetate, propionate, and butyrate, which constitute 95%, while formic, valerian, caproic, and lactic acids comprise approximately 5% and play lesser roles.

SCFAs have several vital functions in the body. They serve as an energy source for the cells lining the colon and are also absorbed into the bloodstream, where they can have systemic effects. For example, butyrate is a primary energy source for colonocytes and helps maintain the integrity and health of the intestinal barrier.

SCFAs also have anti-inflammatory properties, help regulate immune responses, and contribute to overall health and proper gut functioning. They have been associated with various health benefits, including promoting gut motility, improving nutrient absorption, and influencing metabolic processes.

SCFA production in commensal(host) and probiotic strains of bacteria

Commensal (host microbiome) species of bacteria noted to produce beneficial SCFA’s:

Bifidobacterium spp., Blautia hydrogentrophica, Prevotella spp., and Streptococcus spp. have been shown to produce acetic acid. Akkermansia muciniphilia and Bacteroides spp. have both been shown to produce acetic and propionic acid. Dalister succinatiphilus, Eubacterium spp. (e.g., E. halli), Megasphaera elsdenii, Phascolarctobacterium succinatutens, Roseburia spp., Salmonella spp., and Veillonella spp. have all been demonstrated to produce propionic acid.

Coprococcus spp. (e.g., Coprococcus catus), Roseburia inulinivorans produce both propionic and butyric acid. Anaerostipes spp., Coprococcus comes, Coprococcus eutactus, Clostridium symbiosum, Eubacterium rectale, Eubacterium hallii, Faecalibacterium spp. (e.g., Faecalibacterium prausnitzii), Roseburia spp. (e.g., Roseburia intestinalis) are major butyrate producers. Finally, we know that Clostridium spp. and Ruminococcus spp. have been shown to produce acetic, propionic, and butyric acid. I’m sure the database will grow daily and be larger once this article is published!

Let’s take a break here to note that you will find a breakdown of good microbiome labs and testing, which will be discussed at length near the end of this article. Get acquainted with some of the heavy-hitter species you want in your microbiome.  Let me say the same with the upcoming discussion of probiotics, which we are only starting to see being produced for clinical outcomes. Here are the top ones.

Bifidobacterium spp. will produce mainly acetic and lactic acids. Lactobacillus rhamnosus GG (LGG) and Lactobacillus gasseri produce primarily propionic and lactic acids.  Bifidobacterium longum and Bifidobacterium bifidum produce acetic, propionic, and lactic acids. Lactobacillus salivarius spp salcinius and Lactobacillus agilis produce propionic, butyric, and lactic acids. Finally, a well-studied strain, Lactobacillus acidophilus, has been demonstrated to produce acetic, propionic, butyric, and lactic acids.

Now, let’s examine the benefits of the main SCFAs. Butyrate leads the pack for overall health, but acetate and propionate are gaining steam as research progresses. To illustrate the importance of SCFAs, let’s start by discussing the “master SCFA”: butyrate.

Butyrate and gut health

Butyrate is often considered a “master” short-chain fatty acid (SCFA) due to its numerous beneficial effects on the gastrointestinal tract and overall health. Specific gut bacteria primarily produce butyrate through the fermentation of dietary fibers, such as resistant starches and other complex carbohydrates.

Butyrate plays a crucial role in maintaining gut health and function. Some key functions and benefits of butyrate include:

  1. Energy Source: Butyrate is the primary energy source for the cells lining the colon, known as colonocytes. These cells rely on butyrate to fuel their metabolic processes and maintain structural integrity.
  2. Gut Barrier Integrity: Butyrate helps to strengthen the gut barrier by promoting the production of mucin, which forms a protective barrier in the intestinal lining. This barrier helps prevent the entry of harmful substances into the bloodstream.
  3. Anti-Inflammatory Effects: Butyrate has anti-inflammatory properties and can help modulate the immune response in the gut. It can reduce inflammation and promote the balance of immune cells in the gut, which is beneficial for conditions characterized by inflammation, such as inflammatory bowel diseases (IBD).
  4. Regulation of Gene Expression: Butyrate can influence gene expression in colon cells, leading to changes in cellular processes related to inflammation, cell proliferation, and apoptosis (cell death). This regulatory function contributes to the maintenance of a healthy gut environment.
  5. Metabolic Benefits: Butyrate has been shown to influence metabolic processes related to glucose and lipid homeostasis. It can help regulate blood sugar levels, improve insulin sensitivity, and help maintain a healthy metabolism.

In conditions where there is an imbalance in the gut microbiome, leading to a decrease in the number of butyrate-producing bacteria and a reduction in SCFA levels, such as in inflammatory bowel diseases (IBD), irritable bowel syndrome (IBS), type 2 diabetes (T2D), obesity, autoimmune disorders, and cancer, the beneficial effects of butyrate may be disrupted.

This imbalance can contribute to gut barrier dysfunction, low-grade inflammation, and metabolic dysregulation in these conditions.

Therefore, promoting butyrate production and maintaining a healthy balance of SCFAs in the gut through dietary interventions, probiotics, and prebiotics can support gut health, reduce inflammation, and improve metabolic outcomes in these conditions.

Butyrate and the gut-brain barrier

The bidirectional communication between the gut microbiome and the central nervous system, known as the gut-brain axis, is an area of growing research interest. Short-chain fatty acids (SCFAs) influence, particularly butyrate, on neural processes, and neuroinflammation, is critical to this interaction.

While systemic absorption of SCFAs from the intestine into the bloodstream is minimal, with butyrate exhibiting lower concentrations than propionate and acetate, it’s important to note that the concentration of SCFAs in the brain itself is negligible. This means that direct activation of neuronal receptors by SCFAs in the brain is unlikely.

Instead, the proposed mechanism for SCFAs’ influence on neural processes is through the regulation of neuroinflammation. SCFAs, particularly butyrate, have been shown to have anti-inflammatory effects on the gut and systemic circulation.

These anti-inflammatory properties can indirectly impact the brain by modulating immune responses and reducing inflammation.

Neuroinflammation, characterized by activating immune cells and releasing pro-inflammatory molecules in the brain, has been implicated in various neurological disorders and conditions. By regulating neuroinflammation, SCFAs can influence neuronal function, mood, memory, and recovery after injuries.

Moreover, SCFAs can indirectly affect the gut-brain axis by modulating the release of certain neurotransmitters, such as serotonin and gamma-aminobutyric acid (GABA), which play essential roles in mood and cognition.

The specific mechanisms by which SCFAs modulate neuroinflammation and influence neural processes are still an area of ongoing research. However, the emerging evidence suggests that the gut microbiome and its metabolic byproducts, including SCFAs, have the potential to impact brain function and contribute to the pathophysiology of neurological disorders.

Butyrate and Aging

Gut barrier integrity, enhancement of mitochondrial function, enhancement of immune responses, and even beneficial effects on telomeres all point to butyrate’s role in slowing the aging process. Quickly increase your butyrate levels with the consumption of MCT oil. I use this exclusively for cooking: odorless, tasteless, with a low flash point-perfect!

Propionic acid (Propionate)

The gut microbiome has been implicated in developing and progressing atherosclerotic cardiovascular disease (CVD). Compared to healthy controls, individuals with atherosclerotic CVD have observed changes in gut microbial composition, specifically an increased abundance of certain bacteria and a depletion of butyrate and propionate-producing bacteria.

A metagenome-wide association study found that patients with atherosclerotic CVD had higher levels of Enterobacteriaceae and Streptococcus spp. while experiencing a relative depletion of bacteria that produce butyrate and propionate. This suggests that short-chain fatty acids (SCFAs), including butyrate and propionate, may be functional in promoting cardiovascular health.

Propionate has been shown to have vasodilating effects in the vasculature by activating the G protein-coupled receptor 41 (GPR41) in the vascular endothelium. This activation decreases blood pressure.

Consume omega-3-rich fish like sardines, salmon, or mackerel to increase propionate levels. Omega-3 fatty acids, found in abundance in these types of fish, have been associated with beneficial effects on cardiovascular health. Due to propionate levels? At least partially, yes, indeed. Now, let’s turn to our last SCFA, acetate.



Acetate, one of the short-chain fatty acids (SCFAs), plays a role in weight control and metabolic issues, particularly insulin sensitivity. The interplay between the gut microbiota, host metabolism, and metabolic health is an area of growing research interest.

The gut microbiota has been found to regulate various aspects of metabolism and peripheral tissues such as adipose tissue, skeletal muscle, liver, and pancreas through the production of metabolites, including SCFAs. Acetate has been shown to benefit host energy and substrate metabolism.

Animal and human studies have demonstrated that acetate influences metabolism by promoting the secretion of gut hormones such as glucagon-like peptide-1 (GLP-1) and peptide YY (PYY).

These hormones affect appetite regulation, leading to a reduction in food intake. Additionally, acetate has been found to reduce whole-body lipolysis, lower systemic levels of pro-inflammatory cytokines, increase energy expenditure, and enhance fat oxidation.

These effects of acetate on host metabolism contribute to improved insulin sensitivity and may have implications for weight control and metabolic health. Because of the recent social media attention regarding vinegar ingestion and the national obsession with weight loss, let me discuss how to increase your acetate levels.

Acetate from Dietary Sources

Because recommending a TBSP of vinegar daily has become so commonplace, I will spend some time discussing why this might be beneficial. It’s not for the reasons touted in “folklore.” Commonly consumed kinds of vinegar contain between 4% and 8% acetic acid, and vinegar ingestion has gained attention in the scientific literature because of its acute effects on glucose and lipid metabolism.

Oral ingestion of vinegar can rapidly increase circulating acetate levels. In healthy participants, serum acetate levels increased from 120 µmol/L during placebo conditions to 350 µmol/L (after 15 min) and 200 µmol/L (after 30 min) following intake of vinegar (100 mL containing 0.75 g acetic acid) and acetic acid capsules (containing 0.75 g of acetic acid), respectively.

Acetic acid, a bioactive component with a dominant flavor in different types of vinegar (including cider, malt, plum, sherry, tomato, and wine vinegar), increases circulating acetate levels. It is important to consider the type of vinegar used, as its phenolic, flavonoid, and acetic acid content composition may differ.

Some kinds of vinegar, such as apple cider vinegar, grape vinegar, sherry vinegar, and balsamic vinegar, may contain other polyphenol residual components like gallic acid and catechins. These compounds have been linked to various health benefits, including improved blood sugar control, reduced inflammation, and reduced risk of chronic diseases.

In terms of microbiome alterations that produce more acetate-producing species, human fasting and caloric restriction interventions have described an increase in microbial diversity and abundance of essential acetate producers, such as Akkermansia muciniphila (A. muciniphila) and Bifidobacteria. Now, let’s switch gears back to the gut microbiome and what exactly shapes its composition. We’ll start with the basics.

What Shapes the Adult Microbiome?

Diet: Indeed, short—and long-term dietary habits significantly impact the gut microbiome. Short-term changes in diet can lead to rapid but reversible shifts in the microbiome, often accompanied by intermittent gastrointestinal symptoms.

Fiber, particularly microbiota-accessible carbohydrates (MACs), is crucial in nurturing the gut microbiome. When gut microbes ferment MACs, they produce short-chain fatty acids (SCFAs), such as acetate, butyrate, and propionate. These SCFAs have numerous health benefits, including improving gastrointestinal transit by influencing serotonergic pathways.

Low-MAC diets, which are low in fiber, can cause negative shifts in the gut microbiome. The lack of MACs essentially starves the gut microbes, leading them to seek food sources from the host epithelium and mucus. This epithelial barrier disruption can increase the risk of gut inflammation and other gastrointestinal issues.

In addition to low-fiber diets, additives like emulsifiers and artificial sweeteners can adversely affect the gut microbiome and increase the risk of metabolic and inflammatory disorders.

Optimizing fiber and MAC intake is recommended to promote a healthy gut microbiome and overall health. Including fiber-rich foods like fruits, vegetables, whole grains, legumes, and nuts can support the growth and diversity of beneficial gut bacteria. Minimizing the consumption of processed and packaged foods that contain additives can also help maintain a healthy gut microbiome.

Stress: It is well known that stress can negatively impact immune function. When your body perceives stress, it diverts energy and resources from the immune system to prioritize immediate survival responses. This shift in energy allocation can make you more susceptible to infections and result in more severe symptoms. Furthermore, chronic stress can lead to higher levels of inflammation, which can contribute to various health issues.

During stress, immune compounds called cytokines can contribute to the inflammatory response that damages healthy cells. This chronic inflammation can disrupt normal bodily functions and increase the risk of chronic diseases.

Exercise is a natural stress reliever and has numerous benefits for immune function. Physical activity can help lower inflammation, balance hormones, and strengthen the immune system. Exercise can increase the production of antibodies and stimulate the release of endorphins, which are natural mood elevators. These positive effects of exercise can help reduce stress and its impact on the immune system. Let’s delve into that a bit more.

Exercise: Exercise has been shown to positively impact the gut microbiome by increasing the abundance of beneficial bacteria and promoting gut diversity. Studies have found that athletes tend to have a more diverse gut microbiome and lower levels of inflammatory markers. Animal studies have also demonstrated that exercise-related changes in the gut microbiome can reduce susceptibility to inflammation and weight gain.

It’s important to note that the changes in the gut microbiota induced by exercise can be similar in magnitude to, but different from, dietary changes. While exercise can contribute to weight management, sustained weight loss also requires nutritional changes. Both training and a healthy diet are complementary in improving overall health, including the gut microbiome.

To achieve significant changes in the gut microbiota through exercise, it is generally recommended to engage in moderate to high-intensity exercise for 30 to 90 minutes at least three times per week or accumulate between 150 and 270 minutes weekly for a minimum of eight weeks. This consistent exercise routine will likely produce noticeable changes in the gut microbiome.

Vagal nerve stimulation: The brain, gut, and microbiota are connected through a bidirectional communication pathway known as the microbiota-gut-brain axis. This communication involves the autonomic nervous system, particularly the vagus nerve (V.N.). The Vagus nerve is a mixed nerve composed of approximately 80% afferent fibers (transmitting information from organs to the brain) and 20% efferent fibers (transmitting information from the brain to organs).

The Vagus nerve plays a crucial role in interoceptive awareness, allowing it to sense microbiota metabolites through its afferent fibers and transfer this information to the central nervous system. This information is then integrated into the autonomic network, influencing various physiological processes.

One important pathway mediated by the Vagus nerve is the cholinergic anti-inflammatory pathway. Through this pathway, vagal fibers release anti-inflammatory neurotransmitters, dampening peripheral inflammation and reducing intestinal permeability. By modulating inflammation and gut permeability, this pathway may play a role in shaping the composition of the gut microbiota and promoting healing of the gastrointestinal tract, including the “leaky gut” phenomenon.

Conversely, stress, accompanied by the release of cortisol, can inhibit the function of the Vagus nerve. This can negatively impact the gastrointestinal tract and the gut microbiota.

Chronic stress is implicated in the pathophysiology of conditions such as irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD), which are characterized by dysbiosis (microbial imbalance) and increased gut permeability. Vagal nerve stimulation with a device like the one found here has been demonstrated to improve gut permeability and microbial balance.

Sleep: Lack of sleep and poor sleep quality can significantly impact the quality of the gut microbiome. Research has shown that even two days of sleep deprivation can cause a noticeable shift in the ratio of Firmicutes to Bacteroides, two major bacterial phyla in the gut. This shift may have implications for metabolic health and weight regulation.

Sleep disturbances can also lead to changes in the composition of the gut microbiota, favoring less metabolically friendly species. Studies in mice have shown that chronic sleep fragmentation can decrease the abundance of beneficial Lactobacillus species in the gut, which have various health-promoting effects.

Ongoing research illuminates the importance of adequate and restful sleep for maintaining a healthy gut microbiome. Sleep is a critical restorative process for the body, and disruptions can have wide-ranging effects on various physiological systems, including the gut microbiota.

Medications: PPIs, antibiotics, laxatives, statin drugs, metformin, statins, benzodiazepines, hormones, antidepressants, antihistamines, and nonsteroidal anti-inflammatory drugs are examples of all the medications that are associated with changes in the composition of the gut microbiota. Never has it been more apparent that the fewer pharmaceuticals we ingest, the better!

Smoking: Studies show that smokers have lower levels of acetic, propionic, and butyric acid and decreased levels of beneficial Bifidobacterium. Overall, smokers show less microbiome diversity.

Pollution: Data is emerging showing that pollution negatively impacts the gut microbiome. Some studies correlate pollution exposure to increased levels of inflammation associated with decreased butyrate production.

We are learning more and more about the effects of “forever chemicals” on the immune system and, in parallel, on the microbiome. It’s not good. Specific data links the ubiquitous forever chemical PCB to a notable decrease in microbiome diversity.

Geography, urban versus rural living unrelated to pollution per se reveal quite a range of different microbiome compositions, and this data continues to emerge. Undoubtedly, we’ll see data linking the excellent health in the “blue zones” to more diverse and healthy microbiomes.

Shout-out to older siblings and furry pets: Children with older siblings and (moreso) the owners of furry pets have more diverse and generally healthier microbiomes. This bolsters my theory that every child needs a pet!

Now that we know what can disturb the microbiome let’s discuss the best diet to support our microbiomes.

Healthiest Microbiome Diet

Diet plays a crucial role in establishing gut health and supporting the growth of beneficial bacteria in the microbiome. Over the years, research has shown a strong connection between a person’s microbiota, digestion, body weight, and metabolism.

Studies have revealed that the microbiome environments can differ significantly depending on the diet of humans and other mammalian species. Different dietary patterns can lead to variations in the composition and diversity of the gut microbiota.

Conversely, the health of your gut can also affect how your body processes nutrients from your diet and stores fat. The gut microbiota has been found to play a significant role in obesity, and changes in the bacterial strains present in the gut can lead to notable changes in health and body weight in just a few days.

For example, experiments with mice have shown that germ-free mice, which lack any gut microbiota, become fatter when they receive a transplant of gut microbiota from conventional or fat mice, even without any increase in food intake. This suggests that the gut bacteria can influence hormone production, such as insulin, and affect nutrient extraction and fat storage.

These findings highlight the intricate relationship between gut microbiota, diet, and metabolic health. It is becoming increasingly clear that maintaining a balanced and healthy gut microbiome through a nutritious diet is crucial for optimizing digestion, body weight management, and overall metabolic well-being.

Now that you can see why it’s critical to lower inflammation and support gut health let’s examine how to do this.

Foods that promote inflammation= avoid

 The items listed below are commonly associated with adverse effects on gut health and overall well-being. Let’s go over each of them.

  1. Pasteurized dairy products: These can be common allergens for some individuals. Dairy products also contain lactose, a sugar that can be difficult to digest for people with lactose intolerance. Additionally, specific pasteurization processes may reduce the presence of beneficial bacteria in the dairy products.
  2. Trans fats/hydrogenated fats: Trans fats, commonly found in processed and fried foods, can harm gut health. They can disrupt the integrity of the gut lining, promote inflammation, and negatively impact the gut microbiota.
  3. Added sugars: Excessive added sugars, often found in processed foods and beverages, have been linked to adverse effects on gut health. High sugar intake can disrupt the balance of the gut microbiota and contribute to inflammation and various health issues.
  4. Refined carbohydrates and processed grain products: Foods like refined grains, white bread, and processed cereals are often low in fiber and nutrients and can lead to dysbiosis (imbalanced gut microbiota). These foods can also cause rapid spikes in blood sugar levels, negatively impacting gut and overall metabolic health.
  5. Refined vegetable oils: Refined vegetable oils, such as canola, corn, and soybean, are often high in pro-inflammatory omega-6 fatty acids. Imbalanced ratios of omega-6 to omega-3 fatty acids can contribute to systemic inflammation, including in the gut.
  6. Conventional meat, poultry, and eggs: Conventionally raised meat, poultry, and eggs can contain higher levels of omega-6 fatty acids due to the animals’ diets mainly consisting of corn and cheap feed. This can disrupt the body’s balance of omega-3 to omega-6 fatty acids, leading to inflammation and imbalances in the gut microbiota.

To support gut health, it is recommended that people focus on a diet rich in whole, unprocessed foods—including many fruits, vegetables, whole grains, legumes, and lean protein sources. Choosing healthy fats, such as avocados, nuts, seeds, and olive oil, is also beneficial.

Additionally, incorporating fermented foods like yogurt, sauerkraut, and kimchi can provide beneficial bacteria for the gut. Let’s take these general recommendations and spell them out more useably so that you know what you can and should eat.

Anti-inflammatory foods

  1. Fresh vegetables: These are packed with beneficial phytonutrients linked to various health benefits, including reduced cholesterol, triglycerides, and symptoms of multiple diseases. Aim for different vegetables and try to have at least four to five servings daily. Some highly nutritious options include beets, carrots, cruciferous vegetables (broccoli, cabbage, cauliflower, kale), dark leafy greens (collard greens, kale, spinach), onions, peas, salad greens, sea vegetables, and squashes.
  2. Wild-caught fish, cage-free eggs, and grass-fed/pasture-raised meat: These options are higher in omega-3 fatty acids and provide essential nutrients like zinc, selenium, and B vitamins. When including fish, eggs, or meat in your diet, opt for these healthier choices.
  3. Herbs, spices, and teas: Herbs and spices like turmeric, ginger, basil, oregano, and thyme have potent antioxidant and anti-inflammatory properties. Green tea and organic coffee in moderation can also be beneficial.
  4. Whole pieces of fruit: Eating whole fruits instead of fruit juice is essential to get the maximum benefits of the fruits’ nutrients, including antioxidants like resveratrol and flavonoids. Incorporate three to four servings of fruits per day. Some excellent choices include apples, blackberries, blueberries, cherries, nectarines, oranges, pears, pink grapefruit, plums, pomegranates, red grapefruit, or strawberries.
  5. Healthy fats: Grass-fed butter, coconut oil, extra virgin olive oil, nuts, and seeds are all excellent sources of healthy fats that can support gut health and well-being.
  6. Probiotics: Probiotic foods contain beneficial bacteria that populate the gut and help fight off harmful strains. Including probiotic foods like yogurt, kombucha, kvass, kefir, or cultured veggies in your daily diet can promote a healthy gut microbiota.
  7. Ancient grains and legumes/beans: Sprouted and unrefined/whole ancient grains and legumes/beans are a good source of fiber, nutrients, and plant-based protein. Including two to three servings per day or less is recommended. Examples include Anasazi beans, adzuki beans, black beans, black-eyed peas, chickpeas, lentils, black rice, amaranth, buckwheat, and quinoa.

Treats: Red wine and dark chocolate/cocoa in moderation contain prebiotics! These can be consumed several times per week or a small amount daily. Now, what about supplements?

Best gut microbiome supplements

When discussing supplements for the microbiome, we generally talk about prebiotic supplements. I mentioned a few in the discussions above, but here are the main ones used today. Here are some common flavonoid prebiotic supplements that are frequently “multi-use.”

We often use catechins, including EGCG supplements derived from green tea, which have been shown to be anti-cancer in several studies. We also use quercetin and fisetin, both of which are multi-use supplements.

Continuing in the flavonoid class are the curcuminoid polyphenols curcumin and turmeric. Rounding out this class of supplements are stilbenes: resveratrol and pterostilbene.

In the category of resistant starch, potato flakes have gained popularity lately.

Probiotics are next when it comes to supplementation, with species identified to reinforce the gut lining (Akkermansia M.), improve gut microbiome diversity (sporulating species; mostly Bacillus), as well as Lactobacillus and Bifidobacterium species, which help metabolism and mood, and much more. As an example, pouring through PubMed looking for probiotics to help reduce anxiety by increasing GABA yields the following information.

Some probiotic strains that can increase GABA (gamma-aminobutyric acid) include Lactobacillus brevis, Bifidobacterium dentium, Bifidobacterium adolescentis, and Bifidobacterium infantis. These strains are part of the lactic acid bacteria (LAB) and bifidobacteria groups, which have been shown to produce GABA. Additionally, other Bacteroides species have been found to produce large quantities of GABA.

As a reminder, there are many ways to improve SCFA production, from consuming a TBSP of vinegar daily for higher acetate levels to taking fish oil supplements to increase propionate levels and using MCT oil for cooking to increase butyrate levels.

The advent of synbiotics and parabiotics has not developed to the point where I can recommend anything specific regarding these two categories. However, no matter what you plan to do to improve your gut microbiome, isn’t it a good idea to know its composition and whether you have enough diversity and SCFA production?

After reviewing all microbiome tests on the market, I have found only one test with enough data and recommendations to be considered accurate and “actionable.” It’s this one. If you haven’t received it yet, get it on the app and let me explain next.


Best microbiome test=microbiome labs (Yes, there’s an app for it!)

Most microbiome tests out there are, frankly, useless. The Injoy test is different – it integrates microbiome data with dietary, lifestyle, and symptomatic information through Patient-Reported Outcomes (PROs), painting a complete picture of gut health.

1 – In-Depth Longitudinal Analysis:

  • They require three samples, not just a one-off snapshot (which invites uncertainty). This approach allows us to track changes over time, providing diagnostic-grade data even in a wellness test. They have published and patented this.
  • Their database isn’t just extensive (35K+ samples); it’s specifically focused on people with validated GI issues (IBD/IBS). Meaning you are comparing yourself with a relevant dataset.

2 – Cutting-Edge AI, Gutchat:

  • The app’s health check-ins are based on validated questionnaires used in clinical practice, ensuring their relevance.
  • They’ve sifted through 50K+ scientific papers, distilled them, and ensured they’re clinically sound. This allows users to ask their GutChat any gut health question and receive personalized responses from a credible source.

3 – Actionable Recommendations:

  • Because they capture more than just the microbiome, the reports can be shared with healthcare providers in a way no other report currently can. This enables patients to take action and practitioners to develop more personalized treatment plans.
  • Injoy’s recommendations are accompanied by a ‘confidence score,’ indicating the level of evidence from publicly available research articles that support each recommendation.

Bottom line: We all know the field of microbiome testing is full of overhyped promises. Injoy is not about that. They provide tools that work based on solid science. You can find the Injoy app in your Apple or Google app store. Please use my discount code: DRKIM10. You’re welcome!


Hopefully, you have read this article with more knowledge of testing, evaluating, and improving your gut microbiome. You have learned the terminology of the available products to improve your gut health. You have learned what foods help and what foods “hurt.”

Importantly, you have learned what activities and products to utilize and which ones to avoid. If you feel overwhelmed, start cleaning up your diet from ultra-processed foods and getting an Injoy kit. At some point in the not-too-distant future, good medical practices will be based not just on patient history, physical exams, and bloodwork but also on the results of microbiome testing. As an important addendum, there are studies linking various herbal supplements with the production of SCFA in the gut, but rather than give you a huge laundry list, I feel that you will benefit from getting an Injoy kit and then supplementing scientifically with the help of their AI-powered GutChat.



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Seppo Salminen, 1 Maria Carmen Collado,2 Akihito Endo,3 Colin Hill,4,5 Sarah Lebeer,6 Eamonn M. M. Quigley,7 Mary Ellen Sanders,8 Raanan Shamir,9,10 Jonathan R. Swann,11,12 Hania Szajewska,13 and Gabriel Vinderola14


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