The human gut is home to trillions of microorganisms, which are collectively known as the microbiome. These microbes play a vital part in our gut health, supporting digestion and the synthesis of vitamins.

The human microbiome has a profound impact on our health. It has been correlated with a wide range of conditions, including obesity and Type 2 diabetes, as well as inflammatory bowel disease (IBD) and Irritable Bowel Syndrome (IBS).


Why the microbiome matters

Bacteria and other microorganisms carry out important work the body cannot do itself. Some species process dietary fiber, while others synthesize essential vitamins.

A balanced microbiome – the ecosystem of microorganisms living in and on your body – is important for good health.


Butyrate is a short chain fatty acid that is produced by beneficial bacteria in the colon.  Some of its benefits are:

Prevents and fights cancer.
Lowers colon inflammation.
Prevents heart disease and atherosclerosis.
Controls blood sugars.
Controls hunger.
Lowers cholesterol.
Boosting the immune system.
Heals “leaky gut” (kind of what we doctors call “increased intestinal permeability”).
Affect genetic disorders such as cystic fibrosis and blood disorders like thalassemia and sickle cell.
Help improve stroke outcomes.
Mouse studies imply an improvement in Huntington’s Disease outcomes.
Improve memory production and cognition.

In cancer: In in vitro studies (studies done in a lab’s “test tube,” not in humans), butyrate appears to protect against cancer and even “fight” cancer.

Causes cancer cells to die (apoptose).
Causes cancer cells to revert to more normal cellular activity, rather than out-of –control cancerous activity and cancerous propagation.
Keeps cancer cells from spreading (metastasizing) and also from getting the blood flow they need to perpetuate.

In inflammation: Appears to lower inflammation, both in the colon and throughout the rest of the body. (Remember, for inflammation, start thinking type 2 diabetes, obesity, and heart disease.)

Stops active inflammation in the colon.  Develops the immune system.  May lower low-grade, chronic inflammation present in obesity, type 2 diabetes, insulin resistance (pre-diabetes, if you will), high cholesterol, and heart disease: controlling blood sugars, controlling hunger, lowering cholesterol, decreasing atherosclerosis.

Helping the Immune System

By affecting the movement of immune cells, their ability to stick in a particular area, and their ability to make inflammatory substances.
By helping the body regulate cells which help recognize “good, self bacteria” from “bad, non-self bacteria,” decreasing autoimmune possibility.

Improving Brain Neurological Function

Rat studies indicate improvement after “induced strokes” by increasing the amount of brain-derived neurotrophic factor.
Mouse studies suggest prolonged survival and decreased atrophy of neurons in induced Huntington’s Disease.
May enhance synaptic plasticity and memory.

Helping “Leaky Gut”
  • By stimulating mucous production and thickness in the colon.
  • By acting as the main source of energy for the colon cells
  • By increasing substances which protect the GI lining from invasion by foreign bacteria.
  • Stimulating repair after mucosal injury.
  • Decreasing intestinal permeability, perhaps depending on its concentration.
  • May increase satiety (make you less hungry).


Butyrate Producing Bacteria

Bacteria, such as those from the Clostridium, Eubacterium, and Butyrivibrio genera, are able produce butyrate in the gut lumen at mM levels. In addition to producing butyrate as an endpoint, bacteria produce fermentation intermediates, including lactate, succinate or formate, which are used by the bacteria themselves to proliferate and survive.

Butyrate is also utilized by microbiota and serves as the primary energy source of colonocytes (as discussed below), making this a vital and mutually beneficial relationship. High fiber foods, that enable these butyrate-producing bacteria to thrive include resistant starches (e.g., whole grain and legumes) and fructo-oligosaccharides (FOS) (e.g., bananas, onions, and asparagus).

In fact, within two weeks of a high FOS diet, rats showed increase butyrate in the large intestine without changing the total number of anaerobic bacteria.

Similar results were seen in another study with diets containing FOS as well as resistant starches, but were not observed in the starch free wheat bran diet, which produces less butyrate. This study, as well as many others, demonstrates that different sources of fiber yield different levels of butyrate so care must be used in selecting the appropriate fiber diets to increase butyrate levels.

Eating Butter is another way to increase your butyrate levels but for those that have dairy allergies you can increase the levels by eating fiber. Eating fiber increases the production of butyrate in your colon by your gut flora which consumes the fiber and produce butyrate out of it.

Start slow with any fiber supplementation and use Inulin (FOS), chicory root or 100% partially hydrolyzed guar gum as those are the types that your gut flora love.

Potential Benefits of Butyrate (1)

Microbiome and Sleep

Scientists investigating the relationship between sleep and the microbiome are increasingly finding a dynamic connection between gut health and brain health. The microbial ecosystem may affect sleep and sleep-related physiological functions in a variety of ways, including altering the body’s sleep-wake cycle and affecting the hormones that regulate sleep and wakefulness. The quality of our sleep, in turn, may affect the health and diversity of our microbiome.

There’s constant interplay between the gut and the brain, which means that a disturbance in either can influence sleep. The intestinal microbiome actually promotes the release of many of the neurotransmitters — including dopamine, serotonin, and GABA — that help to regulate mood and promote sleep. Studies show a strong connection between imbalance of gut microbes and stress, anxiety, and depression, which in turn can trigger or exacerbate sleep disruptions. Research also links gut health to pain perception. An unhealthy microbiome appears to increase sensitivity to visceral pain, which then can make falling asleep and staying asleep much more difficult.

Just as an imbalanced gut can affect sleep, unhealthy sleep patterns can disrupt the microbiome, as in the common sleep disorder, obstructive sleep apnea. In one study, scientists put mice through a pattern of disrupted breathing that mimicked the effects of OSA. They found that the mice that lived with periods of OSA-like breathing for six weeks showed significant changes to the diversity and makeup of their microbiota.

Gut health also has a significant connection to hormones that affect sleep. Melatonin, the “darkness hormone”, is essential to sleep and a healthy sleep-wake cycle. Melatonin is actually produced in the gut as well as the brain, and evidence suggests intestinal melatonin may operate on a different cyclical rhythm than the pineal melatonin generated in the brain.

Additionally, cortisol is critical to the sleep-wake cycle. This hormone is central to the body’s stress and inflammatory response, and exerts an effect on gut permeability and microbial diversity. Rising levels of cortisol very early in the day help to promote alertness, focus and energy. Changes to cortisol that occur within the gut-brain axis are likely to have an effect on sleep.

Put very simply: our gut affects how well we sleep, and sleep affects the health of our gut. When you improve one, you improve both, which makes for a much healthier – and better rested – you.

A healthy immune system could have roots in your gut

When a summer cold leaves you coughing and sneezing, your gut microbiome is probably the last thing on your mind. The gut microbiome may significantly impact our immune system, which could be good news for those who suffer from a host of conditions, including Alzheimer’s disease, rheumatoid arthritis, inflammatory bowel disease (IBD), and asthma.

A 2014 article in Cell explored the relationship between the microbiota and our immune system. It proposed that, in high-income countries, overuse of antibiotics and changes in diet have rendered microbiomes less diverse and resilient, resulting in a sharp increase of autoimmune and inflammatory diseases over the past few decades. It is widely understood that the microbiota is intrinsic to the regulation of the immune system, and this understanding now informs research in the area.

Recent studies have linked gut health to conditions like Alzheimer’s (a neurodegenerative disease) and multiple sclerosis (a disease of the central nervous system). Scientists are still trying to figure out whether it’s the diseases that cause an imbalance in gut microbes or whether the conditions themselves could possibly stem from a shift in gut microbiota.

What does our gut have to do with autoimmune conditions?

The microbes in our guts have co-evolved with us, forming a symbiotic relationship that promotes immune homeostasis (a balanced immune system), effective immune responses, and protection against pathogen colonization. Pathogens, however, have also evolved ways to replicate within the gut microbiota. A disruption of the gut microbiome—through environmental and genetic factors—can increase the risk of pathogen infections and the development of inflammatory disease.

Our gut microbes communicate with our immune system, and research has shown that microbial exposure early in life can help protect against immune-mediated diseases, such as IBD and asthma. However, beyond childhood, there are many ways in which our gut microbiome can impact our immune systems. A number of recent studies shed light on which microbes impact immunity and how.

One study found that patients with rheumatoid arthritis (RA) had less diverse gut microbes than control groups without the disease. In the same study, gut microbial diversity correlated with disease duration and auto antibody levels. The researchers concluded that dysbiosis in RA patients likely results from a large number of certain rare bacteria. They suggested that a correlation between the intestinal microbiota and metabolic signatures could help predict who might develop RA and how the disease might progress.

Another study tested the use of the bacterium Prevotella histicola in mice. The mice treated with this bacterium had fewer and less severe cases of arthritis compared to control groups. These findings suggest that Prevotella histicola, which is native to the human gut, may suppress arthritis. P. histicola could potentially be explored as a new therapy— with few to no side effects—for RA patients.

Perhaps most promising, a Yale study of mice and humans from March 2018 found that gut bacteria can drive autoimmune disease. Researchers discovered that Enterococcus gallinarum, a bacterium that causes a number of infections, can migrate from the gut to the lymph nodes, liver, and spleen.

The researchers discovered that, in both genetically susceptible mice and in the liver cells of healthy humans, E. gallinarum initiated the production of auto-antibodies and inflammation. Using a vaccine targeted specifically at E. gallinarum, the scientists were able to suppress its growth in the tissues and blunt its effects on the immune system.

Vaccinations against other bacteria were not successful at preventing mortality and autoimmunity. The authors of the study plan to further investigate E. gallinarum, and concluded that there may one day be a vaccine to improve the lives of patients with autoimmune diseases.

Healthy Gut, Healthy Immune System

There is much more research to be done, but what’s clear is that a healthy gut microbiome can aid in keeping your immune system functioning optimally. It has also been established that diet can have a significant impact on gut health and, therefore, immunity.

Doctors may prescribe dietary changes to people who are at risk for autoimmune diseases like diabetes or rheumatoid arthritis or people who’ve already been diagnosed with those conditions. Some doctors are already prescribing medical foods and nutraceuticals.

While unrelated to food, it’s important to point out that researchers have also tried applying beneficial bacterial metabolites directly to disease sites, with positive results. For example, in one study, colonic inflammation in IBD patients decreased when butyrate or Short Chain Fatty Acids cocktails were added to the colon via enema.

Immune problems

As scientists continue to discover just how our gut microbiome impacts our immune system, one thing is clear: microbes can be our immune system’s best friends.

The large intestine is where we see the greatest number of bacterial colonies. Where the small intestine meets the large intestine is the location where we absorb fat-soluble vitamins, and recycle digestive enzymes. The goal of probiotic therapy is not only to properly populate the small intestine, but to repopulate the junction of the small and large intestine with healthful bacteria.

Taking a probiotic with an evening meal can also make the side effects (gas, bloating) more tolerable because you are asleep. As the bacteria make their way through the digestive tract assisting in the digestion of your food, often times hydrogen and methane gases are produced, creating bloating and stomach pain. When you are asleep, you hopefully won’t feel those symptoms.

When making a decision to take probiotics, I suggest evaluating and understanding your gut health to determine what type of probiotic to take.

Comprehensive stool testing is the diagnostic test of choice. Based on what is found in the gut, specific probiotics are recommended to restore normal function and combat disease.

For example, Saccharomyces Boulardii is the bug of choice to help eliminate candida, parasites, and other unwanted pathogenic micro-organisms found in the gastrointestinal tract (GI) tract.

Lactobacillus acidophilus NCFM® and Bifidobacterium lactis Bi-07 are powerful anti-inflammatories. General strains of Lactobacillus and Bifidobacterium are good to repopulate the GI tract if there is small intestinal bacterial overgrowth (SIBO). (*)

While gut health is more complicated than just the population of bacteria that reside there, understanding when to take probiotics will help you quickly rebuild from your chronic gut problems.

Small Intestinal Bacterial Overgrowth (SIBO)

Small intestinal bacterial overgrowth (SIBO) is defined as the presence of excessive bacteria in the small intestine. SIBO is frequently implicated as the cause of chronic diarrhea and malabsorption. Patients with SIBO may also suffer from unintentional weight loss, nutritional deficiencies, and osteoporosis. A common misconception is that SIBO affects only a limited number of patients, such as those with an anatomic abnormality of the upper gastrointestinal (GI) tract or those with a motility disorder. However, SIBO may be more prevalent than previously thought. This apparent increase in prevalence may have occurred, in part, because readily available diagnostic tests have improved our ability to diagnose SIBO. (*)

Limit (eliminate would be better but we all know how hard that is) eating bread, cookies, cake, and cocktails, as well as complex carbohydrates such as whole grains and legumes. These foods are broken down into sugar in your gut, which feed the bacteria.  Instead eat plenty of non-starchy vegetables, leafy greens, lean proteins, and healthy fats, with minimal fruit.

Take a SOIL BASED ORGANISM PROBIOTIC (SBO) because when you have SIBO most of the bad bacteria are lactobacillus or bifidobacterium species which most all the probiotics being sold on the market contain.  So you are just adding to the problem. Have you ever taken a probiotic and the symptoms didn’t improve or your gas, bloating, constipation or diarrhea only got worse?  Well that is why.  Soil based probiotics don’t colonize in the small intestines and they don’t feed the bad bacteria in the small intestine.  Microbiome Labs specializes in gut restoration and only sells soil based organism probiotics.  You can go to our SERVICES page to access their information.


Viome Microbiome Home Test Kit

There is no such thing as universal healthy food. What’s healthy for one person can be inflammatory for another.

Viome analyzes your gut using the most cutting-edge technology developed for National Security at the Los Alamos National Lab. We are the only company to be able to detect the nutrients and toxins being produced by your microbiome and give you personalized recommendations of foods and nutrients to heal your gut with the goal to keep you free from chronic conditions.

How it Works

We believe there is no one-size-fits-all diet for your good health. After all, one man’s food is another man’s poison. In three easy steps, you can be on your way to feeling better, losing weight, getting better sleep, eliminating brain fog and having more energy!

Step 1 – We send your easy to use at-home kit to collect samples from you.

Step 2 – We analyze your samples in order to understand what nutrients and toxins are being produced by your gut organisms.

Step 3 – We recommend which foods to enjoy and which foods to minimize to balance your gut microbiome.

Viome Test Kit


Great website by the University of Utah on the microbiome: