What exactly is the microbiome and why is it important for human health

The microbiome. Open a magazine on health matters or listen to many wellness influencers and it appears to be the holy grail. Rebalance it and live your perfect life. Buy these 12 supplements to take for the next year.

Five years ago, I knew very little about the microbiome and the impact it has on overall health, despite having practiced emergency medicine for decades in a traditional healthcare setting. As part of my integrative medicine fellowship, I learned the basics of what it was, major components, and how it interacts with your immune system as well as impact certain health conditions.

Today, we all know a lot more about the microbiome compared to five years ago and we will know a lot more about it five years from now. My intent here is to explain exactly what it is, its impact on overall health, what happens when the microbiome gets of balance (called dysbiosis), and how to rebalance it.

I’ll also try to state the limitations known about it and why taking prolonged supplements to support it, unless you have certain specific health conditions, is not indicated or supported by the medical literature. 

Definitions and Basics

According to the National Institute of Environmental Health, a microbiome is the entire community of microorganisms—including bacteria, viruses, fungi, and archaea—that live in a specific, well-defined environment, such as the human body, soil, or water. This dynamic ecosystem includes not just the microbes themselves, but also their genes (genomes) and surrounding environmental conditions.

Technically speaking, the microbiota are the actual organisms that make up the larger microbiome environment. For ease of use I will use the term microbiome. While we typically think of the microbiome as on or within the human body, the soil in which our food grows has its own microbiome as does the sandbox in which our kids play. These are the trillions of organisms that interact in unique ways to create a particular environment. The genetic material of the microbiome and how it is expressed can influence the surrounding organism. That environment can be supportive or damaging to the particular species in which it interacts. More on that later.

Everyone generally understands what bacteria, viruses and fungi are but what about the whole ‘archaea’ term. They come from the Greek word archaios, which means ancient, existing long before the typical bacteria that we know today. They also are known to exist in unique environments such as hot springs, extreme acidity and can produce (as well as use) unusual nutrients for metabolism such as methane.

One such archaea, methanobrevibacter smithii (a mouthful, I know) is known to contribute to a particular intestinal condition called Intestinal Methanogen Overgrowth. While all these different organisms are important, how they interact with each other and your body’s metabolism and immune system is very dependent on multiple factors and where much of the ongoing research is focused.

Microbiomes exist in the human being in many places including the skin, respiratory system, urogenital, mouth and gastrointestinal tract (unique from the mouth). There is even evidence of a microbiome in the brain and likely in other places in your body. For the purposes of our detailed discussion we are going to focus on the ‘gut microbiome’ and the impact on health in the rest of the article. 

The gut microbiome exists and has developed for millions of years as part of human evolution in a symbiotic relationship. These organisms helped human beings adapt to our changing dietary patterns over time. They assisted in digesting and breaking down plants and animals for nutrients. They provide specific nutrients the human body can't, such as certain vitamins (a percentage of B vitamins and all of Vitamin K) as well as short chain fatty acids (SCFA). These SCFA provide nutrients to colonocytes (cells in our large intestine) as well as regulate our immune system through anti-inflammatory effects. In this way, the microbiome assists in helping to ‘train’ our overall immune system and provide support to the physical barrier of our intestinal tract. 

Most recent studies estimate that there are approximately 38 trillion organisms which make up the microbiome. That roughly mirrors the number of human cells estimated in our body. If you were to weigh your microbiome it would be less than ½ a pound. That small number belies the fact that the genetic diversity of the microbiome is estimated at 2-20 million unique genes. In comparison the entire human genome, which is estimated at 20,000-23,000 genes. This only underscores how the interaction between these symbiotic partners influences much of our health and wellness. 

Generally speaking, 90% of the microbiome is made up of two major ‘families’ of bacteria named bacteroidites and firmicutes. Interestingly, as an infant, 90% is made up of bfidobacterium which gradually decreases over time. While there is estimated to be 3,000 different species of organisms in human microbiomes, most individuals have about 160 species. This is influenced by diet, geography and physical activity. A major influence on microbial diversity are medications; specifically antibiotics.

Two questions I always ask new patients are whether they were born by natural vaginal birth or by C-section and were they bottle or breast fed. We know that of the 20% or so children born by c-section in the US the microbial diversity is much less due to loss of initial inoculation through the vaginal canal. 

In addition, breast milk helps to build upon diversity through providing the probiotic cocktail found in human milk. Breast milk also provides human milk oligosaccharides (HMOs), which can’t be used for our energy needs but do provide a substrate for bifidobacterium to flourish in the gut. Twenty percent of total carbohydrate concentration in breast milk are HMOs, an amazing fact considering it provides zero energy source for human cells. It is estimated that breast milk alone provides 28% of all the bacteria in the microbiome in the first month of life. 

Important species of bacteria in your gut

As mentioned, 90% of bacteria we can measure fall into one of the two major families, bacteroidetes and firmicutes. Let’s get a little more detailed so you understand what they do and the significance of testing for them later on.

Bacteroidetes are primarily responsible for breaking down fiber and complex carbohydrates called glycans. They account for 30% of all gut bacteria. They immediately release nutrients which helps your cells use these nutrients as an energy source. Important types of bacteria in this class include:

• Bacteroides thetaiotaomicron – helps digest complex plant fibers and supports gut barrier and immune regulation.

• Bacteroides fragilis – contributes to immune balance; some strains can be protective, while others can be opportunistic.

• Bacteroides uniformis, Bacteroides ovatus, Bacteroides dorei – common, abundant species associated with fiber fermentation and metabolic health.

• Prevotella spp. – often higher in high‑fiber, plant‑rich diets; linked to carbohydrate metabolism and mucosal health.

• Alistipes and Parabacteroides – emerging roles in gut–brain axis and inflammation modulation.

Firmicutes are important for fermenting lipids and carbohydrates unlocking higher energy production. They account for 60% of all gut bacteria. Clostridium species are the majority of this class. This class is the major producer of the SCFA butyrate which maintains intestinal homeostasis and is the major energy source for cells in the colon. Important types of bacteria in this class include:

• Faecalibacterium prausnitzii – a major butyrate‑producing species with strong anti‑inflammatory and gut barrier‑supporting effects.

• Roseburia spp. – butyrate‑producing bacteria that support colon health and metabolic balance.

• Eubacterium spp. (e.g., Eubacterium hallii, E. rectale) – help ferment fiber to short‑chain fatty acids and support gut integrity.

• Lactobacillus spp. – common probiotic‑related bacteria that help with fermentation, inhibit pathogens, and modulate immunity.

• Ruminococcus spp. – involved in breaking down complex plant polysaccharides; some species are associated with gut health, others with imbalances.

Another important and separate species is Akkermansia muciniphila which breaks down the mucous gel (hence the name) and provides nutrients to the other microbes as well as maintaining integrity of the barrier. Low levels are associated with increased obesity, type 2 diabetes and inflammatory conditions. 

What is dysbiosis?

The term dysbiosis is frequently bantered about in discussions of the microbiome. What exactly is it?

The microbiome is like a healthy garden. In a healthy garden you should see a large number of plants and a wide variety of those plants. Similarly in a healthy microbiome we should see a wide diversity of bacteria and a healthy number of those bacteria. We will discuss testing your microbiome later and how to interpret those tests.

Dysbiosis results when you have a reduction in the normal amount of beneficial bacteria or an overgrowth of less desirable /inflammatory ones. Many patients describe a constellation of symptoms including excess gas, bloating, vague abdominal discomfort and an abnormal stool pattern, either constipation or loose stools/diarrhea often a combination of both.

The single greatest sign of which to be aware is abnormal stool production. We talk a lot about stools in my practice! A normal healthy person should have 1-2 well formed stools a day. Yes you heard that right. Going more than one day between bowel movements or having chronically loose stool is NOT NORMAL. There is a chart called the Bristol Stool Chart that shows in graphic detail what your stool should look like. Types 3 and 4 are considered normal. 

There are multiple causes of dysbiosis, including a recent gastrointestinal infection, high level of processed food intake, low fiber intake, recent antibiotic use, chronic stress, excessive alcohol use as well as other reasons. The result of the dysbiosis is an imbalance of beneficial and inflammatory bacteria. This causes reduction in production of SCFA mentioned above critical for energy production and immune system modulation. Additionally your gut becomes hyperpermeable when imbalance occurs. The tight junctions between the cells, primarily in your colon or large intestine, start to widen allowing larger molecules to pass through triggering increased activation of the immune system. When people use the term ‘leaky gut,’ it is this to which they are referring. 

Depending on the type and pattern of dysbiosis ,you can predict particular conditions we will discuss below. In truth, we still have a lot to learn about particular bacterial patterns. We do know there is a systematic way to treat most imbalances. 

Relationship to human disease

Specific changes in the microbiome can lead to certain chronic diseases. It’s a bit of chicken vs egg. Did the particular changes of a certain disease lead to changes in the microbiome or the reverse? As I mentioned in the opening, we are continuing to learn more about different metabolic conditions and microbiome changes.

Let’s highlight a few of the more common patterns identified. 

Obesity 

A common finding in obesity is a shift in the ratio of the gut's two dominant bacterial families — Firmicutes and Bacteroidetes. In many studies, people with obesity carry a higher proportion of Firmicutes relative to Bacteroidetes. The practical consequence is that an obesity-associated microbiome appears to be more efficient at extracting calories from food — essentially harvesting more energy from the same meal than a lean person's microbiome would. At the same time, key beneficial species like Akkermansia muciniphila (which helps maintain the gut lining) and the anti-inflammatory Faecalibacterium prausnitzii tend to be depleted. This combination of over-efficient energy harvest plus a weakened gut barrier sets the stage for low-grade chronic inflammation — a driver of metabolic disease.

Anxiety and Depression

The gut produces roughly 90% of the body's serotonin, and the microbiome directly influences how much is made as serotonin made in the gut cannot cross the blood brain barrier. In individuals with anxiety or depression, researchers often find reduced microbial diversity and a drop in short-chain fatty acid–producing bacteria — the same anti-inflammatory species depleted in metabolic disease. Through the gut–brain axis (a bidirectional communication highway involving the vagus nerve, immune signaling, and microbial metabolites), this dysbiosis appears to alter neurotransmitter balance, elevate cortisol, and amplify neuroinflammation. Importantly, recent studies suggest this is not just correlation — gut dysbiosis may be a contributing cause of depression and anxiety, not merely a consequence.

Rheumatoid Arthritis (Autoimmune)

In RA, the dysbiosis pattern has a distinct signature. One of the most replicated findings is an over-expansion of Prevotella copri in early, untreated RA — often at the expense of protective species like Bacteroides fragilis, which helps keep regulatory T cells of your immune system in check. The proposed mechanism is that a Prevotella-dominated gut disrupts the balance between pro-inflammatory Th17 cells and anti-inflammatory regulatory T cells (Tregs), tipping the immune system toward autoimmune activation. Additionally, the gut barrier has been reported to be compromised in RA patients, allowing bacterial fragments (such as peptidoglycan) to translocate into the bloodstream and even into joint tissue, further fueling the inflammatory cycle. 

Cancer

One of the more startling areas of research is how certain microbiome patterns can either stimulate or inhibit specific cancers. While much of this research is at the mouse model level it is active and may lead to future supportive therapies as part of an overall cancer strategy. Research using fecal microbiota transfers from one person to another suggests changes to the immune system in specific cancers using immunotherapy to modulate responses. 

Despite the differences in microbial "fingerprints," a shared pattern emerges: loss of microbial diversity, depletion of beneficial short-chain fatty acid producers, increased gut permeability, and chronic low-grade inflammation. The specific downstream effects — metabolic dysfunction, neuroinflammation, or autoimmunity — depend on the individual's genetic susceptibility, environment, and which part of the immune system is most affected.

Microbiome testing

Perhaps the biggest area of controversy in conventional medicine is the ability to test the microbiome and provide a map to treat imbalances.

Most gastroenterologists will say these tests are inaccurate and not worth the cost. There is some truth to that as they have not been verified in large controlled trials. They are not inexpensive, costing $350-500. However, having used hundreds of these tests over the last five years I find them invaluable to assist and target therapy.

Are they perfect, no. Do they represent the best opportunity to provide guidance on where to focus my attention as an integrative medicine physician when faced with a patient that has struggled, sometimes for years, with chronic issues, having been told by numerous doctors, including gastroenterologists, that ‘nothing significant’ has shown up on traditional testing including endoscopy and colonoscopy? Emphatically for me that answer is yes. 

Most of these testing companies cover the same territory but have slightly different ways to report their findings. The most common ones are GI-MAP, GI Effects and GI Advanced. While the reports are different they generally cover these basics: 

• Evaluation of beneficial bacteria through counts using PCR genetic testing and in some cases what is called shotgun metagenomic test which evaluates all genetic material and gives more expansive results

• Evaluation of less desirable or inflammatory bacteria using same method as above

• Some evaluate the presence of h. Pylori which can cause specific conditions

• Evaluation for intestinal infections and parasites

• Evaluation of yeast > a common cause of chronic inflammatory conditions

• Inflammatory and Immune markers like calprotectin, secretory IgA, and others

• Digestion and absorption markers like pancreatic elastase, fecal fat and sometimes short chain fatty acids

There are consumer tests available to order on your own. I strongly discourage people from using consumer grade tests. I find the reports confusing and generally not helpful. 

Now that you have the test, what do you do with that information? Your doctor would review the results in the context of the symptoms you are having and develop a course of treatment to correct the imbalance. While the particular course of treatment would be specific there are common patterns that occur that point to certain treatment protocols. 

Rebalancing the microbiome

A diet rich in a variety of plants which provides specific nutrients and high fiber acting as substrates for the beneficial bacteria are critical. In addition, fermented foods like yogurt, kimchi, sauerkraut, kombucha, miso and others provide a variety of bacteria to help to support the healthy garden of the microbiome.

Regular physical activity promotes a healthy microbiome by increasing microbial diversity and increasing levels of bifidobacterium and faecalibacterium and boosting SCFA.

Regular sleep maintains gut integrity and reduced sleep, even over a few nights, has been associated with changes in the microbiome and increase in gut hyperpermeability.

High stress levels release catecholamines and cortisol which impact the gut brain axis leading to increase in inflammatory bacteria and increased gut permeability. 

In functional medicine, the 5R protocol has been popularized to rebalance the microbiome. It involves:

• Remove (eliminate) triggers that impact the microbiome such as processed foods, alcohol, and foods causing likely sensitivity such as gluten or dairy (at least temporarily). It may also involve treating issues like candida or rarely parasites found on testing. 

• Replace refers to supporting digestion through the use of digestive enzymes, bile acids and hydrochloric acid for a short period of time.

• Reinoculate refers to the use of targeted probiotics for a period of time to support beneficial bacteria.

• Repair is about providing the nutrients to support the lining of the gut such as glutamine, zinc carnosine, aloe vera and other botanicals.

• Rebalance is about the lifestyle factors mentioned above which result in maintaining a healthy microbiome long term. 

What I have found in my practice is the above process typically takes several months, depending on the level of imbalance and the length of time an individual has been struggling with their symptoms will determine how long it takes to correct. If this is an acute event after a severe case of gastroenteritis then the steps to take are straightforward. If this has been something that has been going on for 10 years then it will likely take 3-6 months to rebalance and correct the issues.

Candidly, this is where there is less science and more art. It is also where people occasionally get placed on supplements for many months with no apparent end in sight. Generally I start with helping to repair the lining for 4-6 weeks before using targeted botanicals to reduce inflammatory bacteria and support beneficial ones. If probiotics are needed they would be used for a few months. Each individual is different and each practitioner has their own process they follow. Reassessment at the 2-3 month mark is always appropriate. 

The red flags to me are someone who is on long term anything. After 2-3 months, there should be a reassessment. This can typically be done following symptoms although occasionally I do repeat GI testing to see where we are. This is especially true if we are dealing with markedly abnormal findings or infections that have been determined to be the likely cause of the symptoms.

Patients who have been diagnosed with SIBO are in a different category and require more intensive treatment and follow up. I’ve written about this in other places. I do not see the need to be on a general probiotic long term. Using food as medicine, following the healthy lifestyles document above and allowing your body to be in balance is usually the best advice to follow.