(Woodpath is an education site focused exclusively on gut health. Our articles are researched by clinical nutritionists and contain citations at the end of the page.)

The gut microbiome is perhaps one of the most crucial elements to your overall health.

A diverse gut microbiome is a critical factor for a strong immune system, healthy mind, and much much more.

Inside and on the surfaces of our bodies are rich environments where various microbes thrive — these populations and their respective genes are known as the microbiome.

The human microbiome in the gut is made up of up to 100 trillion cells. These microbes include bacteria, fungi, protozoa, and viruses. (Ursell et al., 2012)

The gut microbiome is believed to be intimately involved with health and disease since humans co-evolved with it over millennia. (Liang et al., 2018)

When your gut is in poor health, it can lead to complications such as leaky gut syndrome, heart disease, cancer, autoimmune disease, and much more.

What Affects the Gut Microbiome?

There is a range of environmental factors that plays a large role in the development of gut dysbiosis. Gut dysbiosis is an imbalance between beneficial gut bacteria and inflammatory (or harmful) bacteria.

Some of the most common causes of a decline in gut microbiome health are:

Processed foods

Processed foods contain refined carbohydrates and oils, which are inflammatory triggers in the body. These foods lack the beneficial prebiotic fiber and polyphenols that are a foundation of a healthy microbiome.

Diet low in fiber

Fiber helps to fuel gut bacteria. A lack of dietary fiber can deprive the bacteria of what it needs, causing a deficit of beneficial bacteria. (Holscher, 2017)


Chronic stress contributes to the decline in the health of gut microbiota. This is perhaps one of the key reasons why stress has been linked to health decline. (Foster and McVey Neufeld, 2013)


Various types of infections, such as bacterial, fungal, or viral infections can alter the gut microbiome.


Antibiotics, proton pump inhibitors, and NSAIDs have been found to alter gut microbiota significantly. (Francino, 2016)

Lack of sleep

Lack of sleep is thought to influence the makeup of the gut microbiome and contribute to a weak gut barrier. (Deaver et al., 2018)

Gut Dysbiosis

The integrity of the gut can significantly affect overall health. (Vajro et al., 2013)

Dysbiosis is when gut microbiota is out of balance. Gut dysbiosis can contribute to a host of different health issues, including leaky gut.

Bacterial fragments and endotoxins can leak through the gut lining and into the bloodstream. The immune system then generates a response which results in inflammation and various chronic symptoms. (Escobedo, 2014).

This inflammation can then lead to insulin and leptin resistance, which then leads to metabolic conditions such as type 2 diabetes and obesity. Inflammation can also cause a variety of other diseases, as well. (Cani et al., 2012)

Besides inflammation, other issues that may point to gut dysbiosis include:

  • Gastrointestinal Issues (irritable bowel syndrome and inflammatory bowel disease)
  • Halitosis
  • Nausea
  • Diarrhea
  • Recurrent yeast infections
  • Bloating
  • Heartburn and reflux
  • Rashes
  • Fatigue
  • Brain fog
  • Mental health issues (including depression and anxiety)
  • Autoimmune diseases

How to Repair Your Gut Microbiome        

Although it’s almost impossible to avoid some factors that can negatively impact your gut, there are preventative measures you can take to improve your gut health. Some of the best ways to do this include:

Eat whole foods

Remove gluten, dairy, and processed foods. Stick to foods that are nutrient dense and require preparation.

Eat fermentable fibers (prebiotic foods)

These foods fuel good bacteria and heal leaky gut. Eat foods such as:

  • Jerusalem artichoke
  • Onions
  • Garlic
  • Plantains
  • Bananas
  • Chicory root
  • Yams
  • Dandelion greens
  • Leeks
  • Legumes such as lentils, chickpeas, and beans

Eat fermented foods

Fermented foods are packed full of probiotics, which support various health benefits related to gut health. Foods to eat include:

  • Kefir
  • Kimchi
  • Miso
  • Sauerkraut
  • Kombucha

People who are sensitive to histamine-containing foods should always try these foods fermented foods in small amounts — and may instead need to focus on prebiotic foods.

Get enough sleep

And limit screen exposure before bed to minimize blue light that disrupts the circadian rhythm.

Manage stress

Meditation, yoga, and exercising in nature are great ways to do this.

Take a high-quality probiotic

We recommend multi-strain probiotics with a sound evidence base or multiple single strains, such as:

Although probiotics are transient, they still exert beneficial effects on the overall microbiome as they often play a protective role with the various substances they produce.

How to Test Your Gut Microbiome

The first step is to see your healthcare practitioner. They can order a test that uses a 16S rRNA gene polymerase chain reaction (PCR) amplification technique. Through this method, they can analyze selected bacteria in the gut.

A high-quality test will also examine for parasites, yeasts, and viruses.

Tests that also measure short-chain fatty acids, pancreatic elastase, zonulin, and fecal fats also provide a useful picture when assessing gut health.

Here are various tests for you to consider with your healthcare practitioner. Each of these tests has different advantages.

Other Types of Microbiomes

There are other microbiomes other than your gut microbiome that host bacterial species. Below we discuss the most common.

The Skin Microbiome

The skin microbiome hosts up to one thousand bacteria species and around eighty various fungi species such as staph, strep, and candida. Just like the gut, the skin can contain bifidobacterium and lactobacillus species but in a far fewer quantity.

The skin microbiome varies based on what part of the body is being examined. Some bacteria thrive in light, dry areas whereas others thrive in moist, dark areas of the body. The skin microbiome also changes as you age and is different depending on what gender you are.

A healthy skin microbiome is one that protects against infections as well as assists in wound healing, limits UV radiation, oxidative damage, and exposure to allergens.

The oral microbiome

Another type of microbiome is the oral microbiome, which is the second most diverse microbiome in the body — after the gut.

This is because bacteria living in the oral microbiome eventually makes its way through the digestive tract and becomes part of the gut microbiome — there is a 45% species overlap between the oral and gut microbiomes.

Issues such as pathogenic bacteria, which can cause gum disease, can make its way to the gut. This, in turn, can cause disease throughout the body.

Various studies have shown a link between oral disease and systemic disease. (Dhadse, Gattani, & Mishra, 2010)

For example, pathogens within the mouth have been found in rheumatoid arthritis, IBD, as well as cardiovascular disease. This is why the oral microbiome is so crucial to our health.

Oral health equates to overall bodily health.

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Research Citations

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