The Gut Microbiome: A Guide to Digestive, Skin, Immune System & Mental Health

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In this deep dive guide to the gut microbiome, we're exploring what the microbiome is, how it's formed and the science behind why it's so critical to your health. Discover how an imbalance causes problems with gut health, skin health, immune system functioning, depression, anxiety, allergies and–ultimately–many serious and potentially life-threatening diseases like obesity, PCOS, diabetes, cancer and more. Finally, learn how you can take control of your microbiome, including the best foods to eat and avoid. 

In this deep dive guide to the human microbiome, we're exploring what the microbiome is, how it's formed and the science behind why it's so critical to your health. Discover how an imbalance causes problems with gut health, skin health, immune system functioning, depression, anxiety, allergies and--ultimately--many serious and potentially life-threatening diseases like obesity, PCOS, diabetes, cancer and more. Finally, learn how you can take control of your microbiome, including the best foods to eat and avoid. 

This post is sponsored by Mother Dirt. All thoughts and opinions are my own. Thank you for supporting the brands that make it possible for Root + Revel to provide free content and healthy living inspiration.

If you've been following along with R+R for awhile, it should be of no surprise to you by now that inflammation is, at least in part, at the root of all disease.

What is inflammation?

Simply put, inflammation is the body's natural response to protect itself against harm. As we're exposed to all kinds of stressors–toxins from our food supply, cigarette smoke, chemicals in our cleaning and beauty products, extra body fat, chronic stress, recurring infections and over-reactive immune systems, to name a few–our bodies stay in a ongoing state of inflammation.

As a result, our cells start attacking our body and cause a host of diseases and debilitating conditions, or at minimum symptoms like fatigue, digestive problems, skin problems, allergies, brain fog, depression, anxiety, high blood glucose levels and excess fat around your abdomen.

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In order to take control of these issues, it begs the question: how does all of this happen in the body?

If you think the brain is large and in charge, think again! In fact, 90% of all disease can in some way be traced back to the gut and health of the microbiome. (source)

There it is again! That word: microbiome. It's been a total buzzword popping up everywhere recently, right?

In today's post, we're breaking down what the microbiome is, what role it plays in your health and wellness, how it's affected and how you can work towards improving your microbiome and, ultimately, experience optimal health.


First, let's start with layman's terms a definition of the human microbiome, or microbiota (these two terms are often used interchangeably), that we can all understand.

The human microbiome is the name given to all of the genes that live in the body, made up of a wide variety of bacteria, viruses, fungi, and other single-celled animals. (source)

So yep–if you didn't know already, you coexist with trillions of bacteria, archaea, yeast, mold, fungi, bacteriophages, viruses, parasites and more.

For the most part, these microbes aren’t bad; in fact, we rely on them for great health and live in a symbiotic, supportive relationship with most of them.

Well, when were aren’t destroying all the good bacteria, that is. See our recent post on A Guide to Good Bacteria: Why Too Clean Isn't Healthy for the full scoop on the dangers of over-sanitation and how being too clean can lead to many serious diseases and infections, including gut problems and immune disorders.

I highly recommend that post as the perfect compliment to this guide on the human microbiome as the topics go hand in hand; plus, you'll also discover five tips on how to boost health, digestion, and immunity by increasing your exposure to the right kind of good bacteria.

Now, onward to a little game we like to play sometimes here at R+R called Did You Know?

Did you know that…

  • There are over 10,000 different microbe species that have been identified living in the human body, and 10x as many outside organisms as there are human cells in the body? (source)
  • The human microbiome holds 10-100 TRILLION symbiotic microbial cells, primarily in the gut? (source) Other populations of microbes live in the skin and genitals. (source)
  • Over 80% of your immune system resides in the lining of your gut, and your microbiome is in constant contact with it?  (source)
  • Just one round of antibiotics decreases gut microbiome diversity by at least 30%? (source)
  • Individual humans are 99% identical to each other in terms of the host genome, but 80-90% different from one another in terms of the microbiome? (source)
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Some of these stats should be pretty shocking and reveal just how important the microbiome is, as it's involved in most, if not all, biological processes and regularly signals to the brain. Scientists are doing extensive research now on this gut-brain axis, studying the constant communication between the gut and brain along the vagus nerve. Many people even call the microbiome our “second brain.”

Get a tummy ache when you're anxious, like me? That's the brain-gut connection at play!

What is clear are these basic key facts:

  • The health of your gut microbiome is a major indicator of how healthy your immune system will be.
  • The microbiome is key for nutrition, immunity, and effects on the brain and behavior.
  • The microbiome plays a role in a number of diseases caused by a disturbance in the normal balance of microbes. (source)

Ultimately, a healthy, resilient gut microbiome relies on two factors:

  1. richness, the total number of bacterial species in your gut microbiome
  2. biodiversity, the amount of individual bacteria from each of the bacterial species present in your gut microbiome

When there is high richness and diversity of the microbes in your gut, your immune system is stronger and more stable.

Having low gut microbiome diversity matters because it’s associated with a number of chronic illnesses including obesity, insulin resistance, high cholesterol, inflammation, type 1 and type 2 diabetes, colorectal cancer, crohn’s disease, ulcerative colitis, celiac disease, allergies, chronic fatigue syndrome and polycystic ovary syndrome (PCOS). (source)

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Your gut microbiome is as unique to you as your fingerprint but, unlike your fingerprint, your gut microbiome is dynamic and constantly changing.

It all starts at the beginning: in the womb.

Conventional wisdom used to believe that the womb environment was sterile, but in recent years, scientists have been able to detect small amounts of bacteria in the amniotic fluid, the placenta and even in the fetus’ intestines, supporting the idea that the baby’s microbiome actually gets established far earlier than previously thought. (source)

Thus: it's seeming more and more likely that the mother’s health–and the microbes she may harbor–may matter even more than we thought for baby’s development and health, including the types of diseases the baby might be vulnerable to later in life.

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Other studies have found, for example, that mothers who are overweight have different types of bacteria in their gut than those who are normal weight during pregnancy, and an expectant mom’s dental health could also have an effect on her baby’s microbiome and later health. (source)

Post-birth, your journey through your mother’s birth canal plays an important role in inoculating your gut microbiome (that's why an increasing number of OB's are recommending c-section babies be swabbed with bacteria from the mother's vagina after they're born). Then, from the moment you're born into this world, you are immersed in microbes.

During the first week after birth, a mother’s colostrum (the creamy liquid that's a precursor to breast milk) nourishes and further seeds her baby's gut with a megadose of microbiome building elements. Breastfeeding also plays a part in delivering nutrients and building your microbiome as an infant. (source)


More and more studies are coming out demonstrating a strong association between skin disorders and gut health.

Could keeping your gut healthy be the key to having flawless, radiant skin?

In fact, many people don’t know that your skin also has its own microbiome that relies on good bacteria to help us be healthy.

The skin is subject to a variety of challenges, including sun radiation, urban pollution, weather and harsh, often toxic, chemicals in the environment. As a result, the epidermis thins and our skin's microbiome is altered, leading to inflammation.

Just like in the gut, our skin must try to protect against pathogens invading from the outside environment. When the right balance between the good and bacteria is lost, it can contribute to skin disorders and diseases.

Not only is the skin's microbiome trying to keep the surface level in check, but the gut and skin interact through several pathways, especially the microbiome and its metabolites. Thus, these organs influence one another’s health, with the gut having a greater impact on skin health. (source)

There are many skin disorders that are more common in those with gut issues and vice versa. For example:

  • Rosacea has an association with SIBO (small intestine bacteria overgrowth). In one study, there was a higher number of patients with rosacea who tested positive for SIBO than the group without the skin disease. (source)
  • Inflammatory bowel disease (IBD) is also associated with a higher risk of developing an inflammatory skin condition, such as psoriasis, atopic dermatitis, and rosacea. (source)
  • Celiac disease is associated with skin problems, and one subset of the disease, dermatitis herpetiformis, presents with skin problems rather than gut issues.
  • There is also a strong association between gut health and acne. (source)
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So, what can we do to improve our skin's health?

One way to infuse good bacteria into our skin is with probiotic skin care products, like one of my favorite brands, Mother Dirt.

Their preservative-free, hypoallergenic products help restore and maintain good bacteria on your skin and hair. In fact, their products have been proven to improve skin appearance within 2-4 weeks!

Use their AO+ face and body mist on your face, armpits or anywhere you sweat like your hands and feet to help with odor.

They also have an awesome face and body cleanser, moisturizer and shampoo.

While great for anyone to achieve and maintain proper balance, these products are especially supportive if you have skin blotchiness or redness, acne, dry, oily or sensitive skin, or skin infections. You can buy their probiotic skin care line direct on their site at Mother Dirt, or buy them here on Amazon.

What else can you do to improve your skin's microbiome? Taking an oral probiotic can also help give you the healthy bacteria strains you need in your gut (that, as we talked about, will impact your skin), as well as looking at lifestyle factors like stress, environmental toxins or food allergens that may be causing irritations.


It turns out the microbiome has a lot to say when talking to your brain through the use of neurotransmitters, hormones, proteins and other communication factors.

Fascinatingly, your microbes influence how you feel, your emotions, and your happiness in a very real and tangible way. (source)

There are four major ways your gut microbiome can contribute to anxiety and depression (source), including:

  1. Gut Microbiome's influence on your stress response: From an early age, your gut microbiome modulates your stress response. As you get older, changes in the health of your gut microbiome affect how you respond to stressors. This is a growing area of research, but it's amazing to think that anxiety and depression can be treated through the gut!

  2. Gut Microbiome + Leaky Gut Connection: When there is a change in the composition of the gut microbiome, it can cause problems such as leaky gut. Leaky gut is when proteins, viruses, bacteria and more are able to leak out of the gastrointestinal tract and into the bloodstream. This causes a breakdown of communication in the body and results in poor cognitive function and improper emotional responses. 

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  3. Gut Microbiome's link to chronic inflammation: We've already touched on chronic inflammation, which is promoted by harmful microbes. This occurs when these malicious microbes outcompete the beneficial bugs in the gut. When these harmful gut inhabitants takeover and cause inflammation, it can activate the vagus nerve and lead to neuropsychological symptoms.

  4. Gut Microbiome + producing harmful peptides: Harmful bacteria can also create peptides known to send stress signals. These can affect gene expression and your central nervous system, adding to your neurological symptoms. Your gut peptide concentrations are determined by the composition of your gut microbiome, making a healthy gut even more important if you suffer from anxiety or depression.

Given this, it's no surprise that when people struggle with anxiety and depression, it’s likely that they also have digestive symptoms. All too often, these cognitive and digestive symptoms are thought to be independent of one another, ignoring the important link between the gut and the brain.

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What is an Anti-inflammatory Diet? Here, we dive deep into the meaning and causes of inflammation, plus get a list of anti inflammatory foods and what foods to avoid.


Our diet is the most powerful tool we have to affect change in the gut microbiome.

Compared to our ancestors, our microbial diversity has decreased through reduced food variety (on a global scale, the United Nations Food and Agriculture Organization reported that our food diversity has dropped 75% in the last 100 years), eating highly processed foods, moving to cities where there isn’t dirt for us to play in, and the overuse of antibiotics.

Because these microbes play a huge role in keeping our immune system alert, the decrease in microbial diversity has significantly weakened our immune systems. (source)

Because everyone's microbiome is unique, it's hard to list specific foods that will hurt or help your individual gut health (more on that below).

However, there are some general guidelines on foods to avoid because they tend to promote inflammation in the body, like:

  • Refined vegetable oils (like canola, corn and soybean oils)
  • Refined carbs and processed gluten/wheat
  • Conventional meat, poultry and eggs
  • Added sugars (found in the majority of packaged snacks, breads, condiments, canned items, cereals, etc.)
  • Trans fats/hydrogenated fats (used in packaged/processed products and often to fry foods)
  • Pasteurized dairy products (a common allergen)
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On the flip side, many real foods can lower inflammation and help increase good bacteria in the gut. High-antioxidant foods that help reduce gut damage include:

(Source of food lists)

That's a wrap!

Share in the comments below one thing you learned from this post and one step you're going to take to support your optimal microbiome health!

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7 thoughts on “The Gut Microbiome: A Guide to Digestive, Skin, Immune System & Mental Health”

  1. This is so interesting and amazing what is going on inside of us. My company recently added a probiotic to its line up and I didn’t understand why it was such a big deal. But I can see now how everything is so interconnected, definitely going to add them into my daily practice. Thank you for taking the time to research and share this! 

  2. What is the name of the multivitamin you take that you referenced in your Dr. Axe article? It had iodine & other good things in it. I currently take ERFA (Armour Thyroid) & take other supplements separately for my hypothyroidism. Thank you!

  3. Excellent article! I am recovering from both Toxic Mold Poisoning and Lyme infection. My doctor told me that my “pristine diet” (exactly as you described here) for the past 8 years most probably saved my life during the years I was unknowingly inhaling Aspergillus and Penicillium mold spores from mold in our crawl space!!
    I have made great strides from my close to death condition, but still have a hard road ahead of me. I still must liquify all my meals while my gut continues to heal. Otherwise, too painful.
    Please keep writing such well-researched and encouraging articles such as this. Your work is invaluable in teaching the public how to heal our bodies and truly stay well without self-destruction from chemical pharmaceuticals! My best!

  4. This article is utterly fascinating! I love all the research and facts. I have some gut imbalances and am doing whatever I can to balance them out. I also noticed a HUGE impact on my skin when I stopped using Mother Dirt’s AO+ Mist – I started breaking out all over my face, so ordered another bottle and within a couple days the acne is fading and my skin is looking way healthier. TOTALLY recommend that product, thank you Mother Dirt!! <3

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