Are you experiencing gut related challenges? Have you come across the term human microbiome in your search for a solution to the challenges you are facing? And how you just want to know what is meant by the human microbiome? And what does the human microbiome do?

In this article, we will answer these questions and more. You will be able to walk away with a clear understanding of the human microbiome, how it impacts health, disease, and what can be done to improve the human microbiome. Let's get started.

What is the Human Microbiome?

Despite what we may think, our bodies are not really ours. We're not separate and distinct from the world around us, but an inseparable part of the great web of life. Indeed, the vast majority of cells inside of us aren't even human; but bacteria, fungi, and other microorganisms that live alongside our human cells.

Collectively, these non-human cells are known as the microbiome - and they are critical to our health and wellness.

When we talk about the microbiome, we are most commonly referring to what?s inside our gut. Our digestive system is home to many billions of microorganisms?mostly bacteria?that live inside our intestines and directly impact how much we weigh, what we eat, how we absorb nutrients, and how we feel.

Human Microbiome Definition

Many people wonder what the definition of the human microbiome is ?While there are hundreds of strains of bacteria that live in our gut, they can broadly be categorized as either helpful and harmful. Helpful bacteria aid our digestion, boost our mood and otherwise contribute to our well-being. They also play an important part in how we resist or develop immunity to disease.

Harmful bacteria do the opposite - they can cause us to gain weight, crave unhealthy foods, negatively affect our emotional state, and help lead to health conditions like SIBO or leaky gut. Likewise, parasites and fungi can also harm our health. We always have both helpful and harmful bacteria living in our gut, but in order to be healthy, we want to have an abundance of the healthy strains.

All of this knowledge about the human microbiome is at our fingertips because of the government-funded Human Microbiome Project. Let?s find out more about the project. . .

What is the Human Microbiome Project?

The Human Microbiome Project was started in 2007. It is a project that took the rod-shaped bacteria that live not only in, but on the human body and mapped them. This mapping process led to a greater understanding of how clusters and communities of bacteria play a role in the overall wellness of the human body and susceptible risk of disease based on the diversity and health of the human microbiome.

5 Main Areas of the Human Microbiome

The Human Microbiome Project broke the microbes found in and on the human body into the following five areas:

1. Nose

2. Mouth

3. Skin

4. Digestive tract 

5. Vagina

5 Facts About the Human Microbiome Project

Wondering why is the Human Microbiome Project Important? Outside of the map, it provided both scientists and medical professionals with:

1. Time: The map that was created because of the Human Microbiome, the result of a five-year span of research and meditation. 

2. Collaboration: The project is the collaborative efforts of over 80 scientific institutions and higher education colleges and universities. 

3. Publication: The first round of publications for the project occurred on June 13, 2012. 

4. Microbes: There are trillions of microbes hosted by the human body. 

5. Cells: There may be a lot of cells in the human body, but the human body hosts more microbes in the human microbiome than it does cells ? By a 10:1 ratio. 

Now that we know about the Human Microbiome Project and what human microbiome is ? let?s look at how it is related to the gut-brain connection . . .

The Human Microbiome and the Gut-brain Connection

As more information emerges and research is done like the Human Microbiome Project, more and more people have found themselves asking: why is having a diverse and balanced microbiome important?

Part of the reason why the health of our microbiome is so important is that of what is known as the gut-brain connection. That?s exactly what it sounds like?our digestive systems and our brains are intimately linked. Our gut actually contains neurons, which are more colloquially known as brain cells, and are directly connected to our brains through the vagus nerve.

This means that conditions in our gut directly affect conditions in our brains. If our digestive system is working well, and our microbiome contains a high ratio of helpful bacteria to harmful bacteria, this can help improve our mood, our energy, and our mental clarity. Conversely, if our microbiome isn't healthy, we can experience brain fog, depression and anxiety, and a host of other mental and emotional effects simply because we've got too many of the wrong kinds of microorganisms living inside of us.

Let?s take a look at the connection between the human microbiome and disease . . .

The Microbiome, Inflammation, and Disease

Most holistic health professionals see chronic diseases as the result of long-term imbalances within our bodies.

One such imbalance is inflammation - the swelling and reddening of tissue as part of an immune response. Inflammation isn't always a bad thing - acute inflammation is a normal, healthy part of fighting off infection. However, when inflammation becomes chronic, it is a major causal factor for most ongoing forms of illness.

Chronic inflammation is directly linked to the state of our microbiome. When we have too many unhealthy bacteria present, or parasites or fungi or other harmful microorganisms, our digestive system can become inflamed. Likewise, eating foods that aren't good for our gut can also trigger inflammation. So can stress, emotional pain, or trauma?all of which directly impact our gut because of the gut-brain connection.

In other words, taking care of our gut is really important. If you?re struggling with any sort of chronic health condition or disease, there is a good chance that your gut health?and the health of your microbiome?is suffering, and needs to be set right in order for you to feel better.

Wondering which health conditions have been linked to an unbalanced a microbiome that lacks diversity?

6 Conditions linked to an Unbalanced Human Microbiome

A study published in the Frontiers of Microbiology identified the diversity and balanced state of the human microbiome as a controlling attribute of the human body?s ability to defend against disease and maintain wellness. The following conditions were identified as a reproduction of an unbalanced and unhealthy human microbiome:

1. Clostridium difficile infection

2. Inflammatory bowel disease

3. Celiac disease 

4. Obesity

5. Colorectal cancer

6. Autism spectrum disorder

5 Types of Healthcare Professionals to See when Seeking Assessment and Treatment of the Human Microbiome

Some people ask, how do I heal my microbiome? One of the first steps that can be taken to start the healing process of the human microbiome is seeking out the guidance of professionals who view the microbiome as a vital element of healing the human body of ailments, symptoms, and conditions.

Here is a list of five types of healthcare professionals that can be both helpful and effective in assessing, treating, and healing the human microbiome:

1. Nutritionist

2. Health and Wellness Coach

3. Integrative medicine doctor 

4. Naturopathic medicine doctor

5. Functional medicine doctor

Once you choose one of the five types of health care professionals for treating the human microbiome, you will receive the following:

Understanding: You will gain an understanding of and a sense of exactly what is going on with your microbiome and digestive tract.

Advise: You will obtain specific, nuanced advice for how to deal with any particular health conditions you may be dealing with.

However, there are several simple steps you can take right way on your own to support your microbiome and your gut. Let?s look at a few of steps and options you can choose from . . .

How to Improve the Health the Human Gut and Microbiome

Optimal health is what we would all like to achieve. However, more often than not, the human body is not working as well as it could be. Some days it could be a simple headache, bloating, brain fog, or it could be a chronic symptom and condition that is experienced.

Poor microbiome and gut health is a huge part of this. Improving the quality of the human microbiome may be the single biggest step you can take towards boosting your wellness.

Fortunately, there is a lot you can do to do just that! No matter how beat up your digestive system may be, there is room for healing.

To help the microbiome, first look at one thing you should stay away from . . .

The Microbiome and Antibiotics

Many people often ask what impact of antibiotics on the human microbiome? The human microbiome and antibiotics do not mix well. Avoid antibiotics unless medically necessary.

Antibiotics kill the good bacteria inside you along with the bad, and can seriously throw your microbiome out of balance. Antibiotics may be present not just in pills we take, but also in factory-farmed:

- Meat 

- Dairy

- Eggs

So cut back on eating such foods or buy pasture-raised and antibiotic-free if possible.

What is one thing that should be added for a healthier human microbiome . . .

The Microbiome and Probiotics

Take a high-quality probiotic supplement can aid and help in improving the health of the human microbiome. Probiotics contain strains of healthy gut bacteria?the kind your body really needs in order to properly digest food, shed pounds, ward off disease and infection, and feel mentally and emotionally grounded. Taking a daily probiotic is an easy way to boost the levels of healthy bacteria in your microbiome, steering things in the right direction.

Microbiome Diet to Help Improve the Human Microbiome

Fascinatingly, harmful gut bacteria can even make us crave unhealthy foods. Such bacteria thrive on sugar, white flour, and other processed foods.

When present in sufficient numbers, unhealthy gut bacteria can actually stimulate our vagus nerves, sending signals to our brains telling us to eat. We may think we?re hungry for ice cream or pizza, but it's actually the harmful bacteria in our digestive tract looking for their next fix.

One of the best ways to help heal and improve the human microbiome is to eat a microbiome-friendly diet. One of the best diets for the human microbiome is the Mediterranean diet.

Let?s take a deeper look at what a microbiome-friendly diet looks like and what it does not look like . . .

8 Foods to Avoid for a Healthy Human Microbiome

To ensure that the diet and nutrition you are eating is helping the microbiome, there are eight foods that should be avoided:

1. Sugar

2. White flour

3. Processed foods

4. Vegetable oils

5. Trans-fats

6. Corn syrup

7. Junk food 

8. Alcohol

These eight foods all tend to feed the unhealthy bacteria in your gut while harming the healthy bacteria. Avoid those foods as much as possible,

Want to know what foods are good for the human microbiome? Let?s find out . . .

What Foods are Good for Microbiome?

Here is a list of six types of foods and examples of each type of food;

1. Probiotic-rich foods: yogurt, miso, dark chocolate, kefir, kimchi or sauerkraut

2. Gut-healthy fats: extra virgin olive oil, coconut or MCT oil, or grass-fed butter or ghee

3. Healthy proteins: legumes, lentils or pasture-raised meat or eggs

4. Greens: spinach, fresh herbs, kale, broccoli or cabbage 

5. Berries: blueberries, blackberries, raspberries, huckleberries or lingonberry 

6. Whole grains: brown rice, quinoa, freekeh, oatmeal, buckwheat, amaranth, and sorghum

One other option for helping the human microbiome through nutrition and diet is intermittent fasting. Don?t know what that is?

The Microbiome and Intermittent Fasting

For an extra dietary boost, consider intermittent fasting. This is a practice where you fast for at least 12 hours straight out of every 24. Doing so gives your body time to burn off all the glucose?sugar?that comes from eating even healthy carbs like fruits. Since the unhealthy bacteria in your gut live off of sugar, intermittent fasting can help keep them in line. Want to know more about intermittent fasting? Read more: What is Intermittent Fasting?

Improve the Human Microbiome Through Sleep

You might be experiencing insomnia or other sleep challenges and wondering, does gut health affect sleep? In short, yes. Getting enough sleep can help improve the functioning and balance of the human microbiome. Most people need at least 8 hours a night, often more. Make an effort to get that much if you can?sleep is a time for your gut to repair itself. It also boosts your overall immunity, helping you ward off infection and parasites.

Interestingly, the human microbiome is also responsible for a good night's sleep. Want to know how?

Your Microbiome Helps with a Good Night?s Sleep

Want to get a good night?s sleep? A study published in The Journal of Medical Food found that a healthy microbiome is vital to sleeping well and dreaming. It was discovered that the gut and human microbiome interacts with the hypothalamic-pituitary-adrenal (HPA) axis ? A pathway between the brain and nervous system. It acts as an avenue to responding to stress.

The interaction between the hypothalamic-pituitary-adrenal (HPA) axis aids to shape the flow of a normal and restful of sleep. The human microbiome has bacterial peptides. This leads to intestinal macrophages and T-cells and the production of:

- Cytokines interleukin-1beta (IL-1b)

- Tumor necrosis factor alpha (TNFa)

- Bacterial cell wall lipopolysaccharides (LPS) 

An adult human biome that is balanced, and healthy is estimated to have about one gram The of LPS. IL-1b, There are two elements of the human microbiome are stimulators of non-rapid eye movement (nREM) sleep ? they are TNFa and IL-18.

The Microbiome and Emotional Health

Due to the connection of the human microbiome and the hypothalamic-pituitary-adrenal (HPA) axis, it is important to nurture your emotional health and do what you can to lower your stress.

You know what it?s like to have feelings in your gut?and well, those feelings affect the health of your microbiome. Looking for supportive treatments and strategies to help not only your emotional health but also the microbiome? Let?s find out . . .

10 Supportive Treatments and Strategies for Emotional Health and the Microbiome

Here is a list of ideas of supportive treatments and strategies to help not only your emotional health but also the microbiome:

1. Meditate

2. Tai Chi

3. Chiropractic

4. Emotional Freedom Techniques

5. Acupuncture

6. Massage

7. Yoga

8. Nutritionist

9. Health and Wellness Coaching

10. Exercise and go for walks in nature

Be kind to yourself and others and spend time with people who are kind to you. Essentially, do whatever helps you feel more grounded and at ease.

It can also be useful to work with a counselor or psychotherapist if you have any major unresolved emotional pain or trauma.

Exercise is important the human microbiome. Wondering why?

How and Why Exercise for the Human Microbiome

Move. Spending too much time sitting is no good for our digestive health. Do what you can to stand, walk and otherwise move about as much as possible during the day. This can be a yoga class or going to the gym, or just taking an hourly short walk. If you are home and have a dog, they will surely enjoy a few extra walks. Or start strolling around the block after work. The more you stretch your legs, the better it is for your body.

In fact, exercise plays a large role in the health of the human microbiome as well as helping it improve and heal. In one study called: Exercise Modifies the Gut Microbiota with Positive Health Effects found that exercise enables stool to move faster through the human body which in turn reduces the time contact is made between pathogens and the gastrointestinal mucus layer of the digestive system. This leads to a healthier human microbiome and a reduction in the following three conditions:

1. Colon cancer

2. Diverticulosis

3. Inflammatory bowel disease 

Microbiome Testing

There are many companies that offer microbiome testing. Want to get your microbiome tested at home but would like a better idea of which microbiome testing best fits your individual needs? Check out: Top Microbiome Testing Companies: A Review.


Kho, Y., Z., Lal, & K., S. (2018, July 23). The Human Gut Microbiome ? A Potential Controller of Wellness and Disease. Retrieved December 24, 2018, from

Monda, V., Villano, I., Messina, A., Valenzano, A., Esposito, T., Moscatelli, F., . . . Messina, G. (n.d.). Exercise Modifies the Gut Microbiota with Positive Health Effects. Retrieved from

The Gut Microbiome and the Brain - PubMed Central (PMC). (n.d.). Retrieved December 24, 2018, from

The Healthy Human Microbiome. (2018, November 28). Retrieved December 24, 2018, from