Microbiome science is exciting and is just now coming to the forefront in research. Each month approximately 2000 articles are published about the microbiome and its health influences. The human microbiome consist of approximately 38 trillion microbes including bacteria, fungi, viruses, parasites and more. We are a lot more microbe DNA than human DNA. Understanding this, we are now beginning to see that these microbes have deep influences to our health.

Our gut microbiome is the gateway to our health, regardless if it is  poor health or good health. In fact, our gut microbiome influences conditions such as aging, allergies, obesity, diabetes, cancer, heart disease, anxiety, depression, dementia, IBS, Crohns, autoimmune conditions like chronic fatigue, arthritis and Lupus, athletic performance, liver and even our skin health.

What is our microbiome?

Our microbiome is the totality of all organisms in and on our body. ( Just take a moment and think about that!)

The microbiome is the community of microorganisms (such as fungi, bacteria and viruses) that exists in a particular environment. In humans, the term is often used to describe the microorganisms that live in or on a particular part of the body, such as the skin or gastrointestinal tract. These groups of microorganisms are dynamic and change in response to a host of environmental factors, such as exercise, diet, medication and other exposures. https://www.genome.gov/genetics-glossary/Microbiome

Our lungs, mouth, nose and throat also have there own microbiome. However today lets focus on our gut microbiome.

Dysbiosis, the imbalance of gut flora, our microbiome

Most American have dysbiosis also known as gut microbiome imbalances due to diet, lifestyle, environment and daily stresses.

Digestive Health

Obviously since most of our microbiome is in our digestive system it is certainly going to effect every aspect of our digestive health. If your microbiome are out of balance (dysbiosis) you may have many different digestive conditions such as GERD, heartburn, bloating, excessive gas, sensitivities to certain foods, allergies, IBS, Crohns and Colitis.

With excessive gas your flatulence and bathroom trips might be very smelly. If you get your gut flora in balance the majority of the foul smell most likely will go away and can reduce the amount of gas produced . Some exceptions are; if you ingest a stomach bug it can cause a lot of putrid gas, and, in some cases food sensitivities can cause smelly gas. For example, Brussels sprouts and cabbage can cause smelly gas and bloating in some people sensitive to the type of fiber and sulfur compounds cruciferous plants contain.   Additionally, legumes such as beans can cause a lot of gas in some individuals. However, there are ways to get your digestive system to adapt to those foods so they are not as prone to make you as gassy. The more balance your gut flora has the less offensive, less smelly your emissions should be. Did you know that even cooking methods also have an impact on the amount of gas and bloating from our foods?

Diet and Lifestyle Changes the Microbiome

Most of my clients are skeptical that a diet and lifestyle change can really have an effect on certain health issues they have. Until it does!!!!  I had a coaching client this week tell me they noticed their gas was barley noticeable now. I have fibromyalgia clients that see a marked reduction in pain and IBS symptoms and an increase in energy.  I have athletes that see an increase in performance. I also have clients with type 2 diabetics that not only improve their numbers but they get off medications completely. Realize it takes time to heal the gut and bring balance to our microbiome. For some, change can be quicker and for others it may take longer. Our gut has approximately 1,000 different strains of bacteria both good and bad and number in the trillions of microbes. Most Americans that eat the standard American Diet have a poor microbiome balance.

Brain Health

Are you battling depression or anxiety? Do you have trouble concentrating on task? It could be a gut flora imbalance. The gut-brain axis is real. Our gut is called our second brain for good reason. Our gut health can affect our cognitive ability, memory, moods and more.  Our gut produces several neurotransmitter chemicals. An imbalance in our gut microbiome can affect the balance of these brain chemicals. Studies show that a lack of, or too much of certain microbe strains can increase the risk of dementia.

These good bacteria do many things including the following;

  • Break down foods
  • Supply the gut with energy
  • Make some vitamins
  • Produce anti-inflammatory compounds in the colon (called postbiotics)
  • Break down toxins
  • Protect against pathogens, (by setting up camp where the harmful bacteria normally would, and by producing anti-microbial chemicals that defend the host against them)
  • Help make neurotransmitters. Our gut flora is essential for producing at least 5 neurotransmitter compounds.
  • Improve our bone, brain, gut, heart, immune system health, and skin.

Best Ways to Improve Your Healthy Gut Flora.

  • Increase your fiber intake through your diet. Foods with digestive resistant starch are great at populating beneficial gut bacteria in our colon.
  • Take a quality probiotic (only if your diet is low in fiber or for a short term boost or if recommended by a qualified health professional)
  • Eat and drink fermented foods.
  • Eat a whole foods plant based diet. It will contain lots of fiber.
  • Limit the intake of processed foods. They have chemicals that kill your gut flora.
  • Avoid sucralose (Splenda). Studies show it kills gut flora if consumed on a regular basis.


If your microbiome contains trillions of microbes including beneficial bacteria most probiotic supplements are not going to be very effective, even if they have 100 billion bacteria. How do we even know if they contain the strains of bacteria you need?  You really need a comprehensive microbiome test to determine the probiotics you need. Did you know ….it is even possible to have too many of certain good bacteria? Contact a qualified health care practitioner like myself for a reliable test, results and strategies for correcting the imbalance. I work with the company Jona and provide a discounted price for my clients.

 If you have specific digestive problems like colitis, ulcerative colitis or Crohn’s, specific types of fiber can do more harm than good. Make sure you work with a qualified health professional that is experienced with digestive disorders.


What Kills and Damages Our Gut Flora?

The American diet is loaded with gut inflammation producing ingredients and very little fiber. Processed foods have little fiber and a host of chemicals that can actually kill our good bacteria as well as feed the bad bacteria and funguses.  Artificial sweeteners like Splenda also known as sucralose kill your gut flora. Additionally, some medications like antibiotics kill all the gut flora good and bad, food preservatives, pesticides, fungicides, herbicides, food colorings, unhealthy fats like soybean and corn oil and hydrogenated fats, GMO foods, gluten, water with chlorine, mercury in vaccines and in foods.

Our digestive system has many parts. Most of the imbalances happen in the small intestines and the large intestines.

Your microbiome, the types and amount of microbes living in your gut are critical to your overall health as well as very critical to the health of your digestive system!! The wrong foods produce the wrong kinds of microbes that cause gut and whole body inflammation.

Fiber and Its Benefits

Fibers act as prebiotics providing food for the good bacteria in our gut. And, some fibers act as postbiotics creating healthy compounds in our colon such as short chain fatty acids like butyrate.

The subject of fiber intake and weight loss has mixed opinions and studies are not conclusive in either direction. However, the studies tend to more strongly support the premise that the increase of fiber in the diet does increase weight loss potential, a reduction of cholesterol, improve the management of type 2 diabetes cut the risk of heart disease and some cancers.

There are two types of fiber in our diet; insoluble and soluble fiber. Both are non-digestible and provide no caloric energy that is either burned as energy or stored as fat.  Soluble fiber is soluble in water, swells, absorbing water becoming a gelatinous substance in our gut during the digestive process. It is soothing to the digestive tract and binds with fats helping to lower cholesterol and triglycerides and slows down the absorption of sugars, thus lowering blood sugar levels.  Ground flax seeds and chia seeds are great sources of soluble fiber. Soluble fiber may help with diarrhea and constipation. Insoluble fiber helps with constipation and keeps the digestive tract clean by move the digestive process along. It’s very important to drink plenty of water when increasing your fiber intake.

Both types of fiber are filling providing satiation leading to lower calorie consumption. However it is important that those looking to lose weight follow a lower glycemic diet that is higher in fiber. Fiber sources in the diet should be from low starch vegetables like avocados, broccoli, cauliflower, Brussels sprouts, asparagus, spinach and winter squashes, Also, low sugar fruits like berries and the powerhouse of fiber, legumes. Legumes (beans, lentils and peas) are the highest source of fiber in our diet.

Dietary fiber does many great things for us. I believe that fiber should be a part of everyone’s diet. There is no question that fiber from low starch plant foods is a vital part of a healthy diet.  A diet rich in vegetables, fruits, legumes, nut and seeds is rich in fiber and offer an abundance of vitamins, minerals, enzymes, essential fatty acids, antioxidants and additional phytonutrients. The average American is only getting 1/4 to 1/3 of their minimum daily fiber requirements. Maybe its one of the contributing reasons there is so much obesity, disease and illness in our great country.

Increase Your Fiber Intake and You Can Increase Your Good Gut Flora

The only negative to fiber intake is increasing the intake too quickly. If you increase your fiber intake too quickly it can cause bloating, gas and potentially loser stools. It is very important that individuals who have been following a lower fiber diet increase their fiber intake slowly. A simple way to increase your fiber intake is to increase it by 5 grams per week until you get to a healthy level. If you can understand that fiber is the only food your healthy bacteria get, then you should see that the more fiber you get the healthy your gut flora and microbiome balance will be. Personally I think a minimum of 30 grams of fiber daily should be a goal for everyone. If you increase you intake slowly you will minimize any negative side effects such as extra gas and bloating.

The best fiber sources are avocados, low starch vegetables, low sugar fruits, beans, lentils, peas, nuts and seeds. You will find a list at this link https://webnd.com/pages/high-fiber-foods  Whole grains provide fiber but can be higher in glycemic values which means they can raise blood sugar and insulin levels quickly (not a good thing to happen).  The best sources from grains are found in the bran and germ such as rice bran and germ. Fiber supplements can help but food sources provide the fiber and nutrients in one beneficial package and are therefore preferred.  Vive shake is the ultimate whole food, fiber, nutrient, and, antioxidant food! Check it out at https://www.viveshake.com

Improve Your Gut Flora and Improve Your Health

To summarize; Fiber is the only food your gut bacteria get. Fiber is filling, satiating, soothing, cleansing, removes bad fats, slows blood sugar absorption, provides food for our healthy gut bacteria, makes some nutrients, reduces the risk of heart disease and some cancers. Remember that a balanced gut helps maintain a balanced immune system. This can help prevent some autoimmune conditions that are caused by an overactive and nervous immune system. Additionally, a healthy gut can help reduce anxiety and depression in some people!

Healthy Wishes
Wally Bishop I.N.H.C., C.N.C., C.I.C.P.

Board Certified Holistic Health Practitioner

Board Certified Functional Nutrition Coach

The contents of this blog is not and should not be considered medical advice. This blog is for informational purposes only. Always consult with your doctor before making any dietary or lifestyle changes. Never quit taking prescription medications unless advised to do so by your doctor.


Nutr Rev. 2001 May;59(5):129-39. Dietary fiber and weight regulation. Howarth NC, Saltzman E, Roberts SB. Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA 02111, USA. http://www.ncbi.nlm.nih.gov/pubmed/11396693
Nutrition. 2005 Mar;21(3):411-8. Dietary fiber and body weight. Slavin JL.Department of Food Science and Nutrition, University of Minnesota, St. Paul, Minnesota, USA. jslavin@umn.edu http://www.ncbi.nlm.nih.gov/pubmed/11494646
Pediatr Clin North Am. 2001 Aug;48(4):969-80. Dietary fiber and body-weight regulation. Observations and mechanisms. Pereira MA, Ludwig DS. Division of Endocrinology, Departments of Pediatrics and Medicine, Harvard Medical School and Children’s Hospital, Boston, Massachusetts, USA. mark.pereira@tch.harvard.edu http://www.ncbi.nlm.nih.gov/pubmed/15797686

Front. Nutr., 25 February 2022
Sec. Nutrition and Microbes  Low Dose of Sucralose Alter Gut Microbiome in Mice https://www.frontiersin.org/articles/10.3389/fnut.2022.848392/full_______


The Link Between Gut Health and Depression  https://psychcentral.com/depression/gut-health-and-depression#symptoms______________________________________________________________________

Neurotransmitter Modulation by the Gut Microbiota  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6005194/