First Step to Cleanse Your Microbiome of Harmful Bacteria

First Step to Cleanse Your Microbiome of Harmful Bacteria

For centuries, man has sought the elusive fountain of youth.  Do you know any so-called “old people” who seem to have more energy and zest for life than “younger people”?  I have a friend who is 88 years old and who has always said she was 16. She is always healthy in mind and spirit and loves life.  But instead of indulging in anti-aging products, medicating her symptoms, and fighting her age, she embraces it and lives as natural and healthy life as possible.  She has more “young” friends than older ones.  In fact, she doesn’t really like to be around old people.  Why?  Because she doesn’t feel like one of them.  By contrast, I know of many people half her age suffering from diabetes, anxiety, depression, obesity, and general fatigue. 


Longevity is estimated to be 25% genetic and 75% environmental, which means we actually have the ability to control most of the elements that have an effect on our health and lifespan.[1]  And this “environment” includes the microbes we are constantly in contact with. 


What if the fountain of youth was simply a balanced microbiome?  Having a healthy microbiome rids you of hunger, cravings, and helps end depression, anxiety, brain fog, fatigue, and the inability to concentrate.  A healthy microbiome can clear your skin, improve your hair, and boost your energy levels.  It can also put you on the road to maintaining your proper weight and relieve the stress and worry that comes from thinking you are “too fat”.[2]


Reset Your Microbiome and Regain Normal Metabolism

The first step to having a normal microbiome is to remove the unhealthy bacteria from your system by depriving it of the food it needs to thrive, replace your digestive enzymes, reinoculated your system with probiotics (intestinal bacteria) and prebiotics (foods and supplements that nourish your “good” bacteria and keep it healthy) and finally to repair the lining of your intestinal walls, which have likely become preamble and are releasing partially digested food particles into your bloodstream.[3]  These foods are essentially fiber-rich substances, such as dandelion greens, garlic, chicory root, onions, Jerusalem artichokes, bananas, whole oats, apples, leeks, asparagus, barley, koinjac root, cocoa, burdock root, flaxseeds, yacon root, jicama, wheat bran, and seaweed; and fermented foods, such as yogurt, kimchi, kefir, sauerkraut, pickles, miso, and kombucha.


You can never get rid of all the unhealthy bacteria, but you can reduce the food it thrives on and maximize the effectiveness of the beneficial bacteria using the simple tools given to you in this book.  That way, the unhealthy bacteria will not be able to reproduce in large enough numbers to be harmful.[4]


All of this can be accomplished by resetting your microbiome by avoiding foods that damage it and replacing them with foods that nourish it.  This is not really a “diet” in the sense of the word that we usually think of it, such as a fad diet one goes on to try to lose weight, but a change of lifestyle where you can enjoy eating your fill of tasty foods without having to suffer or deprive yourself of anything.  When you alter your diet, such as switching to a high-fiber, low-fat diet, changes to the microbiome can be detected within three days.  In fact, changes in diet account for over half of the variation of the gut microbiome.[5] This makes you understand “you are what you eat” in a whole new light.


But first, there is going to be just a little suffering involved as you must clear your system and reset your unhealthy microbiome.  But not a lot of suffering, as I propose only a three-week cleansing period, during which time you are going to be strict about what you eat (and what you don’t eat) but you will neither go hungry nor suffer.


Remove Unhealthy Foods from Your Diet

This is a permanent removal of everything that will wreak havoc on your microbiome and help you to maintain a healthy microbial balance.  Here is the list, but the most important rule of thumb is not to eat anything that comes out of a box, or drink anything that comes out of a bottle, and scrutinize the ingredients on every can carefully:


Processed sugar


Artificial sweeteners

Trans Fats

Hydrogenated fats

High Fructose Corn Syrup

Non-organic foods

Foods treated with insecticide, such as Iceberg lettuce

All GMO foods

Dried or canned fruits

Fruit juices

Corn and cornstarch

Processed meats or deli meats

Soy and Soy products

White rice


Artificial sweeteners, such as aspartame, convert to harmful compounds such as formaldehyde. If you keep consuming them, you will be well on your way to being a mummy in a coffin before your time. Sweeteners containing sucralose cause your blood sugar levels to spike and put you at the risk for weight gain and insulin resistance.  Moreover, since our bodies are conditioned to associate sweetness with a high amount of calorie intake, eating sweet foods with no calories teaches the body to break that connection, which can cause us to remain hungry even after consuming many calories and this causes us to consume even more. [6]


Trans fats and hydrogenated fats were invented to extend the shelf life of food products.  They are not natural and promote weight gain and can lead to the production of free radicals, which destroy the health of your cells.  Since cell walls are made of fat, it is important to consume only healthy fats, such as Omega 3 fats found in fish oil, olive oil, flaxseed oil, nuts and seeds, and Omega 6, such as is found in olive oil and avocado.[7]


Additives, such as high fructose corn syrup (HFCS), feed unhealthy bacteria, disrupt your hormones for hunger and fullness, and blunt your appetite for healthier foods. Chemical additives and preservatives found in processed foods stress your liver, which makes it less efficient at metabolizing fat.[8]


Dried or canned fruits often contain added sugar and can imbalance your microbiome by feeding unhealthy bacteria.  They also set up a craving for sweets by feeding yeasts and other sugar loving microbes.[9]


Juices contain no fiber and are generally too high in fructose, which feeds your unhealthy bacteria. After the cleansing phase, you may occasionally indulge in drinking fresh-squeezed juices but should try to avoid them as much as possible.[10]


Corn and all products made from corn are usually genetically modified. Even conventional corn can feed your unhealthy bacteria.[11]


Temporarily Remove the Following Foods from Your Diet

To reset your microbiome, you will have to make a little sacrifice for the first three weeks of your road back to good health.  This involves removing the following foods from your dietary consumption:





Dairy and Dairy Products, except for butter

Rice and grains

Soy and Soy products

Peanuts and peanut butter

Canola oil or cottonseed oil

Potatoes and sweet potatoes

Nuts and nut butters

Legumes, including black, white read or kidney beans, and string beans (except for chickpeas and lentils)[12]


Whole grain and basmati rice


These are the most common foods that your immune system overreacts to if you have leaky gut. The goal is to normalize your system, so it does not see these items as invaders.[13]


Gluten is a form of protein found in wheat, but it is used as a preservative so frequently, you can find it in almost any kind of baked goods and of course pasta.  Gluten triggers the production of zonulin, a biochemical that opens the tight junctions of your intestinal wall.  When you consume gluten in moderate amounts, your body has the chance to tighten up those junctions.  But when you are continually exposed to gluten, the tight junctions remain open, causing you to have leaky gut.  After the first three weeks, you can add back in gluten-free grains such as quinoa, rice, and spelt, and after four weeks, you can resume moderate consumption of whole-grain, barley, bulgur, wheat berries, and millet.[14]


Sugar is a major culprit, as it spikes your blood sugar and triggers a flood of insulin, which in turn triggers the storage of fat and could, over the long term, set your body up for insulin resistance.  It also nourishes the disruptive (bad) bacteria in your microbiome.[15] 


Eggs are normally one of the most nutritious foods, but they may cause a reaction in your immune system if you have leaky gut, so cut them out for the first three weeks of cleansing.  Don’t worry, you can do it. 


Remove Parasites, Fungi and Yeast

Too much yeast in your microbiome can leave it imbalanced, and you crave sugar and starches as a result.  This and parasites can lead to symptoms such as bloating, gas, constipation, diarrhea, and abdominal discomfort, as well as skin rashes, vaginal yeast, fatigue, brain fog, anxiety, depression, muscle, and joint pain.  To break through the biofilm that protects the yeast and remove natural parasites, Dr. Kellman recommends taking berberine, wormwood, caprylic acid, grapefruit seed extract, oregano oil and garlic.[16] These components can be found in most candida-control supplements.


Remove Environmental Toxins

Our environment has a profound effect on our microbiome.  Environmental toxins can disrupt your endocrine system and affect your metabolism and weight; creating inflammation which stresses your immune system and your liver.  Make every effort to eat non-GMO organic or farm fresh foods and meats, drink fresh, filtered water and avoid polluted air.  Also use household and cosmetic products that do not contain toxic chemicals, such as can be purchased online or from your local health food store.[17] 


Avoid hand sanitizers. Hand sanitizers kill most of the microbes on your hands, both good and bad.  However, it is good old soap and water that will kill most of the harmful microbes that can cause infection.  In fact, hand sanitizers do not kill spores of clostridium difficile, a common pathogen in healthcare settings that causes diarrhea and other complications.[18]  Sticking with hand washing is the better bet, and your hands won’t end up being so cracked and dry.  And avoid antibacterial soaps.  Our skin has a microbiome as well, and beneficial bacteria on your skin’s microbiome help block pathogens to ward off infection, prevent eczema, maintain skin moisture and ph balance, and keep acne in check.[19]


One thing we did not learn from the Covid pandemic was that we need to be exposed to bacteria to keep our immune system functioning.  One of the best ways to do this is to have a dog.[20] A dog is close to the ground and will transport a lot of the good bacteria you need for your immune system from the outside world into your home. 


Avoid nonsteroidal anti-inflammatory drugs, such as aspirin and especially ibuprofen.  They damage the lining of the gut.


Key Takeaways

The first step to a healthy microbiome is removing the unhealthy bacteria from your system by depriving it of the resources that are nourishing it.  Next time, you will learn what foods to eat during the first three weeks, as well as how to reset your digestive acids and enzymes and enrich your microbiome with probiotics which can be done with a few simple supplements.  For more information on Dr. Gutman's Digestive Health supplements, click here.


[1] Finlay, B. Brett, The Whole Body Microbiome

[2] Kellman, Rafael, M.D., The Microbiome Diet., page 32.

[3] Kellman, Rafael, M.D., The Microbiome Diet., page 49.

[4] Raj, Roshini, M.D., Gut Renovation, page 5-6.

[5] Finlay, B. Brett, The Whole Body Microbiome, Chapter 7.

[6] Kellman, Rafael, M.D., The Microbiome Diet., page 63.

[7] Kellman, Rafael, M.D., The Microbiome Diet., page 64.

[8] Kellman, Rafael, M.D., The Microbiome Diet., page 65.

[9] Kellman, Rafael, M.D., The Microbiome Diet., page 188.

[10] Kellman, Rafael, M.D., The Microbiome Diet., page 189.

[11] Kellman, Rafael, M.D., The Microbiome Diet., page 189.

[12] Kellman, Rafael, M.D., The Microbiome Diet., page 186-187.

[13] Kellman, Rafael, M.D., The Microbiome Diet., page 58.

[14] Kellman, Rafael, M.D., The Microbiome Diet., page 61, 62.

[15] Kellman, Rafael, M.D., The Microbiome Diet., page 62.

[16] Kellman, Rafael, M.D., The Microbiome Diet., page 67.

[17] Kellman, Rafael, M.D., The Microbiome Diet., page 67.

[18] Finlay, B. Brett, The Whole Body Microbiome, Chapter 2.

[19] Finlay, B. Brett, The Whole Body Microbiome, Chapter 2.

[20] How Pets May Improve Our Immunity, Psychology Today, September 11, 2020.





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