9 Ways to Improve Your Microbiome


1 – CHOOSE CARBS CAREFULLY – Focus on Fiber and Prebiotics

All carbs are not created equal. Avoid simple carbs like sodas, refined sugars, and processed foods. They spike insulin levels leading to weight gain, diabetes, gut inflammation and a microbiome out of balance.

Choose complex carbohydrates, especially fiber rich veggies, fruit, some ancient grains and brown rice. Ingestible or insoluble fiber is incredibly important. It’s technically a carb, but we absorb it as a fat. Not having enough ingestible fiber can be more challenging to the gut than moderate amounts of sugar. Bacteria in the gut eat the fiber we can’t digest creating short chain fatty acids (SCFA) which are the fermentation byproduct of dietary polysaccharides. SCFA include acetate, propionate, and the most popular, butyrate.

Butyrate is very beneficial. It can powerfully modulate gut mucosal immunity without which leaky gut can be expressed. It also crossed the blood-brain barrier making bdnf – (brain derived neurotrophic factor) which supports neuroplasticity and long-term memory. 95% of butyrate is used by the colon cells. It’s anti-inflammatory and anti-carcinogenic. Butyrate also increases mineral absorption and can regulate gene expression.

Include Resistant Starches. These starches are 1.5 calories per gram. Simple carbs are 4 calories per gram. That’s less calories for you, more food for the microbes. They have anti-inflammatory and anti-carcinogenic properties especially in support of the lower bowel and colon. They also create short chain fatty acids.
Resistant starches include green banana flour, green peas, lentils and uncooked rolled oats. It also includes rice and potatoes that have been cooked and cooled before eating.

Prebiotic Foods that have inulin include artichokes, asparagus, green bananas, chicory root, dandelion root, garlic, leeks and onions. Remember every veggie fuels a different type of bacteria.

2 – PREBIOTICS & FERMENTED FOODS – Retrain the Taste Buds, Especially the Bitters

Fermented foods are microbiome rock stars because they contain live bacteria (probiotics) and prebiotic fiber to nourish gut bacteria. Include some of these fermented foods in your diet every day. They include kefir or coconut kefir, sauerkraut, kombucha, natto, yogurt, kvass, raw cheese, apple cider vinegar, fermented pickles or veggies, olives, miso or tempeh probiotic supplements can be very beneficial. They can support digestion when taken on an empty stomach. But… they can be like the tourist passing through a community. They support the economy but they don’t take root. A tablespoon of sauerkraut can have as many probiotics as a full bottle of probiotics.

Gradually training the taste buds to accept more bitter-tasting greens and cutting down on intake of added sugar are key elements of retraining a picky palate. And you really should think of this as training – it can take months, if not years, for people to get to the point where they’re eating vegetables at every meal without rebelling, or enjoying more savory rather than sweet desserts. It’s also important to remember that food is medicine: you’re not really feeding your picky eater; you’re feeding the microbes that have effects on every aspect of our health.


There’s only so much room on your plate, and it’s vitally important to make sure that the microbe-boosting foods are well represented. So ideally, you should think of veggies as the main course and meat as a condiment. Make sure you’re eating the best-quality, grass-fed meat available, with no antibiotics, since cows raised on corn or treated with antibiotics produce more pathogenic bacteria that can disrupt the microbiome. Strive for about ½ your weight in grams of protein per day. Balance is critical here. Not too much, not too little. Anyone with heavy workout schedules might find they need more protein per day.


There’s no debate that eating more plants is the most important strategy for improving gut flora. Indigestible fiber from plants provides raw material for bacterial fermentation, which feeds your microbes… the diversity and number of plants you eat will be reflected in the diversity and number of bacteria in your gut garden, so eating lots of different plants every day is immensely valuable. Eating the whole plant is also a habit your microbiome will thank you for.

Polyphenols are another favorite of the microbiome. They are found in dark red, purple, and blue parts of plants. They can change the composition of your gut bacteria increasing the amount of healthy bacteria and inhibiting the growth of harmful bacteria. In one study, people who drank a blueberry extract high in polyphenols for 6 weeks saw dramatic improvement in their gut bacteria. Benefits included lower inflammation and brain support. Polyphenols also protect your gut from dangerous pathogens such as staphylococcus and even salmonella. Polyphenols work more efficiently when consumed with fat. Put some cream or coconut milk on those blueberries.

The 1-2-3 rule is simple. That’s part of what makes it so easy to follow. It’s just one veggie at breakfast, two at lunch, three at dinner. Build the meal around plants and use meat as a condiment. Also, buy organic whenever possible. Following the “Dirty Dozen and Clean 15” can save some funds when necessary.


Being told what we cannot eat is never as fun or easy as adding things to the diet first. And even when eliminating foods that really are harmful to our health, focusing on what is being added can make the process more manageable. Then with foods like insoluble fiber, not having enough can be more critical than what we eat. Replacing is a great strategy as well. When one food is taken away, replace it with something that is healthier.


Microbiota health starts in the soil. Plants can only use what is in the soil. Depleted soil creates depleted nutritional value in the plants and healthy soil creates nutritious food. These days our produce travels long distances – sometimes thousands of miles and from other continents – before it gets to us. The enzymatic activity and nutrient value of these foods starts to decline right after harvesting, and therefore its microbial value is significantly diminished. Buying locally grown food from small farmers generally means that the food has travelled a shorter distance to get to you, so more of the nutrients and bacteria are intact. Take advantage of local farmers markets when in season or grow a garden of your own. That’s when you can really “know” the dirt.


Food is information. When it is synthetically created or manipulated, the body doesn’t recognize it the same way and doesn’t inform the body as intended. It’s NOT the same information. So many altered or synthetic foods challenge the body. The amazing ability of the body can handle it… for a time, until a tipping point is reached and disease occurs. Sugar feeds gut bacteria, but not the kind whose growth you want to encourage. Studies have shown that a diet high in sugar can lead to overgrowth of yeast species (candida) and other pathogenic bacteria. Sugar also interferes with the immune system causing white blood cells to
slow their response in fighting toxins. This decline in immune response begins within minutes of ingesting refined sugars and lasts for hours. Artificial sweeteners can be worse on the body than refined sugars. They promote glucose intolerance. Whether you gradually reduce your sugar consumption or do a more drastic sugar detox, your gut bacteria should eventually get to the point where the sugar-craving microbes are outnumbered and your cravings become easier to control. Sometimes eating or drinking something fermented can subside that sugar craving.

Frankenfoods include processed foods loaded with preservatives, artificial flavors and sweeteners, genetically modified foods or foods covered with toxins, herbicides or pesticides, etc. Gluten, commercial dairy, refined carbs, vegetable oils including canola, safflower or sunflower oils, and artificial sweeteners are also very detrimental to the microbiome and overall health.


The Antibiotic family of drugs is at the top of the list. Remember that 80% of antibiotics produced are used on commercially raised animals. These animals are also given hormones that can disrupt our natural hormone balance. There are also many non “Antibiotic” drugs that also disrupt the delicate balance of the gut microbiome, especially antacids, PPIs like Prilosec, Metformin, chemotherapy drugs and calcium-channel blockers (used to treat high blood pressure). Another area of “anti’s” include all the antibacterial cleaners, soaps, and detergents we use every day. Personal care products, makeup, and so many other products in our homes can have damaging effects on our health.  In the office we are able to test your toxic load if you are interested.  Opt for more natural cleaners including many that take advantage of essential oils. The enormous amount of environmental toxins also needs to be acknowledged and addressed. This includes the EMF frequencies from cell phone and electronic devices. An easy idea is to turn off your router at night. Put it on a timer and you don’t have to think about it again. Your home and everyone in it will benefit and possibly get a safer more healthy night’s sleep.

The exceptions are the herbs and food that are Anti-inflammatory and so protective and beneficial for the body. These can include turmeric and ginger, green leafy veggies, bok choy, celery, beets, broccoli, blueberries, pineapple, salmon, bone broth, coconut oil, chia seeds and flax seeds.


Enjoy nature as often as possible and in as many exotic places as you can. It’s amazing that breathing the air in strange and different areas can add to our microbial diversity. Pets also support that “enjoying the dirt” idea. Whether they are yours or even the neighbors, they add diversity to the microbiome which supports immune strength.

Let the enjoyment of nature include the decrease in stress it can support as well. Stress can be very detrimental to the microbiome. Even how you view stress makes a difference. If you believe that stress, which we all experience, can be beneficial, by prepping you to better handle whatever is stressing you, your body responds much more positively. Imagine that, how we think is reflected in our health. The parasympathetic (rest and digest) side of the autonomic nervous system is directly connected to our microbiome health. Left-nostril breathing (breathing just through the left nostril for a few minutes) encourages the relaxing parasympathetic state so necessary for rebuilding and restoration. Movement or the lack of it also has an impact on microbiome health. In fact Burst Training (HIIT) has been shown to improve the health of the gut. Our sleep quality also affects the gut microbiome. Add these all together and you’ve got a triple dose of “great” for mind, body and soul.

Written by Cathy Phillips, Health Coach

Inspiration for this list came from many sources including excerpts from
The Microbiome Solution by Dr. Robynne Chutkan.

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Hi! We are the Balanced Health Care Team. We are passionate about getting to the root cause of chronic conditions & reducing the need for prescription drugs.

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