As a young girl, I was on penicillin daily for six years, so I know first hand the affects of a compromised microbiome. Over the years, I had to work hard on healing the gut and even today I still need to be proactive, using many of the methods I explain below.

The term “microbiome” typically refers to the bacteria in our gastrointestinal tract (or gut), specifically in the large intestines. These bacteria live in harmony with other microbes in our gut such as viruses, fungi, and parasites. Some report up to 100 trillion bacterial cells reside in our gut microbiome, which cumulatively comprise more genetic makeup than all the other cells in our body.

These bacteria consists of commensal (friendly or good) bacteria and pathogenic (harmful or bad) bacteria. In the past, the common thought was that we had to kill off the “bad” bacteria and replenish the “good.” The problem is that when you try killing off the harmful bacteria, you also kill the good.

More recent research indicates that both types of bacteria, the good and the bad, live in harmony with each other. The key is to have enough good bacteria at all times so that the commensal bacteria keep the pathogenic bacteria in check.

You want to improve and maintain a balanced microbiome by eliminating the things that disrupt the microbiome and create a well rounded strategy to encourage bacteria diversity. Hint: It is more than just taking a probiotic (or prebiotic) supplement. Some of the suggestions below may surprise you!

Microbiome Out of Balance

When our gut microbiome is out of balance, called gut dybiosis, it can cause a wide variety of health issues. Most importantly, 80% of our immune system is contained in the gut. So, when our gut is compromised, our immune system is also compromised. The gut also activates close to 20% of your thyroid hormones and produces many of the neurotransmitters needed by the brain. An unbalanced microbiome can also cause inflammation (in the gut and elsewhere in the body), make us crave the wrong foods, cause unexplained weight gain, among other things.

You should also know that there is more than one microbiome in the body. New ones are being discovered every year – we have bacteria that live on our skin, in our mouth, in our eyes, etc. Even our brain contains its own unique microbiome. If the gut microbiome is compromised, most likely one or more other areas of your body are also compromised.

What Disrupts the Gut Microbiome

Before I get into ways to replenish your gut bacteria and help bring your microbiome back into balance, lets discuss the many things that cause the disruption in the first place. Often the first thing that comes to mind is antibiotics. However, as explained below, there are many things we do on a daily basis that kill our good bacteria.

Eating the Wrong Foods – The foods you chose to eat on a daily basis can shape your microbiome. Poor food selections like the ones shown here can drastically reduce the quality of your gut microbiome.

• Sugar – Too much refined sugars, including processed baked goods, feed the bad bacteria, making it propagate and push out the good bacteria. Sugar also runs down your immune system.
• Diet Sodas and Other Products with Artificial Sweeteners – The newest studies show that artificial sweeteners are modifying the gut bacteria. (The studies also show that when you drink diet sodas regularly you have a higher probability of diabetes and dementia.)
• Pesticides and Herbicides – Farmers use pesticides to kill bugs, bacteria, fungus, etc. to keep them from harming plants. However, when we ingest pesticide laden foods, it also kills the bugs and bacteria in our gut. (Contrary to popular belief, pesticides cannot be washed off but rather are inherent in many plants since the chemicals are also in the soil and get absorbed through the plant’s roots.) Even more disturbing are the many crops, including many grains, legumes (think humus), and sugar cane, that are sprayed with the herbicide glyphosate right before harvesting so they are easier to process.
• Genetically Modified Foods (GMOs) – GMO crops are made to withstand high amounts of herbicides so you are getting an extra dose of pesticides when you eat GMO foods. However, GMO crops additionally have modified genes resulting in plants that our bodies (and our bacteria) do not recognize, effecting our gut microbiome even more. Find out more here.
• CAFO Animal Products – When we eat conventionally raised (CAFO) animal products as found in your typical grocery store, we are ingesting meat, eggs, and dairy that have been raised on GMO feed, GMO hormones, and antibiotics. Many live in inhumane conditions. The genes from these compromised animal products get transferred into our bodies when we eat them and contaminate our microbiome.
• Gluten – Whether you notice the effects or not, research has shown that gluten causes the tight junctions in the gut to weaken each time you eat it, which in turn affects the balance of gut bacteria. This happens to everyone. (If you are healthy, the tight junctions repair themselves between meals.)

Taking Medications – There are a number of medications that are known to affect the gut microbiome. These are the most common: 

• Antibiotics – We now know that taking too many antibiotics can create super bugs and bacteria that become resistant to antibiotics. This is a clear example of how a medication can directly impact the gut bacteria: it directly modifies the microbiome, killing off the good bacteria along with the bad. This includes prescription antibiotics as well as the antibiotics found in conventional animal products (see above) and sprayed on produce such as apples. Every time you take or use an antibiotic, you are changing your gut microbiome and in some cases eliminating strains of bacteria that are difficult to replenish. (A recent large Danish study indicated that antibiotics also increases your risk of diabetes, even from one course.)
• Acne Medications – Acne medications such as Accutane and Tetracycline modify the gut microbiome.
• NSAIDs – Nonsteroidal anti-inflammatory drugs (NSAIDs) are medications that relieve or reduce pain and include aspirin, ibuprofen, naproxen among many other prescription NSAIDs. Interestingly, studies have shown that those taking NSAIDs are also found to have higher levels of clostridium difficile (c. diff.) which is a pathogenic bacteria.
• Proton-pump inhibitors – Proton-pump inhibitors as well as your basic acid blocking medications (even things like Tums) can modify your gut microbiome. More recent studies indicate they also increase your risk of heart attack, which is due in a large part to the change in the gut’s acid level, which in turn changes in the diversity of gut bacteria.

Using Antimicrobial Products – This includes antimicrobial soap and hand gels as well as the antimicrobial clothes and sneakers and other products you use on your body. (Be sure to read your labels.) The chemicals in these products get absorbed by the skin and eventually enter the gut and affect the gut microbiome. The good news is that the FDA banned some of the worst chemicals, including triclosan and triclocargen, which are suppose to be phased out by end of 2017. However, other chemicals will still be in use. Studies show that using plain soap and water can be just as effective. (You can also add your own antimicrobial essential oils, such as tea tree oil, to natural liquid soaps.)

Using Birth Control – Oral birth control is notorious for killing off the gut bacteria. However, other devices such as copper-based contraceptives can also affect the balance of bacteria in the vaginal microbiome and the gut microbiome.

Ingesting Chlorinated and/or Fluoridated Water – The chlorine and fluoride found in tap water kills the bacteria in your gut when ingested. This can also occur when swimming and you inadvertently gulp pool water.

Environmental Toxins – In addition to pesticides and chlorine/fluoride mentioned above, there are a number of other toxins in our environment that can affect the microbiome. Toxic metals, for instance, are another big culprit. Aluminum and heavy metals such as lead, nickel, and mercury are found in the air we breath, the foods we eat (both from pesticides and food containers), the cookware we use, the body products we apply, etc. (Learn more about toxic body products here.)

Certain Medical Procedures – Prepping for a colonoscopy, for example, totally flushes out the large intestine over a short period of time which in turn flushes out a good amount of gut bacteria. Chemotherapy is also known to disrupt the gut bacteria.

Chronic Stress – High stress levels stops your body from its normal pattern of resting, digesting, relaxing and healing. This constant stress keeps your cortisol levels high which can lead to insulin issues (and possible diabetes), sleep issues, among other things that disrupt your gut microbiome.

How to Rebuild Your Microbiome

Most people at this point know that when taking antibiotics, you need to replenish the good bacteria in your gut. In fact, some medical doctors now prescribe a probiotic supplement to be taken in conjunction with the antibiotic. (They should be taken at separate times of the day.)

However, as you saw above, there are many ways to damage your gut bacteria and disrupt your gut microbiome, not just antibiotics. In today’s world, you need to be proactive on a daily basis to make sure you are rebuilding the good bacteria so that you have a good defense against the pathogenic (or bad) bacteria. Keeping this balance keeps your immune system strong.

Building good bacteria starts with eliminating as many of the things discussed above as you can. First and foremost, you need to eat quality foods. You also have to be diligent about restocking your good bacteria by using a variety of probiotic sources.  It also means that you need to actively feed the good bacteria you already have by regularly consuming prebiotics.

Below are a wide variety of ways to help replenish and maintain a strong microbiome. No two people are the same, so different combinations will work better for some than others. When you try something new, start will a little and work your way up to larger quantities, if needed. Or, work with a health professional.

Supplements – Probiotic and prebiotic supplements can be good and sometimes are necessary, especially when you know you have done something to compromise your gut. Taking a higher concentration or specific strains of probiotics may be necessary after an antibiotic, for example, or to help with specific health issues. Some probiotic strains may work better for you than others.

The problem with taking a particular probiotic supplement for an extended period of time, however, is that you can create a mono-culture in your gut – essentially creating a mono-biome rather than a microbiome. For example, if you keep taking a lactobacillus based probiotic long-term, you may create an overabundance of lactobacillus bacteria in the gut and therefore crowd out other beneficial bacteria that are needed.

If you do take a probiotic supplement, it is best not to stay on it long term. Use different strains and brands over time. (Note that there are also some probiotic strains that help your body build and maintain the bacteria you already have.)

Eat Fermented Foods and Drinks – Fermented foods is one of my favorite ways to replenish good gut bacteria. A good fermented food or drink can have thousands of bacteria strains as compared to a typical supplement with an average of 8 to 12 strains. Eating a spoonful of ferments a couple times a day or with each meal can help counter some of the substandard foods we eat.

If you are new to ferments it is important that you start slow or you can shift your microbiome too fast, causing die off and flu-like symptoms. Making your own fermented items like kefir, kombucha, or sauerkraut is optimal. Another good choice is a quality apple cider vinegar, like this one that still has “the mother” in it. You can start by drinking a teaspoon or less first thing in the morning in a small glass of water and build up from there.

More fermented options are becoming available in stores as well, but you still need to be cautious. Most yogurt brands, for example, contain lots of sugar and have many other suspect ingredients. Kombucha is fermented but it is a sweet ferment and when bought in a store can also be paired with not so favorable ingredients. If you use kombucha, keep it to a minimum (i.e.: 1/4 cup per day).

You are better off eating fermented vegetables. Not only do they provide you with good bacteria, but the fermenting process increases the nutritional value of the veggie. Each veggie will give you different family of microbes so it is good to vary them.

It is best to use organic when you can, because the fermenting process can possibly increase the pesticide load. More importantly, you should only use ferments that are in glass containers. The process of fermenting makes the contents acidic and will cause plastic and/or metal containers to leach toxins into the ferment. (I recently spilled a fermented drink on the dashboard in my car and it actually “ate through” the top finish.) Click here for fermented food and drink sources.

Consume Prebiotic Foods – Certain plant-based foods directly feed our good gut bacteria and help them flourish, especially when the food comes from good quality sources. Known as prebiotics, the fibrous part of theses foods are typically non-digestible by the stomach and small intestine. When they reach the colon, these food components ferment and selectively feed the good bacteria.

Prebiotic foods are often categorized as insoluble fiber, soluble fiber and digestive-resistant starch. Components include things like inulin, oligosaccharides, and arabinogalactans. Eating a variety of prebiotics is usually the best, so that you feed a wide range of good bacteria. However, there are some people that may be more sensitive to the effects of a prebiotic (like those with gas, bloating, and reflux), so you may want to start with small amounts and increase slowly.

Examples of prebiotic foods include:

• Artichokes and asparagus as well as herbs like dandelion root and chicory root. Dandelion greens are also good.
• Sulfur containing foods such as onions, leeks, and garlic. Use them raw and cooked.
• Raw nuts and seeds, although these are most digestible if soaked and rinsed before eating. Learn how to traditionally prepare nuts and seeds here. Ground flax seeds spread on salads is another good option.
• Green bananas and under-ripe papaya and mango.
• Starchy vegetables such as potatoes and yams are best if consumed after they are cooked and cooled. Other root vegetables with good soluble fiber include beets, carrots, turnips, and parsnips.
• Legumes and lentils if you can tolerate them. If you have not consumed beans in a while, you may experience gas and bloating as bacteria start to regrow. Start slow, like a tablespoon at a time, and prepare your legumes the traditional way as explained here.
• Whole grains contain insoluble fiber. If you eat grains be sure they are organic (and GMO-free). Gluten-free prebiotic baked goods include potato starch, tapioca starch, and brown rice flour.
• Pectin fiber, found in apples, can also be good. Stewing the apples on low heat and letting them cool brings out the pectin even more. Other good prebiotic fruit options include grapefruit, nectarines, and pomegranate.

Eat as much variety as you can. Restricted diets such as eating a low carb diet or one that is grain-free and/or legume-free, can actually change the diversity of your microbiome. (You should limit processed foods that advertise prebiotic ingredients since many also contain sugar.)

Eat Polyphenol-rich Foods – Similar to prebiotics, polyphenol-rich foods nourish our good bacteria. Sources include grape skins, onions, broccoli, blueberries, and Matcha green tea. Raw cacao (dark chocolate) also contains pholyphenols but watch the sugar content.

Eat Quality Meats, Dairy and Eggs – If you are a meat or dairy eater, be sure you are eating quality animal products. In the same way that conventionally raised (or mainstream) animal products can transfer damaged genes and antibiotics to our bodies (see CAFO Animal Products above), healthy animals can transfer their healthy genes and microbes to us. Examples of quality animal products include:

• Salmon that is wild caught (not farmed with GMO grains and antibiotics).
• Beef and milk products from cows that are grass fed (on pesticide-free fields) and not given antibiotics or hormones. It is best if they are not “grain finished” either.
• Eggs and meat from free-range chickens that eat bugs and worms (along with organic grains, not GMO grains).

Animal product suppliers have gotten creative with their advertising and package wording. For example, some farmed salmon may say “wild” but not wild caught. Other meat suppliers may say “no administered antibiotics” but they may be using it in the feed instead. Finding a local farmer who consciously raises their animals is optimal. Other sources are available here.

Eating quality animal products is also difficult when eating out, unless you really know your restaurant sources. That is why I suggest people only eat meat they prepare themselves and eat vegetarian when dining out.

Consume Quality Bone Broth – Studies show that chicken broth is especially beneficial to gut bacteria. If you are not sensitive to glutamine, consuming bone broth daily is a good habit. You can drink it plain or add it to cooked rice, soups, etc. To learn how to make it your self, click here and here. If you purchase it from the store, brands that are packaged in glass are best since the fat in the broth can absorb the toxins in the plastic containers and liners. (You can usually find glass in the refrigerator section.)

Play In the Dirt – It is good for kids to play in the dirt, especially real dirt in nature that has not been sprayed with chemicals. As adults we can garden, work in the yard, hike in the woods, and even hug a tree. Good quality dirt is full of good microbes. That is what makes plants grow and thrive. When you move dirt around, you are breathing in bacteria that is beneficial to your gut.

Play With Your Pets – We share parts of our microbiome with the people around us and the animals we play with – similar to how we share genes and microbes with the animal products we eat. Bacteria gets shared as you play and breath around your pet, pickup their poop, share licks and kisses, etc. The key here is that your pet has to be eating and living right too. If they are eating pet foods full of GMO grains, drinking tap water, and regularly taking medications, for example, their microbiome will be compromised and there will be a higher ratio of bad bacteria. You should apply all the principles in this article to your pets too!

Empowerment – Believe if or not, your attitude as you move through life can also affect your gut microbiome. If you have not worked through adverse childhood experiences and/or traumas, they can negatively affect the balance of bacteria in your gut. Dr. Raphael Kellman actually found that if his patients overcame these childhood obstacles (through therapy, etc.) and became empowered as a result, they could change their microbiome even without changing or adding anything to their diet.

Stool Implants – A stool implant is a medical procedure that is used more often in other countries. Depending on the damage you have done to your microbiome, there are some strains of bacteria that once killed off are more difficult to obtain. Many have found that having stool implanted from a healthy donor (often a close relative) helped them to create a state of health they were not able to accomplish any other way. (Stool implants work best if you are committed to making many of the other changes discussed above, otherwise the microbiome can revert back to the way it was.)

Our First Exposure to Bacteria as a Baby

Our first exposure to the bacteria that resides in our gut comes from our mothers. When a baby passes through the vaginal canal at birth, the mother’s vaginal bacteria gets ingested by the baby. Breast milk delivers additional bacteria.

Those of us that were c-section babies and/or not breast fed, may need to be more diligent about creating bacteria diversity in our gut. Long-term gut dysbiosis (imbalance) can result in a number of digestive issues as a child (and as an adult), show up as acne as a teenager, and even infertility issues later on. You need to actively rebalance the gut as early as possible. Be sure you are using a variety of the suggestions above.

If a c-section becomes necessary, the newest trend is to soak some gauze in the mother’s vaginal cavity to gather the bacteria there and then swab the baby’s mouth and face with this bacteria laden gauze as soon as delivery occurs. If breast feeding becomes an issue, there are children-based probiotic supplements available that provide very specific strains. (Some probiotics and bacteria are too strong for newborns and small children.)

As the child grows and starts eating solid foods, be sure to include all the good things mentioned above at the age appropriate time.

Moving Forward

As you can see, being conscious of our gut microbiome is a daily commitment. We need to be proactive about feeding the good bacteria we already have and adding to it on a regular basis in order to keep a balanced gut microbiome.

The bad news is that in today’s world the medications we take and even the toxins we are exposed to can kill off some bacteria strains that may be difficult to replace. You will want to limit these microbe killers as much as possible.

You also want to make sure you are not limiting too many foods over a long period of time. There are times when limiting foods is necessary for healing. However, as you heal it is important to reintroduce whole, nutritious foods back into the diet as much as possible.

The good news is that we can still thrive by constantly adding to the diversity of our good bacteria. Lab testing shows that changes to the gut bacteria can occur within 30 hours of changing the diet. Other changes may take longer, but at least you know you can make a difference in your microbiome and your health!

---

This article was written by Sharon Harmon, founder of Life Design for Health. She has a passion for helping people find their way back to optimum health. Please contact her if you would like to know more. There is a great deal of health-related information in her blog articles and on her website.