Graphic showing key components of feeding the microbiome

How To Feed Your Microbiome- Part 2





As we explained in part 1, new research confirms something that has long been accepted anecdotally- eat a varied diet, especially one full of fruits and vegetables. Eating the same oatmeal and banana breakfast every day? Change it up! The more varied your diet, the happier your microbiome. It’s suggested that you eat at least 30 different fruits, vegetables, and grains/grasses per week, and even more is better. Seems daunting? Here’s how to make it happen:


  1. Rotate your breakfast each day. Vary the type of fiber and fruit you use. This can be easy to do with a smoothie or soaking a bowl of fiber overnight in the fridge with milk, yogurt, or a non-dairy alternative. Top with different fruits.
  2. Pick up new or different vegetables each time you go to the store, or join a local co-op that delivers seasonal fruits and vegetables. If you eat with the seasons, you tend to get more variety in your diet over time. 
  3. Mix it up for dinner. Try not to eat the same thing continuously throughout the week. Master some simple meals where you can swap out different vegetables. Stir fries, curries, sheet pan roasts, casseroles, and stews are all easy to change up with different vegetables. Try using sweet potatoes, turnips, rutabagas, parsnips, celeriac, or kohlrabi instead of potatoes every time. Swap your greens around. Add different toppings to a salad. If you insist on keeping taco Tuesday, then vary the fillings, toppings, or type of tortilla. 
  4. Don’t forget the herbs and spices! They count as well for promoting the microbiome. You’ll find it easy to hit that 30-type mark if you integrate different herbs and spices into your cooking. Change the profile of your dishes by slanting them towards different flavor profiles. Group spices by cuisine- add seaweed, sesame, soy etc for a Japanese profile; or cumin, coriander, cayenne, and cinnamon for a more North African take- you get the picture. It’s especially easy to wake up roast vegetables by varying the spices. Be creative!


Eat Lots of Fiber


As we mentioned in our last piece, there is almost nothing that you can change in your diet that will have a more beneficial effect than eating lots of fiber. Why? Not only does fiber increase the motility of your waste products (meaning it moves them through your system more quickly and you’ll avoid constipation), but at the same time it also helps prevent watery stools which means you’ll likely avoid cramping and diarrhea. Just these two things help avoid irritation to the gut, which prevents trauma and can help keep the lining of the intestines intact, preserving the tight junctions and helping prevent a leaky gut. Fiber can also directly benefit specific bacteria that populate your microbiome and help your gut. Fiber also slows digestion and has been directly tied to a healthy heart and brain. There are two types of fiber you should try to consume:


  1. Soluble Fiber: Soluble fibers mix with water and slow digestion. They are associated with a decreased risk of heart disease, decreased cholesterol levels, and better blood sugar control. Soluble fiber is the type that can also directly benefit good bacteria in your microbiome. Depending upon the mix of your population of gut bacteria, different fibers can benefit different bacteria (another reason to vary your diet). For instance, long-chain inulin (LCI) was associated with increased Bifidobacterium, a beneficial gut bacteria. The short chain fatty acids, found in soluble fibers can lower inflammation and help to regulate your appetite and blood sugar levels.

Soluble fibers are found in some grains, seeds, legumes, and various vegetables. Examples include oats, beans, peas, and most fruits. Oats, many seeds, LCI, and even peas can be integrated into breakfast fairly easily. Look as well for high-fiber breads, tortillas, and wraps at the grocery store. Fiber-enriched powders are also useful for smoothies and mix-ins and help guarantee you get enough soluble fiber.

  1. Insoluble Fiber: This type of fiber is not absorbed, but passes through your gut. Why eat it if it’s not absorbed? Insoluble fiber, found in foods such as whole grains, beans, and root vegetables, acts as bulk that can help food and waste pass through the gut more easily. This increase in motility means no constipation and a healthier gut. Nuts are also a good source of dietary fiber. The type of fiber in nuts is primarily insoluble, which adds bulk to the diet and can help to prevent constipation1. However, the exact composition can vary from one type of nut to another. It’s always a good idea to include a variety of nuts in your diet to get a mix of different types of fiber and other nutrients.
  2. Increase your fiber use slowly so your body can get used to it. This also allows your microbiome to react steadily to the change in diet. Increase your hydration as you increase your fiber content so that you maximize the benefit of the fiber and don’t risk getting dehydrated. Studies have found that the people who have the most robust and varied populations of good bacteria in the gut are those that eat the most varied high fiber diet.


Limit Processed Foods


Your microbiome doesn’t just depend on a large and robust population of different bacteria, it also matters what your ratio of good bacteria to bad bacteria is. Those who have far more good bacteria than bad bacteria are more likely to have healthy microbiomes A study of 1,100 people published last year in Nature Medicine, classified good gut fauna that protected people against cardiovascular disease, obesity, and diabetes, and bad fauna that promoted inflammation, heart disease and poor metabolic health. The study found that the greatest correlation between out-of-balanced microbiomes, where too much bad bacteria was found, was in how much processed food each study participant ate. 


  1. When possible, make foods yourself instead of buying prepackaged foods- that way you’ll know what is going into your diet. Batch cooked foods on the weekend and freeze portions for use during the week. Make a double batch of dinner items and freeze the leftovers. 
  2. If you do buy packaged foods, look for natural or organic products that are likely to have fewer additives. Read the label and reject products that have fillers, preservatives, flavor enhancers, dyes, and modified starches and proteins. 
  3. When eating out, avoid fast food chains and other lower-quality eateries. Choose simpler dishes with fresh products that include grains and vegetables if possible.
  4. When snacking, choose natural products, nuts, vegetables, whole grain crackers, and chips. If you eat chips, look for natural products with no additives. This means you should pass on the zesty buttermilk fried cajun dill pickle kettle chips.
  5. Strive to eat a healthy, varied diet full of fruits, vegetables, and whole grains. If you aren’t, transition as best you can to one. It’s not all or nothing, making a start is good- go as far as you can toward health!


Eliminate Toxins


This seems to go without saying, but it’s easier said than done. We are surrounded by toxins, and they are increasing all the time. Some, like alcohol, are self-inflicted. Others, like microplastics, forever chemicals, ozone, and biochemical contaminants are ubiquitous, and difficult to avoid. Although clean living has much to recommend it, not every toxin will impact the microbiome directly. Again, taking steps to limit your intake of toxins can make a big difference- do what you can, and for those you have no control over, consider cleansing toxins through a number of means.


  1. Limit your consumption of alcohol. Alcohol consumption can dramatically impact the microbiome, especially if you consume more than you should. It can lead to changes in the composition of the intestinal microbiota. These changes can lead to dysbiosis, a condition where the balance of the gut microbiota is disrupted. It can also increase the permeability of the gut, allowing bacteria and bacterial toxins to leak from the gut into the bloodstream. This can result in endotoxemia, systemic inflammation, and tissue damage. Alcohol consumption can also cause intestinal inflammation through multiple pathways. This inflammation can exacerbate alcohol-induced organ damage, creating a vicious cycle. Studies have also confirmed that alcohol can increase intestinal bacteria. This overgrowth could be a direct result of alcohol, or an indirect byproduct of poor digestive and intestinal function caused by alcohol consumption.
  2. Stop using tobacco products. Tobacco can cause all of the same effects that alcohol can. Using both together can exacerbate the effects. Tobacco can cause changes in the composition of the intestinal microbiota. These changes can lead to dysbiosis, a condition where the balance of the gut microbiota is disrupted. Tobacco use can increase the permeability of the gut, allowing bacteria and bacterial toxins to leak from the gut into the bloodstream. Tobacco and its metabolites can promote intestinal inflammation through multiple pathways
  3. Only use antibiotics when absolutely necessary. Antibiotics act as a bomb in your microbiome, killing bad and good bacteria indiscriminately. The problem is that the bad bacteria tend to repopulate more aggressively and more effectively than the beneficial gut bugs do. Antibiotics can be overprescribed, often because patients demand them for conditions that don’t warrant their use. Antibiotics do not ever work against viruses. The problem is that some doctors will prescribe antibiotics without knowing whether an infection is viral or bacterial. Be sure. Ask for a culture. Don’t use them whenever it seems convenient. Studies have found that Changes in people’s gut microbiomes due to diet or antibiotic use can directly alter nutrient absorption.
  4. Environmental toxins. Air pollution can alter the microbiome.  Research funded by the National Institute of Environmental Health Sciences (NIEHS) found that breathing ultrafine particles, a component of air pollution, altered the gut microbiome and changed lipid metabolism in mice with atherosclerosis. If you live in a densely populated city or an area with a lot of air pollution, make sure you spend some time in parks or outside the city. Consider a good environmental air filter. 
  5. Heavy metals. Exposure to heavy metals such as arsenic and cadmium can also impact the gut microbiome. For example, arsenic exposure in mice changed the gut microbiome and altered molecular pathways in bacteria that are important to biological functions like DNA repair. A separate study suggested that the microbiome could protect mice from arsenic or methylmercury toxicity. In addition, research in a mouse model of Alzheimer’s disease demonstrated that exposure to cadmium altered an important communication pathway between the gut microbiome and the central nervous system called the gut-brain axis. If you have been exposed to heavy metals, there are several things that you can do to help alleviate the problem. First, assess your risk. Take a reliable heavy metal exposure test. Next, depending on your exposure level, consider mild to medium treatment through sauna therapy, or biomat therapy, especially combined with a quality detox powder to help move things along. Especially if your exposure is heavier, consider IV therapy to help chelate the toxins out of your body. 


Consider Food Sensitivity


Food allergies can wreak havoc on your microbiome and on the lining of your gut. Most of us are familiar with immediate allergic reactions (IgE reactions- true allergies), that cause hives, swelling, itchiness, etc. You can certainly have igE allergies to foods, but when you do, you tend to pick up right away which foods are causing the problem, since these reactions tend to occur within 20 minutes or so. Food sensitivities are more delayed. They involve IgG reactions, sometimes amplified by complement (C3d). IgG reactions can take up to 72 hours to manifest, and when they do, not only might you not be able to immediately correlate to a certain food you consumed, but the symptoms can be different as well. Instead of hives, think bloating, brain fog, gut cramping, low energy, and interference with memory. Because most people don’t trace these food sensitivities to a particular food, they keep eating that food. Doing so risks chronic damage to the gut by causing inflammation that can cause a leaky gut and spread the inflammation throughout the body. Many people with chronic inflammation (a silent killer), can eventually link it to the gut. So how can you discover if you are sensitive to foods that may be harming you? What should you do about it?


  1. Take a comprehensive food allergy and sensitivity test. You won’t be able to do anything about food sensitivities unless you first investigate. Many food tests merely test for food allergies (IgG). To really get to the root cause, you must test for more delayed reactions (IgG) that are harder to trace foods to on your own. Ideally, you’ll also be testing complement, which magnifies IgG reactions in the same way that some viral infections are magnified when it’s triggered. Taking a comprehensive test will allow you to identify your various degrees of reactivity so that you can address the hidden problem.
  2. Start an elimination diet. Once you’ve gotten your results back, the next step is to start an elimination diet. You’ll start by temporarily eliminating all the foods you are sensitive to and replacing them with “safe” foods. If you are sensitive to a lot of foods, then you might only eliminate those that you are moderately or severely sensitive to. Generally, you won’t see foods you don’t normally eat- but there may be a few surprises because of cross-reactivity. For instance, you might see bananas if you have a latex allergy, or clams might show up if you have an environmental allergy to roaches. A dietician or nutritionist can help guide you through the process. After a period of time you’ll start reintroducing foods into the diet that you tested sensitive to. This is a “double-check” on the testing process and helps eliminate cross-reactive reactions and checks to see how your body actually handles each food. Bananas may actually be perfectly fine for you! If a food causes a reaction when introduced (makes you tired, induces brain fog, etc- and you’ll know because you are only reintroducing one food at a time), you keep it out and keep testing the other foods.
  3. Repeat the food sensitivity test. Once 6 months to a year has gone by, and you’ve completed your elimination diet, retest. The great news is that even if you’ve tested as reactive to certain foods after you’ve eliminated them from your diet for a period of time, they may be safe to eat again! Highly reactive foods may take a few years before (if)  you can safely consume them again, but others may clear up more quickly. If you were highly reactive to some foods, keep testing once a year to see how your immune system is now reacting to those foods. Eventually, you may find you can enjoy them again!


Add probiotics to your health regimen


Probably everybody has heard of probiotics by this point, but simply put, a good probiotic supplement consists of billions of beneficial gut flora to help restore and keep healthy your microbiome. Even very conventional doctors will now recommend a probiotic when you are prescribed antibiotics. Probiotics are useful for much more than just ameliorating the effects of an antibiotic. In fact, not only do probiotics help with dysbiosis, but taking one regular will help keep your microbiome thriving. Prebiotics, probiotics, and postbiotics all work together to make sure that the balance in your microbiome stays positive. All are available as supplements. Although these can make a huge difference, don’t think you should ignore the rest of the advice in this article- prevention is the best policy. All of these tips work together to feed your microbiome.


  1. Take a probiotic at least once a day. Double, or triple up if you are on a course of antibiotics. 
  2. Eat fermented foods. Fermented foods like sauerkraut, kimchi, kombucha, natto, yogurt, kefir, etc. can contribute positively to your microbiome. These foods all contribute to the diversity of the bacteria and other flora in your microbiome, and help feed the beneficial flora. Focusing on adding these foods to your diet helps the microbiome thrive- and lowers inflammation.


Implementing all of these tips into your health regimen can have a profound effect on your microbiome, and therefore on the health of your gut, your brain, your heart, your glucose levels, and how you feel in general. Even if you can’t do everything on the list, get started! At least assess yourself for food sensitivities, take a probiotic, decrease your toxic exposure, and change your diet as much as you can toward one that supports your health. Any start is a good start!