After reading the scientific literature on the gut microbiome, working with thousands of patients, and testing the gut microbiomes of hundreds of individuals struggling with gut issues, difficulty losing weight, blood glucose issues, mood disorders, autoimmune disease, learning and memory disorders, and other chronic conditions, I now know that our society is suffering from a serious epidemic that is not receiving the attention that it deserves — in the media and in mainstream medicine.

What is this epidemic, you ask? The epidemic is the mass extinction of beneficial microbial species that are supposed to live in our guts and help us digest our food, metabolize vitamins and minerals, control our blood glucose, modulate our immune system, and even influence our brain health and moods.

And what is the cause of this epidemic? The cause is predominantly the misuse and overuse of antibiotics. However, antibiotics in the medical setting are not the only issue. This mass extinction of our beneficial microbes is also a result of our modern lifestyles of lack of physical activity, almost non-existent contact with nature, and an over-reliance on processed foods and animal-based foods (many of which also contain antibiotics) as our main sources of calories.

There is a growing amount of scientific research now showing that our microbiomes may not fully recover after a round of antibiotics, even with the concurrent use of probiotic supplements. The reason why probiotics aren’t the quick “post-antibiotic remedy” we once thought they were is simply because the most fragile beneficial bacterial species that we are likely to lose when taking antibiotics cannot be encapsulated and sold in pill form with current technologies for producing probiotic supplements.

And it is precisely these more fragile species that are missing in the guts of individuals who suffer from the chronic diseases that keep doctors’ waiting rooms full and pad the pockets of pharmaceutical manufacturers and their sales reps. Moreover, the specific species of bacteria that are missing in an individual patient tend to correspond with the condition from which he or she is suffering. For instance, individuals with low numbers of Roseburia bacteria tend to have type 2 diabetes. Obese patients are typically missing several different species of bacteria, including a mucus-degrading species called Akkermansia. People who are suffering from inflammatory bowel disease have been found to not only have low numbers of beneficial bacteria, but they also have an overgrowth pf pathogenic and opportunistic species such as the bile-tolerant organisms and proteobacteria. Those with recurrent kidney stones are often found to be lacking in a species called Oxalobacter formigenes, which is a beneficial bacterial species that helps us metabolize and break down oxalates in the digestive tract. (Oxalates are components found in a wide variety of plant foods, including spinach, berries, whole grains, nuts, and soybeans.)

Now the devil’s advocate may say that perhaps the chronic illness is what caused the shift in the types of species found in the gut microbiome, rather than a shift in the microbiome causing the disease. This doesn’t appear to be the case. When specific dietary and lifestyle strategies are put into place, the microbiome shifts back towards a more “balanced” state. Then the individual recovers from the chronic disease.

By incorporating specific foods into your diet (and avoiding some other specific types of foods) you can indeed encourage the growth of beneficial species of bacteria that are not found in probiotic supplements and discourage the growth of pathogenic and opportunistic strains of bacteria that tend to crowd out beneficial bacteria. Put simply, whenever you choose to eat or drink anything, you are choosing to either feed “good” bacteria that play a role in keeping you healthy or you are feeding “bad” bacteria that can influence your body and your mind in a negative way.

So here are the specific foods for you to start adding to your meal plan. Be sure to include at least one of these foods at each meal and each of these foods at least a few times every week.

Pea Protein

The specific types of protein you eat dramatically influence the composition of your gut microbiome. Research studies have found that pea protein has an extremely beneficial impact on the microbiome. Specifically, isolated pea protein powders increase lactobacilli and bifidobacteria, as well as the abundance of the beneficial bacterial metabolites acetate, propionate lactate, and butyrate. These bacterial metabolites help feed the cells lining the walls of your colon (your large intestine), thus helping to heal a leaky gut and keep the cells of your colon healthy.

The pea protein powder I use every day (and highly recommend) can be purchased online by clicking this link. I like this one because it’s made from organically grown peas, has a complete amino acid profile for muscle repair, mixes smooth with no clumps or lumps, and comes in 3 different flavors that all taste amazing. In addition, third party testing of this pea protein powder has verified that the nutritional label is accurate and the product actually contains what’s stated in the ingredients. (The same cannot be said for many of the protein powders on the market, which often have much less protein than what’s stated on the label and can be contaminated with non-stated ingredients such as gluten or even plastics.)


You may have heard that sweet date fruits were unhealthy due to high sugar content. However, solid scientific research clearly shows that the sugars and other components of dates have many beneficial properties that promote a healthy gut and help prevent chronic disease. Dates are high in a wide variety of different polyphenols, flavonoids, anthocyanins, and fibers that inhibit the growth of cancer cells and promote an increase of beneficial bacteria that are involved in short chain fatty acid production. The short chain fatty acids that are produced by good bacteria in your gut help to seal up holes in the gut and keep your colon cells happy.

Eating just 2 oz of dates every day can promote the recovery of chronic conditions such as inflammatory bowel disease, type 2 diabetes, autoimmune disease, and obesity if consumed as part of an overall healthy dietary strategy. There are many different kinds of dates being grown in hot, desert climates, and each type of date contains different types of polyphenols and flavonoids as well as different flavors and textures. I recommend trying several different types of dates instead of just one varietal, not only so you can explore the different flavors and textures nature provides, but also to get a wider range of polyphenols and flavonoids which could have pleiotropic health benefits. You can purchase several different types of fresh, juicy dates online from this ranch in California.


Another food often considered “off limits” for anyone trying to lose weight or manage their blood glucose, mangos are scientifically proven to actually help with weight loss and blood glucose control. One of the ways mangos can help you heal your gut, lose weight, and reverse type 2 diabetes is by increasing the amount of Akkermansia bacteria in your gut. Studies have also found that mangos not only help to lower overall blood glucose, but they also can protect the liver from developing insulin resistance and nonalcoholic fatty liver disease (two conditions that underlie the development of metabolic syndrome and diabetes).


Spirulina is actually a form of bacteria called cyanobacteria or “blue-green algae.” Nutritionally, spirulina is high in protein, iron, and a variety of antioxidants and anti-viral, anti-fungal, and anti-inflammatory compounds including phycocyanobilin. Scientists and herbalists have known for many years that spirulina supplementation can reverse type 2 diabetes, fatty liver disease, insulin resistance, high cholesterol, high blood pressure, and anemia when added as a supplemental component of an overall healthy nutrition plan. More recently, scientists have discovered that spirulina supplementation increases Roseburia and Lactobacillus bacteria in the gut, which may be one of the ways in which spirulina has such a powerful healing effect in the body.

As with any type of supplement or food, it’s extremely important to choose a high quality source/brand. Aways get your spirulina from a company that does frequent testing to make sure the spirulina is free of contaminants. The spirulina I recommend for safety and quality reasons is this one.

Celery Juice

Celery juice is an old remedy for digestive ailments, chronic pain and inflammation, and water retention. There is a type of polysaccharide (a long chain of sugar molecules) in celery called apiuman that can help to rebuild damaged stomach lining. Other phytonutrients found in celery juice have been found to prevent inflammation of the digestive tract and liver.  This may be why celery juice can have such powerful healing effects for people with irritable bowel syndrome, Crohn’s disease, ulcerative colitis, and stomach ulcers.

Another category of phytonutrients found in celery juice are phthalides, which are diuretics as well as smooth muscle relaxants. These particular phytonutrients are likely responsible for the blood-pressure lowering and “anti-bloating” effect of celery juice.

Other research on celery has found that it modulates the immune system by decreasing levels of pro-inflammatory cytokines interleukin 1B and interkeukin 8 as well as tumor-necrosis factor (TNF-alpha). For this reason, celery juice may be a promising therapy for autoimmune conditions, allergies, and other conditions associated with chronic inflammation and immune system dysregulation.

Now this was certainly not an exhaustive list of everything you should include in your diet to heal your gut. However, if you make it a point to eat at least one of these 5 foods at each meal, and all 5 of these foods at least a few times per week, you will begin to shift your microbiome towards a healthier state.

Make sure you’re signed up for my free newsletter to be notified when the next article in this series is posted, in which I’ll discuss the foods that you MUST avoid in order to heal your gut microbiome.