Microbiome & Diet: The Two-Way Relationship


And How to Select the Right Therapeutic Diet for Your Client’s Personalized Nutrition Needs

If you’re a nutrition or healthcare professional, you’ve definitely run into clients with at least one of the following conditions:

  • Gastrointestinal disorders
  • Neurologic symptoms such as anxiety, depression, brain fog
  • Autism
  • Infertility
  • Lyme Disease
  • Chronic Fatigue Syndrome
  • Autoimmune disorders like thyroid disease, diabetes, fibromyalgia

 And you’re certainly aware that, to truly help your clients, you need to address the root cause of these issues. So, what’s the underlying ‘culprit’ here?

The root cause is often a damaged gut and imbalanced microbiome. These underlying gastrointestinal conditions result in a struggle with inflammatory and digestive disorders.

As such, it’s important to balance the microbiome, remove inflammatory foods, and repair the gut lining in order to restore food tolerance and alleviate symptoms, with the best therapeutic diet tailored to the personalized nutrition (BioIndividual Nutrition) needs of the individual. 

To do so, it is crucial for you to know (i) how foods can repair or harm the microbiome and (ii) how the microbiome’s health can influence tolerance so that you can effectively tailor diet and nutrition advice based on your client’s unique biochemical needs. 

But first, let’s do a quick overview of factors that can harm the microbiome.

How the Microbiome Gets Damaged

At birth and during infancy

The development of the gut microbiome during the first three years of life is influenced by the gut-brain axis as well as [1]:

Maternal exposures like maternal obesity, stress, and infection

Neonatal exposures including mode of delivery (vaginal vs.c-section), antibiotic exposure during labor, and feeding patterns

Adverse childhood experiences or trauma 

Stress and emotions can change the composition of the gut microbiome by affecting bacterial growth and compromising the integrity of the gut lining. This may allow bacteria and toxins to enter the bloodstream. 

Research shows that adverse childhood experiences and trauma were associated with increased gastrointestinal symptoms, and that GI symptoms were associated with anxiety. [2] Furthermore, this particular study showed that in a subset of children, adverse childhood experiences were associated with changes in diversity of the microbiome and in bacteria levels.

Poor dietary choices

A diet high in processed meats, sugars, inflammatory oils, and low in fiber can increase inflammation in the gut.

Pesticides, herbicides, and exposure to pathogens

These can damage intestinal tight junctions, promoting gut inflammation which can adversely modulate the microbiome. 


An increasing number of studies indicate that antibiotics can result in microbial dysbiosis and the disruption of the microbiota, leading to various diseases. [3]

Proton pump inhibitors 

PPI use is linked with reduced bacterial diversity and profound changes in the gut microbiome, accompanied by an increase in oral bacteria and potential pathogenic bacteria in the gut microbiota of PPI users. [4]

Foods That Cause Inflammation and Damage the Microbiome

How long do you think it takes for diet to alter the microbiome?

According to research [5], the relative abundance of various bacteria species can shift within a day after the food reaches the gut – the microbiota will revert back to its original structure two days after the diet is stopped. The scientists also reported that sticking to a diet for around three days can, not only change the makeup of the microbiota, but alter the behavior of the gut microbes as well.

One proposed mechanism is that foods can also directly disrupt the microbiome since our microbes get to eat what we eat. In one study, researchers found that a Western diet can cause both structural and behavioral changes in the resident microbiome. [6] For instance, a highly processed diet can lead to (i) a permanent loss of bacteria critical for the proper functioning of the microbiome and (ii) an increased levels of endotoxin-producing bacteria in the gut as well as their virulence factors.

Inflammation can directly cause dysbiosis by favoring the growth of Enterobacterial species as well as other pathogenic microbes. Studies suggest that an inflamed gut creates a favorable environment for bacteria that can produce antimicrobials. For instance, Enterobacteriacae can produce colicins which are peptidic toxins that prevent the growth of similar or closely related bacterial strains. [7] 

Specific foods and food components can also damage the mucosal layer, triggering an inflammatory response as described below. The following are foods that can cause inflammation as well as damage the microbiome. 


What is gluten? Gluten is a type of prolamin, a toxic lectin known to interact strongly with the brush borders of the intestinal lining. This can damage the gut barrier and cause inflammation. [8] Gluten is the most common food intolerance.

Moreover, numerous studies on gluten, or more specifically, gliadin, the protein component of gluten indicate that it may not be completely broken down during the normal digestive process due to (i) the protein’s structure being incompatible with our digestive enzymes and (ii) the presence of protease inhibitors which neutralize the digestive enzymes in charge of degrading the proteins (and toxins) in food.

Therefore, these protein fragments and toxins can cross the gut barrier largely intact, thereby further damaging the barrier and causing a leaky gut. 


Found in plants, salicylates are a type of phenol which protects the plant against diseases, insects, fungi, and bacterial infection. The body breaks phenols down via a biochemical process known as sulfation which also helps with intestinal integrity.

However, insufficient sulfate supply, having a condition that impairs sulfate use, depletion of sulfates by pathogens, renal sulfate wasting or poor renal reabsorption can cause tissues to be starved for sulfate. [9] This can lead to inadequate sulfation, resulting in leaky gut, gastrointestinal symptoms, and salicylate intolerance. Additionally, pathogens can release phenolic compounds as a defense mechanism and can deplete sulfate and sulfation, either causing or exacerbating salicylate intolerance and digestive distress.


Oxalate is a type of organic acid salt which is naturally present in many plant foods, and can also be produced endogenously. For individuals with a SLC26A1 mutation – that’s the gene involved in oxalate breakdown – oxalates can be toxic and irritate the mucosal lining throughout the body, thereby triggering inflammation. [10] 

Excessive oxalate consumption may also kill beneficial bacteria. [11] For more information about oxalates and their role in chronic illness, click here.


Histamine is a biogenic amine which is endogenously produced by mast cells and basophils in response to an inflammatory immune reaction.

In susceptible individuals, histamine may contribute to epithelial dysfunction thereby affecting DAO secretion by the gut enterocytes. [12] This can result in an imbalance between accumulated histamine and the body’s ability to break it down.


Glutamate is an excitatory neurotransmitter which can increase intestinal permeability by triggering inflammation in the gut. This can allow microbial overgrowth in the gut, thus affecting the microbiome.


These short chain carbohydrates, rich in fructose molecules, are inefficiently absorbed in the small intestine, even in healthy people. Research suggests that, in individuals with a FODMAP-intolerance, a significantly larger amount of these molecules can enter the colon unabsorbed where they act as fuel for pathogens, leading to dysbiosis. Scientists explain that a FODMAP-intolerance can be triggered by a lack of digestive enzymes or a deficiency of GLUT5 which can be further blocked by polyols. [13] 


 For instance, high-carbohydrate diets consisting mostly of wheat, refined sugar, grains, and processed foods have the ability to damage the gut lining, promoting a leaky gut. As such, elimination of these foods can allow the gut and the microbiome to heal.

Low carbohydrates

The ketogenic diet is very high in fat and very low in carbohydrates, it can either improve the microbiome or be difficult on it. The ketogenic diet is usually low in fiber – gut bacteria ar break down plant fiber to create SCFAs which are anti-inflammatory and protect the gut lining, and thus the microbiome. However, in other cases, the ketogenic diet has been found to improve the diversity of the microbiome.

The Microbiome Can Also Affect Food Intolerance

Scientists who study the gut microbiome have discovered unique microbial differences in patients with food allergies compared to healthy patients. They suggest that the dysbiosis of the microbiome precedes the development of food intolerance.

 For instance:

  • SIBO can thwart the body’s ability to digest FODMAPs.
  • Gut dysbiosis can lead to  sulfate depletion – this could result in an overgrowth of intestinal bacteria which produce phenol and p-cresol and would therefore, reduce tolerance to salicylates and phenols.
  • Antibiotics can wipe out healthy bacteria including oxalobacter formigenes which are involved in oxalate degradation in the gut. This could result in high oxalate levels.
  • H.pylori infections, which can promote GERD and cause peptic ulcers, can also trigger a complex immune response which activates mast cells and histamine release. As such, these infections may decrease tolerance to histamines.

One way to improve your microbiome is via therapeutic diets. Think of it as your client’s personalized microbiome diet.

How Therapeutic Diets Can Help

For nutrition and dietary interventions to be effective, these need to be tailored to individual patients’ specific requirements based on their unique biochemistry, health history, nutrient deficiencies, microbiome state, and genetics.

By addressing these underlying factors, diets can be customized to control the intake of certain foods or food components which could damage enterocytes and the junctions between them, promote bacterial overgrowth, and trigger a cytokine storm.

As such, elimination of these food components can help alleviate symptoms while taking the burden off the system. Moreover, therapeutic diets also promote the consumption of various foods which help our gut bacteria produce various bioactive compounds. These regulate the proteins that form the tight junction complexes and can help heal the gut barrier.

The latest nutrition research indicates that people with an imbalanced or unhealthy microbiome are more likely to react to food compounds such as phenols, salicylates, histamine, oxalates, glutamate, and FODMAPs. 

How to Select the Right Therapeutic / Microbiome Diet

Here’s a brief overview of the various types of therapeutic diets and when they can be useful to personalize the right microbiome diet for your client. Remember to tailor the selected diet to your clients’ needs. You might also want to recommend intake of ceylon cinnamon and turmeric if your client isn’t salicylate intolerant. 

To recap: when your client has a microbiome imbalance or has inflammation from certain foods, a personalized dietary strategy can be very helpful. I always teach the practitioners in my BioIndividual Nutrition Training that dietary intervention is key to healing, and explain how the right diet:

  1. Provides the client relief
  2. Takes the burden off the system
  3. Then allows time to work on underlying factors: microbiome and biochemical pathways/nutrients depleted 

Here’s more on some of my favorite approaches I use when bioindividualizing a dietary strategy.

Diets that Reduce Inflammation and Support the Microbiome

Gluten-free, casein-free, and soy-free diet

The gluten-free, dairy-free, and soy-free diet is definitely the most common and popular low inflammation diet, and a great starting point for most clients.

In one study, investigating the effects of a gluten-free diet on the gut microbiota, scientists found that levels of Veillonellaceae dropped. This bacterium is thought to trigger gut inflammation and is linked to Crohn’s and other digestive diseases. [14]

I advise my clients to eliminate these major gut-disrupting foods for at least 3-6 months to see the full effects of this diet. However, if symptoms are acute, after 2 to 3 weeks on a GFCFSF diet you may consider eliminating further food compounds (in addition to gluten, casein, and soy) in the diets described below.

Low salicylate diet

As we discussed earlier, salicylates can cause leaky gut, gastrointestinal symptoms, and inflammation. And people with dysbiosis may be more intolerant to salicylates. As such, a low salicylate diet can help some people with GI distress. 

If your client presents with gastrointestinal symptoms and has asthma-related or behavior symptoms consistent with salicylate intolerance (such as hyperactivity, aggression, or trouble falling issues, among others), you might want to consider a low salicylate diet such as the Feingold diet or the FAILSAFE diet.

Low histamine (and low amine) diet

A low salicylate/low amine diet may be useful for individuals with low sulfate levels caused by dysbiosis and poor sulfation capacity from genetic or other biochemical reasons.

A low histamine diet is recommended for individuals who often experience facial flushing, itchiness, or nausea after meals, or for those with an H.pylori infection.

Low oxalate diet

As oxalate can irritate the intestinal tract, cause gut inflammation, and kill beneficial bacteria, a low oxalate diet can help with gut and microbiome issues.

Consider a low oxalate diet if your client has kidney stones, or oxalate-related muscle and joint pain. The diet might also be useful for clients with a history of antibiotic use, when the good bacteria that breaks down oxalate may have been wiped out.

Low FODMAP diet

For individuals where FODMAPs fuel pathogens and dysbiosis, as well as cause inflammation and pain, the Low FODMAPs diet can be very helpful.  Clients with SIBO and who have a hard time managing symptoms, especially diarrhea, might want to try this diet especially if more serious culprits have been ruled out.

Low glutamate diet

Individuals with allergies, obesity, diabetes, digestive issues, asthma and other autoimmune diseases may benefit from reducing their glutamate consumption. While this may not reverse their disease, it can help alleviate inflammation, thus allowing easier management of their condition and support healing of the gut.

Ketogenic diet

The ketogenic diet may help individuals with metabolic syndrome, neurological conditions, as well as seizures. However, as they work with their physician, they might want to include resistant starch for SCFA production and to modify the macronutrient composition of the diet for those with a thyroid dysfunction.

Grain-free diet 

The Specific Carbohydrate diet, GAPS diet, and Paleo diet are all wonderful diets to help support the gut by reducing grains and starches which can feed bacteria and pathogens and cause inflammation in the gut. The autoimmune paleo diet protocol is more comprehensive than the paleo diet since it focuses on the elimination of all food components and lifestyle habits that have the potential to damage the gut lining and trigger inflammation including eggs, nuts, nightshades, and more.

Additional healthy diet principles and Foods that reduce inflammation

Fermented foods contain probiotics that can help reduce inflammation and heal the gut lining, which in turn helps improve the microbiome. You want to be cautious with fermented foods though, especially when working with clients who are histamine intolerant.

Prebiotic foods such as chicory root, dandelion greens, Jerusalem artichokes, garlic, onions, leeks, and asparagus can help stimulate the growth of beneficial bacteria in the gut and help reduce inflammation. However, like most substances, always consider BioIndividual Nutrition factors, as they may cause issues in individuals with a FODMAP intolerance.


The microbiome is essential for optimal health and longevity. There is a two-way relationship between diet and the microbiome since (i) what we eat can either support the microbiome or damage it and (ii) the state of the microbiome will ultimately determine what the person can safely tolerate.  

As such, healthcare professionals, especially those who are new to BioIndividual Nutrition, may find it difficult to help clients heal their gut especially if they present with complex medical diagnoses.

My professional Bioindividual Nutrition Training provides a methodology and framework for determining the best interventions for personalized nutrition for clients with specific health concerns and demonstrates how to tailor those plans to meet clients where they are in their health journey, along with all the tools, food lists, and meal plans you need. Check it out here.



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9.  Sonestedt, E., Wirfält, E., Wallström, P., Gullberg, B., Orho-Melander, M., & Hedblad, B. (2011). Dairy products and its association with incidence of cardiovascular disease: the Malmö diet and cancer cohort. European journal of epidemiology, 26(8), 609-618.

10.  Williams, R. J. (2020). Sulfate deficiency as a risk factor for autism. Journal of Autism and Developmental Disorders, 50(1), 153-161.

11.  Peck, A. B., Canales, B. K., & Nguyen, C. Q. (2016). Oxalate-degrading microorganisms or oxalate-degrading enzymes: which is the future therapy for enzymatic dissolution of calcium-oxalate uroliths in recurrent stone disease?. Urolithiasis, 44(1), 45-50.

12.  Suryavanshi, M. V., Bhute, S. S., Jadhav, S. D., Bhatia, M. S., Gune, R. P., & Shouche, Y. S. (2016). Hyperoxaluria leads to dysbiosis and drives selective enrichment of oxalate metabolizing bacterial species in recurrent kidney stone endures. Scientific reports, 6, 34712.

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