November 27, 2022 1:39 am

gut health, microbiome, histamine intolerance, autoimmunity, mast cell activation, Alison Vickery, Health

Over the last ten years, significant advances in microbiome sequencing have enabled real breakthroughs in our understanding of the microbiome.

We must now divide our knowledge between old-world and new-world thinking.

Old-world thinking was based on researching single microbes, which was all we could afford to study.

Much of this research is compromised, in my experience.  Gut health is not simply about the presence of individual microbes,  probiotics, and prebiotics. This is old-world thinking.

New-world thinking is based on researching the whole microbiome, which has found that individual microbes live symbiotically with other microbes, ourselves, and our environment.

Central to this emerging research is the role of the gastrointestinal tract in maintaining our body’s homeostasis necessary for health. Changes in the diversity of the microbiome are directly linked to health outcomes.

Furthermore, there is a bidirectional interaction between our microbiome and our environment.

This means our microbiome is shaped by our diet, sleep, exercise, perceived stress, toxin exposure, and the medicines we take. But equally, we can eat all the right foods,  sleep, exercise, manage stress, and reduce toxin exposure, but if our microbiome is compromised, it will not be able to keep up.

Microbial health is won or lost in an environment. And health is won or lost in a microbiome.

Fortunately, this means that we (not our genes) control our destiny.


gut health, microbiome diversity, histamine intolerance, mast cell activation, Alison Vickery, Health, Australia

Microbiome Diversity

We all have a unique microbiome that is as unique as fingerprints.

The old-world view is that the individual inhabitants are what determines health.

However, the new-world view is that microbial diversity is associated with health.

The factors which affect our microbiome diversity are complex, interrelated, and not yet fully understood.

The remainder of this blog post will look at recent advances in understanding the gut microbiome and what influences microbiome diversity.


gut health, histamine intolerance, autoimmunity, mast cell activation, Alison Vickery, Health, Australia

Dietary Composition

Diet is a crucial factor influencing the gut microbiome.

A loss of microbial diversity is associated with a:

1 Decreased ability of our microbiome to metabolize different foods, and

2 Decreased ability of our microbiome to manufacture anti-inflammation compounds such as butyrate from dietary fibers.


Changing our dietary composition changes the microbiome composition. While changing our microbiome will change the anti-inflammatory compounds our microbiome can manufacture.

Importantly, there is a bidirectional interaction between dietary fiber and the microbiome.  We need microbes to digest dietary fiber, but we also need dietary fiber to feed the microbes that are digesting the fiber!

Similarly, the higher the diversity, the more issues can be resolved with increasing food diversity. The lower the diversity, the more the issue will need supplements to build a bridge to reintroducing foods.


Recent studies have important implications for understanding this dynamic:

1 Immigrants from Southeast Asia to the United States immediately lost 15% of their microbiome diversity.

2 One addition to the diet, within a relatively short time, leads to a significant positive change in microbiome structure without the need to remodel the entire diet regime.

3  Antioxidants (and other anti-inflammatory foods) are poorly absorbed from food. The microbiome produces anti-inflammatory benefits in the form of Short-chain fatty acids.


What does this mean for those with histamine intolerance, autoimmunity, and mast cell activation?

The risks and benefits of eliminating foods need to be carefully evaluated.


Old World Thinking

1 Eliminating foods or only eating a handful of “safe” foods” without working on the microbiome is a lose-lose situation.

2 Removing Salicylates and FODMAPs will remove the fibers that short-chain fatty acids feed on and significantly alter the microbiome diversity. It is quicker and easier, in my experience, to work on the underlying cause than implement an elimination diet.


New World Thinking

1  If we do not tolerate a particular food, particularly fibrous foods, we must identify what drives the reaction and work on the underlying cause.

2 Simple dietary changes (even one food) can significantly and positively improve the diversity and abundance of the microbiome in a short amount of time.

3 Reintroducing foods slowly and building microbiome capacity may explain why slowly reintroducing new foods may be more successful.

4 We need to feed microbiome inhabitants for them to grow.  Even when beneficial bacteria are below detectable levels, they may still be hanging around and able to be grown.

5 Feeding short-chain fatty acid-producing microbes, including butyrate, is paramount in managing inflammation throughout the body.

6 A high-quality diet is more critical than antioxidant supplements to provide antioxidants.

7  Adding probiotics (such as MegasSporeBiotic) and prebiotics (such as ZinoBiotic) can break the vicious cycle by raising microbiome diversity. Similarly, adding butyrate (such as SunButyrate) can provide a vital workaround until fiber can be reintroduced.


More Information

For more information on the importance of butyrate, you can read my blog post All About Butyrate: The Ultimate Mast Cell Stabilizer.  There is also a blog post on MegaSporeBiotic, which explains how to modulate the microbiome in a new world view.

Sleep, Insomnia, Microbiome, Gut Health, Alison Vickery, Health, Australia


The microbiome produces many internal cues in the sleep-wake cycle.

There is a  bi-directional interaction between sleep or circadian rhythms and the microbiome.

Insufficient sleep changes the microbiome and reduces anti-inflammatory short-chain fatty acid-producing microbes. At the same time, alterations in the microbiome alter the immune system regulation leading to sleep disruption.


Recent studies on the link between sleep and the microbiome include:

1 Disturbed sleep altered the microbiome composition and decreased anti-inflammatory butyrate-producing bacteria in an animal study.

2 People who sleep less than 6 – 8 hours a night saw alterations in the microbiome composition, including reduced butyrate-producing bacteria.

3 Disrupted sleep changes the microbiome composition, decreasing health-promoting bacteria and increasing pathogenic bacteria.

4 There is a direct correlation between sleep quality, microbial diversity, and microbiome composition, including reducing anti-inflammatory butyrate producers and increasing histamine-producing gram-negative bacteria.


What does this mean for those with histamine intolerance, autoimmunity, and mast cell activation?

1 A balance in the gut-brain axis, including histamine-producing bacteria and anti-inflammatory short-chain fatty acid-producing bacteria, is vital.

2 A balance of histamine neurotransmitters to GABA neurotransmitters is vital.  This often requires supplementation, including GABA and binders, until the underlying cause is resolved.

3 A balance of cortisol and melatonin is crucial to sleep. This often requires intervention as cortisol is often altered with changes to the cell danger response, and melatonin is often altered with gut dysbiosis.


exercise, gut health, microbiome, histamine intolerance, autoimmunity, mast cell activation, alison vickery, health, Australia


There is also a bi-directional interaction between exercise and the microbiome; however, this is less understood than other factors.

Exercise increases microbiome diversity, anti-inflammatory short-chain fatty acids, and modulates the gut-brain axis.


A recent study found:

1 There are significant differences in the butyrate-producing microbes between people with sleep disorders and healthy people and exercise significantly improved the butyrate-producing microbiome in sleep-disordered persons.

What does this mean for those with histamine intolerance, autoimmunity, and mast cell activation?

1 For many with leaky gut, exercise can cause histamine release.  Yet, exercise is an essential part of building up anti-inflammatory butyrate-producing microbes. The challenge may be balancing the amount of exercise with the immune reaction to exercise. This may include exercising before eating, including upon awakening, to have a bowel movement.


Stress, Microbiome, Gut Health, Histamine Intolerance, Autoimmunity, Mast Cell Activation, Alison Vickery, Health, Australia

Perceived Stress

Perceived stress profoundly impacts gut health, including:

1 Intestinal permeability

2 The gut brain-axis

3 Increases inflammatory microbes

4 Decreases anti-inflammatory microbes


Recent studies have important implications for understanding this dynamic:

1 Depressed people possess a higher level of  gram-negative (histamine-producing and inflammatory) bacteria

2 High stress during pregnancy is also associated with a change in the vaginal microbiome

3 Newborns of high-stress mothers had an altered microbiome linked to gut inflammation and the development of allergies

4. In an animal study, children of highly stressed mothers had an altered microbiome linked to decreased cognitive functioning and increased anxiety.


What does this mean for those with histamine intolerance, autoimmunity, and mast cell activation?

1 Anyone familiar with my work will know that perceived stress alters our autonomic nervous system, which instructs our bodies’ organs and cells to adapt to stressors.

2 It has long been known that the body carries the burden when a load of stressors exceeds its ability to process them at the moment.  The HPA Axis carries part of that burden and adrenals when in an adrenalized state, and some of it is carried somatically when in a shut-down state. This emerging research clarifies that the microbiome also carries part of the burden.  How amazing is that!


toxins, microbiome, gut health, histamine intolerance, autoimmunity, mast cell activation, alison vickery, health, Australia


There is a dual relationship between toxins and the microbiome.

Toxins can impact the microbiome, while the microbiome can metabolize toxins.

Toxins are either absorbed in the small intestine and metabolized by the liver or pass through the small intestine into the colon, where they can be metabolized by the microbiome, which acts like a ‘second liver’. Furthermore, toxins can return to the intestine via bile and interact with the microbiome.

Many different bacterial species interact with toxins, and the metabolism of a toxin often depends on the composition of the gut microbiota.


Some of the environmental toxins known to be transformed by the microbiome are:

1 Melamine (used in adhesives, paints, tables, and engineered wood.

2 Halogens (used as pesticides, in pharmaceuticals, and as bleaching and disinfecting agents).

3 Polychlorinated biphenyls (PCBs) are still present in the environment and have been strongly associated with variations in a pregnant mother’s microbiome.

4 Organophosphates used as pesticides.

5 Glyphosate the weedicide.

6 Cadmium and lead.

7 Azodyes (used widely in pharmaceutical, textile, food, and cosmetics production)

8 Triclocarban (an antibacterial ingredient in personal care products such as toothpaste and hand soap).

9 Triclosan (another broad-spectrum antimicrobial added to personal use products, including cosmetics and toys.

10 N-nitrosamines (predominantly in tobacco smoke)

11 Mycotyoxins (predominantly found in foods and water-damaged houses)

This list is incomplete – this is just the highly researched toxins. It is not a requirement for chemical companies to research the effect on the microbiome before selling the toxin.


Recent research is starting to clarify the impact of toxins on our microbiome:

1 The microbiome from remains of ancient human feces was found to be similar to pre-industrial humans, particularly species linked to complex carbohydrates.

2 Young adults in Southern California, exposed to high levels of atmospheric ozone, show lower gut microbial diversity with an alteration in the microbiome.

3. The skin microbiome is altered in urban populations and changes the skin’s physiological response.

4 Smoking alters the nose, mouth, and gastrointestinal microbiome by decreasing the commensal microbial population and increasing the pathogenic microbes.

5 E-cigarettes also alter the oral bacteria, reducing diversity, decreasing beneficial bacteria, and increasing pathogenic bacteria.

6 Alternaria mycotoxins alter the human microbiome and create biofilms. It also found that the microbial strains could adsorb some Alternaria toxins.

7 A study identified critical bacteria involved in hydrolyzing mycotoxin-glucosides and de-acetylating type A trichothecenes in the human gut.


What does this mean for those with histamine intolerance, autoimmunity, and mast cell activation?

1 The build-up of toxins is a crucial feature of escalating histamine and mast cell issues.

2 The microbiome plays a vital role in addressing toxins. The issue, therefore, is one of balance. Our body is working to address toxins, but at a point, it cannot keep up.

3 Changes in the microbiome can account for changes in the levels of toxins on test results. I am seeing this increasingly as an issue.

4 The level of toxins endemic to the environment has escalated substantially over the last several decades. It is not realistic to expect that we can avoid toxins. Instead, we need a dual strategy of both avoiding and supporting the body to metabolize toxins.

5 The emerging research around mycotoxins is fascinating.  What if the microbiome helped us so that extreme mold avoidance was unnecessary?


More Information

If you want more information on the link between toxins and histamine intolerance, autoimmunity, and mast cell activation, please check out my free e-Course, The Roadmap To Resolution.


medicines, gut health, microbiome, Alison Vickery, Health, Australia


There is a dual relationship between medicines and the microbiome.

Medicines can profoundly impact the microbiome composition, while microbiomes can metabolize medicines and determine their tolerance and effectiveness.


The study of antibiotics (intended to alter the microbiome) has been extensively studied and shown to deplete the microbiome for years, and overuse leads to antibiotic resistance.

However, little research has been done into the effect on the microbiome of other medicines not designed to alter the microbiome. Studies to date have identified the following as altering the microbiome:

1 All antibiotics (including in any animals we consume)

2 Steroids

3 Platelet aggregation inhibitors

4 Antidepressants

5 Benzodiazepine

6 Opiates

7 Digoxin

8 Evodopa

9 Antipsychotics

10 Statins

11 Beta-blockers

12 Angiotensin-converting enzyme (ACE) inhibitors

This list is incomplete. It is not a requirement for pharmaceutical companies to research the effect of medicines on the microbiome to be listed with The Therapeutic Goods Administration (or any other regulatory body).


A recent meta-analysis showed that 17 drug categories were associated with changes to the microbiome, including extreme changes with:

1 Proton pump inhibitors*

2 Antidiabetic drugs (Metformin)*

3 Laxatives*

4 Polypharmacy (using two or more medicines) increased microbiome alteration.*


What does this mean for those with histamine intolerance, autoimmunity, and mast cell activation?

1 Medicines can cause histamine intolerance, autoimmunity, and mast cell activation.

2 All medicines have benefits and risks. These need to be carefully weighed up with your medical doctor and not skipped over.  Sometimes the benefits outweigh the risks (yes, I take medicines). Sometimes they do not.

3 The risks of adverse events and changes in the microbiome increase exponentially with the each addition of medicine.

4 The microbiome’s health can improve our tolerance of life-saving medicines.


More Information

If you want more information on which medicines cause histamine intolerance, autoimmunity, and mast cell activation, please check out my blog post, Medicines That Cause Histamine Intolerance.



There is so much that we still do not know about the microbiome.  A  2020 pioneering study estimates 35.5 million functions of bacteria, of which only 0.02% are known.

Furthermore, the microbiome’s function depends on its structure and diversity, which is highly unique among individuals, and shaped by many factors.

What is clear, however, is that our microbiome plays a vital role in restoring our health and protecting us from stressors.

Far from being an overwhelming prospect, in many ways, it is pretty simple.

We can support our microbiome by building an environment where health can emerge.  Our microbiome supports and protects us. We can help support and protect it too.

It is a balancing act.





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Perceived Stress

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