November 27, 2022 1:39 am

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

In this blog post, we delve into recent discoveries about gut health, a topic of crucial importance for anyone dealing with histamine intolerance, autoimmunity, or mast cell activation.

Symptoms happen in an environment, and creating an environment where true healing is possible is vital to restoring health. Gut health is no different.

Here, you’ll find insights into how our environment shapes gut health.

Gut Health

Over the past decade, groundbreaking advances in microbiome sequencing have transformed our understanding.

Consequently, we’ve shifted from old-world approaches focused on single microbes to new-world thinking that examines the entire microbiome ecosystem.

This holistic view reveals that microbes live symbiotically, influencing health through complex interactions within the gastrointestinal tract and our environment.

Central to this is the understanding that our lifestyle choices—such as diet, exercise, and stress management—as well as external factors like toxin exposure and medication, profoundly shape our microbiome health.

Ultimately, this paradigm shift suggests that diversity in our microbiome is crucial for overall health, highlighting the interdependence between our bodies and the microbial world.

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

Diet and Gut Health

Diet significantly impacts the gut microbiome. Specifically, a diverse microbiome enhances our ability to metabolize various foods and produce anti-inflammatory compounds like butyrate.

Conversely, a lack of dietary diversity can reduce microbial diversity, thereby limiting these abilities.

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!

Consequently, dietary changes can swiftly alter microbiome composition and its functional capabilities.

For those with histamine intolerance, autoimmunity, and mast cell activation, it is crucial to balance food elimination strategies with efforts to maintain or enhance microbial diversity.

Recent findings suggest that even minor dietary adjustments can quickly improve microbiome health, emphasizing the importance of reintroducing diverse foods gradually to support microbial growth and manage inflammation effectively.

For more information on the importance of butyrate, you can read my blog post All About Butyrate: The Ultimate Mast Cell Stabilizer. 

Alternatively, my blog post, All About MegaSporeBiotic and why it is the next generation probiotic, explains how to modulate the microbiome in a new worldview.

fatigue, insomnia, histamine intolerance, autoimmunity, mast cell activation, EMF health effects, Alison Vickery, Health, Australia

Sleep and Gut Health

Sleep and the microbiome have a two-way relationship, significantly impacting each other. Specifically, the microbiome influences the sleep-wake cycle, while inadequate sleep alters the microbiome, reducing microbes that produce anti-inflammatory short-chain fatty acids.

Consequently, this disruption can also affect immune system regulation, leading to further sleep issues.

Moreover, recent studies have linked poor sleep with changes in microbiome composition, notably decreasing health-promoting bacteria and increasing pathogenic ones.

Therefore, for those with histamine intolerance, autoimmunity, and mast cell activation, maintaining a balance in the gut-brain axis, neurotransmitters like GABA and histamine, and hormones such as cortisol and melatonin is crucial.

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

Exercise and Gut Health

Exercise and the microbiome interact in ways that are not yet fully understood. However, exercise boosts microbiome diversity, increases anti-inflammatory short-chain fatty acids, and affects the gut-brain axis.

Notably, a recent study shows that exercise significantly enhances the butyrate-producing microbiome in individuals with sleep disorders compared to those who are healthy.

For those dealing with histamine intolerance, autoimmunity, and mast cell activation, exercise might trigger histamine release, posing a challenge in balancing exercise with potential immune reactions.

Therefore, this balance might involve timing exercise strategically, such as before meals or right after waking up, to stimulate bowel movements.

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

Perceived Stress and Gut Health

Perceived stress significantly affects gut health, impacting intestinal permeability and the gut-brain axis. Specifically, it increases inflammatory microbes while decreasing those that are anti-inflammatory.

Recent research underscores these effects, showing that people with depression have higher levels of inflammatory bacteria.

Moreover, high stress during pregnancy alters the vaginal microbiome and, in turn, affects the newborn’s microbiome, leading to potential gut inflammation and allergy development.

Additionally, stress impacts cognitive function and anxiety in offspring through microbiome changes.

Furthermore, emerging research highlights that the microbiome also shares in managing this stress burden, adding a fascinating layer to our understanding of stress’s physiological impacts.

Therefore, for those with histamine intolerance, autoimmunity, and mast cell activation, the impact of perceived stress is significant.

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

Toxins and Gut Health

Toxins and the microbiome share a dynamic relationship. Specifically, toxins affect the microbiome’s health, while the microbiome can metabolize toxins, acting like a “second liver.” 

For example, toxins can be absorbed in the small intestine and processed by the liver, or they can pass into the colon, where the microbiome breaks them down.

Furthermore, various bacterial species interact with these toxins, and their metabolic outcomes often depend on the gut microbiota’s composition. 

Notably, the microbiome transforms numerous environmental toxins, including melamine, halogens, polychlorinated biphenyls (PCBs), organophosphates, glyphosate, cadmium, lead, azodyes, triclocarban, triclosan, nitrosamines, and mycotoxins, amongst others.

This interaction highlights how critical our microbiome is in managing toxin exposure and underscores the balance needed between toxin buildup and our body’s detoxification efforts. 

Moreover, recent studies reveal that shifts in the microbiome can significantly alter how our body responds to toxins, affecting everything from histamine tolerance to immune responses.

Understanding these interactions helps us devise strategies to avoid toxins and enhance our body’s capacity to neutralize them effectively.

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 and Gut Health

Medicines and the microbiome have a dual relationship.

Specifically, medicines can dramatically alter the microbiome’s composition, while the microbiome itself can affect how medicines are metabolized, influencing their tolerance and effectiveness.

For instance, research has shown that antibiotics can deplete the microbiome for years, leading to antibiotic resistance.

However, the impact of non-antibiotic drugs on the microbiome needs to be studied more, even though they also cause changes.

For example, medicines such as steroids, platelet aggregation inhibitors, antidepressants, benzodiazepines, opiates, antipsychotics, statins, beta-blockers, and ACE inhibitors, amongst others, can alter the microbiome.

Moreover, this interaction might explain why some people experience histamine intolerance, autoimmunity, or mast cell activation after taking certain medications.

Therefore, each medicine has its benefits and risks, which must be carefully considered. Importantly, maintaining a healthy microbiome can enhance our ability to tolerate life-saving medications.

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.


To sum up, our understanding of the microbiome still has many gaps.

For instance, a groundbreaking 2020 study discovered around 35.5 million bacterial functions, yet we’ve barely scratched the surface with only 0.02% identified.

Moreover, the microbiome’s role is profoundly influenced by its structure and the unique diversity found in each individual, shaped by numerous factors.

Clearly, our microbiome is crucial for maintaining health and defending against stressors.

Fortunately, supporting our microbiome isn’t as daunting as it might seem. By fostering an environment conducive to health, we not only support our microbiome but also fortify its ability to protect us.

Ultimately, it’s all about maintaining balance.

Additional References


Mousa, Walaa K., et al. “Recent Advances in Understanding the Structure and Function of the Human Microbiome.” Frontiers in Microbiology 13 (2022): 825338.


von Schwartzenberg, Reiner Jumpertz, et al. “Caloric restriction disrupts the microbiota and colonization resistance.” Nature 595.7866 (2021): 272-277.

Moszak, Małgorzata, et al. “You are what you eat—The relationship between diet, microbiota, and metabolic disorders—A review.” Nutrients 12.4 (2020): 1096.


Agrawal, Ritwick, et al. “Habitual sleep duration and the colonic mucosa-associated gut microbiota in humans—a pilot study.” Clocks & sleep 3.3 (2021): 387-397.

Sato, Mika, and Yoshio Suzuki. “Alterations in intestinal microbiota in ultramarathon runners.” Scientific reports 12.1 (2022): 1-9.

Matenchuk, Brittany A., et al. “Sleep, circadian rhythm, and gut microbiota.” Sleep medicine reviews 53 (2020): 101340.

Wang, Zhe, et al. “The microbiota-gut-brain axis in sleep disorders.” Sleep Medicine Reviews (2022): 101691.


Allen, Jacob M., et al. “Exercise alters gut microbiota composition and function in lean and obese humans.” Med Sci Sports Exerc 50.4 (2018): 747-57.

Aya, Viviana, et al. “Association between physical activity and changes in intestinal microbiota composition: A systematic review.” PLoS One 16.2 (2021): e0247039.

Qiu, Liangwu, et al. “Exercise Interventions Improved Sleep Quality through Regulating Intestinal Microbiota Composition.” International Journal of Environmental Research and Public Health 19.19 (2022): 12385.

Perceived Stress

Maltz, Ross M., et al. “Social stress affects colonic inflammation, the gut microbiome, and short-chain fatty acid levels and receptors.” Journal of pediatric gastroenterology and nutrition 68.4 (2019): 533.

Herselman, Mauritz F., et al. “The Effects of Stress and Diet on the “Brain-Gut” and “Gut–Brain” Pathways in Animal Models of Stress and Depression.” International Journal of Molecular Sciences 23.4 (2022): 2013.


Fouladi, Farnaz, et al. “Air pollution exposure is associated with the gut microbiome as revealed by shotgun metagenomic sequencing.” Environment international 138 (2020): 105604.

Al-Zyoud, Walid, et al. “Salivary microbiome and cigarette smoking: A first of its kind investigation in Jordan.” International Journal of Environmental Research and Public Health 17.1 (2020): 256.

Chopyk, Jessica, et al. “Compositional differences in the oral microbiome of e-cigarette users.” Frontiers in Microbiology 12 (2021): 599664.

Lindell, Anna E., et al. “Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota.” Nature Reviews Microbiology (2022): 1-13.


Vich Vila, Arnau, et al. “Impact of commonly used drugs on the composition and metabolic function of the gut microbiota.” Nature communications 11.1 (2020): 1-11.

Weersma, Rinse K., Alexandra Zhernakova, and Jingyuan Fu. “Interaction between drugs and the gut microbiome.” Gut 69.8 (2020): 1510-1519.

Lindell, Anna E., et al. “Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota.” Nature Reviews Microbiology (2022): 1-13.

Maier, Lisa, et al. “Unravelling the collateral damage of antibiotics on gut bacteria.” Nature 599.7883 (2021): 120-124.