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Our body contains at least as many microbes as it does human cells. [1] These microbes, collectively named the microbiome [i], inhabit almost all of our anatomy, including the oral cavity, stomach, intestines, lung, liver, urogenital tract and skin. [2] Bacteria are the most well- studied microbes of the microbiome but viruses, fungi and bacteriophages also play important roles [ii].

The microbiome has numerous functions in human physiology, including aiding digestion and absorption of food and certain minerals, production of some vitamins and hormone-like substances, and recycling of different nutrients, hormones and bile acids [3] [4].  Microbial-derived metabolites have such a broad influence on human physiology [5] that gut microbiota have been labelled as a neglected endocrine organ. [6] The microbiome also plays a critical role in protection from infectious disease through a number of mechanisms including supporting healthy mucosal barriers, helping shape appropriate immune responses and preventing adherence, colonization and overgrowth of potentially pathogenic microorganisms. [7] [8] The gut-microbiota-brain axis influences various aspects of mental health, including activity of the hypothalamic pituitary adrenal (HPA) axis and other neuroendocrine pathways associated with the stress response. [9] [10]


The microbiome also influences drug metabolism and host detoxification processes and therefore, alters effects of xenobiotics, including drugs and environmental pollutants. [11] [12] [13] Moreover, a reciprocal relationship exists with environmental pollutants also affecting the health and function of the microbiome. [14] The closely intertwined relationship between the microbiome, human health and the environment we live in suggests we are meta-organisms [15] or holobionts [16], unable to survive without a well-functioning and diverse microbiome.

[i] Microbiome: There are a number of different definitions of microbiome including the most commonly referenced one “Ecological community of commensal, symbiotic and pathogenic microorganisms within a body space or other environment”, and the most recent one “Ecological community of commensal, symbiotic and pathogenic microorganisms within a body space or other environment, including the microorganism themselves and their theatre of activity.” Berg G, Rybakova D, Fischer D, et al. Microbiome definition re-visited: old concepts and new challenges [published correction appears in Microbiome. 2020 Aug 20;8(1):119]. Microbiome. 2020;8(1):103


[ii] Dysbiosis: There are number of different definitions of dysbiosis. This document refers to the most commonly used definitions which are: “pathological imbalance with the intestinal microbiota” or “alterations in the homeostasis of the microbiota.” Hooks KB, O'Malley MA. Dysbiosis and Its Discontents. mBio. 2017;8(5):e01492-17

Where Do They Come From?

Numerous environmental pollutants can have a negative impact on the microbiome including heavy metals [17] such as arsenic [18] and lead [19], plasticizers, such as bisphenol A [20], microplastics, [21] and air pollution. [22] Food additives, including emulsifiers such as polysorbate 80 and carboxymethylcellulose, [23] artificial sweeteners such as saccharin, aspartame and sucralose, [24] [25] and other food contaminants such as polycyclic aromatic hydrocarbons, polychlorobiphenyls, brominated flame retardants and heterocyclic amines [26] cause dysbiosis. [ii]  Glyphosate-based herbicides, [27] dioxin-like chemicals [28]  and other endocrine disruptors [29] [30] also may negatively impact gut microbiota.  Importantly, pharmaceutical drugs other than antibiotics also affect the microbiome, such as proton pump inhibitors, [31] metformin [32], NSAIDs [33] and atypical antipsychotics. [34]


Host genetics does influence the microbiome, [35] but the local environment with which one lives (eg. urban or rural) has the dominant role in shaping the overall composition. [36] Many other factors including dietary patterns specific to different cultures and geography, a vaginal or Caesarian birth, the extent and length of breast-feeding, age, [37] [38] psychological stress, [39] and physical exercise [40] also influence the microbiome. Recent evidence also indicates the microbiome has a circadian rhythm, [15] suggesting it could be affected by factors that shift circadian biology including jet lag, lack of sleep and working night shifts.

How They Affect You

Gut microbiota have been described as the missing link between nutrients and the traits of humans [41] because they exist at a critical interface between the food we eat and its beneficial effects. [42] This means that anything that negatively affects the microbiome will potentially have a widespread, systems-wide impact on our physiology. Indeed because  numerous diseases and disorders are associated with dysbiosis, the human gut microbiome is positioned as a key controller of health and wellness. [43]


Emerging evidence suggests the microbiome influences a number of different human sensations including pain, [44] taste, [45] smell, [46]  appetite [47] and eating behaviours. [48] Quality of sleep, [49] mood and risk of stress-related disorders, such as anxiety and depression, also are influenced by our microbiome. [50] [51] [52] Interactions between us, our microbiome and the environment we live in also may also influence different social activities including our behaviour to seek and spend time in Nature. [53]


Irritable bowel syndrome, [54] inflammatory bowel disease, [55] celiac disease, [56] lactose intolerance [57], non-alcoholic fatty liver disease [58] and other disorders associated with the gastrointestinal tract are associated with dysbiosis. Moreover, many different disorders and diseases seemly unrelated to the gut, including hypertension [59] [60], hypercholesteremia [61], bone and joint diseases [62] such as osteoarthritis [63], lung diseases such as asthma[64], kidney disease [65] and different types of cancer [66], also are associated with altered numbers and types of gut microbiota. Dysbiosis also is a contributing factor to various metabolic diseases including obesity [67] [68], metabolic syndrome [69] and diabetes type I [70] and type II. [71] The ability of the microbiome to alter metabolism provides an additional mechanism to shape immune system responses through a relatively newly discovered mechanism named immunometabolism. [72] Alterations in gut microbiota also could impact energy levels via their influence on mitochondrial health. [73] [74] Human circadian rhythms, metabolism and disease risk also could be profoundly affected by altered numbers, types and circadian rhythms of gut microbiota. [75] [76] [77] Healthy aging also is associated with maintenance of a heathy microbiome. [78]


Recent studies indicate the composition of gut microbiota and their gene products [79] affects drug metabolism [11] [12] and therefore, dysbiosis could affect the therapeutic potential and individual responses to any ingested medicinal substances, including natural health products and pharmaceutical drugs. Gut microbiome toxicity might be considered as a potential contributor to various human diseases, in addition to liver, kidney and brain toxicity. [80]


Many of the environmental factors influencing the microbiome have their most profound and long-lasting impact in early childhood when the microbiome is the most amenable to internal and external perturbations. [81] [82] Accumulating evidence suggests that changes to the microbiome also occur in utero, [83] [84] although this evidence is not without controversy. [85]

How To Protect Yourself

The best way to protect yourself from the potential consequences of an altered microbiome is to become aware of factors and environmental pollutants that may negatively influence the microbiota and either avoid them or support their removal if they are already present. Moreover, supporting a healthful microbiome before and during interventions known to be disruptive, such as antibiotic treatments, can help ensure minimal lasting damage occurs. Eating a healthful diet consisting of mostly raw and unprocessed vegetables is one of the best ways to support the diversity and health of the gut microbiota. Regular consumption of fermented food, including plain unrefined yogurt, kimchi, raw cheeses, miso and fermented drinks such as kombucha, also could add to the health of the microbiome. Different strains of probiotics and different types of prebiotics also have a good evidence base of therapeutic benefit in alleviating symptoms of disease and helping to restore a healthful microbiome. In patients with certain conditions or where the microbiota has been drastically altered, a more aggressive treatment protocol using antibiotics and stool replacement therapy might be necessary to help regain a balanced, healthy microbiome.

Work with a naturopathic doctor / naturopath to help you assess for environmental pollutants and to understand how they may be affecting your health. The information on this website is a guide for ways to protect you and your family from environmental pollutants.  It is not meant to replace advice from a healthcare professional.

3 Essentials

  1. Establishing a healthy microbiome early on in childhood is the most important intervention to prevent future diseases.

  2. Awareness and avoidance of what could negatively affect the microbiome is critical to minimizing any potential negative health effects

  3. A healthy diet and appropriate use of probiotics can be used to help restore a microbiome that is altered. Although they have a wide margin of safety, the best therapeutic effect of probiotics is achieved when the appropriate dose, type and strains of bacteria are used. Probiotic therapy is best initiated under the supervision of health care professionals such as Naturopathic doctors who are well trained in their appropriate use.

Additional Key Recommendations

  • Due to its widespread influence on human biology, [86] is useful to consider an altered microbiome as a potential contributing factor to many human diseases and address any imbalances that can be identified.

  • Therapeutic removal of environmental pollutants including heavy metals, plastics etc. that could negatively affect the microbiome [14] [87] are important interventions to restore healthy types and numbers of microflora in certain patients. 

  • It is important to be aware that numerous types of drugs in addition to antibiotics can negatively affect the microbiome including NSAIDs, proton-pump inhibitors and metformin. [88]

  • Due to the close relationship between the circadian rhythm in gut microbiota, [89] and other circadian rhythms, [75] interventions to help restore balance in the microbiome such as probiotics and healthy food choices could help avoid any lasting negative health consequences from activities that disrupt circadian rhythms such jet lag, lack of sleep, shift work, social jet lag etc.

  • An altered microbiome could contribute to the signs and symptoms of disease in patients as well as interfere with the effectiveness of the medications they are taking to treat that disease. This evidence suggests that dysbiosis should be considered and addressed not only prior to initiating treatment but also in treatments where an altered microflora is known to have a negative impact on drug pharmacokinetics including chemotherapy and response to statin drugs and antihypertensives. [90]

  • Although an exact description of what constitutes a ‘healthy’ microbiome has yet to be defined, stool transit time has been identified as a key indicator of microbial richness, [91] [92] one of the key features of a more healthful microbiome. With this in mind, anything that leads to constipation and/or abnormally increased stool frequency also could negatively affect the health of the microbiome.


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