The Human Microbiome, Health And Disease

Within our complex environment, we encounter a large variety of microbial species every day. Some of these can be threatening to our health, and many others are essential for our survival.

Humans have a robust immune system to protect us from environmental pathogens, but certain microbes residing in our gut may actually be supporting our immune function. Some scientists consider the gut microbiome as a sort of organ, based on its numerous essential functions such as nutrient transformation, vitamin supply, immune function, gut-brain communication and even tumor progression. Our bodies house microbes from all different kingdoms of life: bacteria, fungus, viruses, and ancient archaea. Research has just begun to unravel the complexity behind the gut microbiome and its diverse interplay with human biology. 


Microbes exist in every cavity of our body that is exposed to the external environment, including our nasal cavity, mouth, skin, and our gastrointestinal tract. Although some of these species can cause problems, we live in harmony with the vast majority of microbes that reside in our bodies and leverage their capabilities for our advantage. Research on the human microbiome continues to further our understanding of its multitude of functions, but simultaneously highlights how much more there is to learn.

Many studies are being conducted to understand the implications of gut microbiome health in bowel diseases such as IBD and IBS, but these investigations have found strong indications that microbiome health may also be linked to neuropsychiatric diseases like Alzheimer’s disease, Autism spectrum disorder, multiple sclerosis, Parkinson’s disease, and stroke (2). Gut dysbiosis is characterized by an imbalance of the microbial species in the gut leading to negative health outcomes. Leading causes of dysbiosis can include an unhealthy diet high in processed foods, irregular sleep, and overuse of antibiotics. In patients who are impacted by dysbiosis, treatments like probiotics and prebiotics are sometimes used in an attempt to repopulate the gut with healthy microbes. While these therapies show promise, much more research is required to fully understand their utility and impact. 

Although our understanding of the gut microbiome is limited, there are things we can do to promote the cultivation of healthy gut microbiota. Studies have shown that many factors like diet, nutrition, exercise, and meditation can all have a significant positive impact on microbiome function. 


One of the long standing dietary components that has been recommended for gut health is dietary fiber. Including a healthy variety of dietary fiber in the form of different vegetables can be highly beneficial for the cultivation of bacterial diversity (4). The more diverse fiber we eat, the better equipped our gut bacteria will be to digest complex fibers.

Although physicians have recommended fiber for a long time, recent studies have revealed that fermented foods could have an even greater impact on our gut health. A recent study from Stanford found that inclusion of fermented foods in a standard diet can confer great benefits by reducing biomarkers associated with chronic inflammation. When looking for fermented foods at the grocery store, focus on the foods located in the refrigerated section, as this is a likely indicator that the food will contain the live microbes that provide health benefits.  

Physical activity is touted as one of the most valuable tools for our health and has been shown to affect gut health by changing the microbiome in a way that modulates immune pathways to reduce oxidative stress and inflammation (6). Exercise is a valuable tool that can influence the gut microbiome to promote positive changes towards tissue metabolism, cardiorespiratory fitness and metabolic disorders.

There is a lot we have yet to learn about the microbiome and its complex role in our gut, but until we further our understanding of its function, it’s important to be persistent in our habits to maintain a healthy community in our gut and cultivate the beautiful symbiotic relationship we depend on. 

Keep reading our newsletter to learn more with our in-clinic specialists about the relationship between gut microbiome health, nutrition and active living, and what you can do to improve it starting today.


Dr. Rohan Bissoondath,
Medical Director

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