Your Gut Microbiome – Where your Health Begins

The latest big health topic is the gut microbiome and its effect on our health. I’m sure you’ve heard some other doctors mention it numerous times, so I thought I’d start my website’s blog by giving you a basic overview of this fascinating system.

So what exactly is the gut microbiome? I think the easiest way to envision it is to imagine the planet we live on; our Earth is incredibly diverse, consisting of many different environments, like deserts, swamps, and forests. Each of these ecosystems is kept in a balance, with every plant and animal living contributing to keeping the place in order and thriving. Our body, especially our gut, is very similar. Our gut is home to 39 trillion microorganisms, including viruses, bacteria, fungi, archaea (single-celled organisms) and microbial eukaryotes. These organisms have evolved alongside us and are specially adapted to survive inside our gut.


Just like the various organisms in a rainforest help keep that ecosystem thriving, these tiny organisms play a crucial role in keeping us healthy. A healthy gut environment is a breeding ground for beneficial microbes. As they flourish, they crowd out other, pathogenic, microbes that cause disease. Furthermore, various studies have shown that a healthy microbiome may help to prevent and combat already existing conditions such as obesity, heart disease, diabetes, cancer, autoimmune disorders, inflammatory bowel disease, and mental and neurological disorders.


The gut microbiome is significantly influenced by our environment and behaviors. This is particularly true for those of us who live in urbanized and overly sterile places. The more sterile our lives, the less diverse our gut flora tends to be. This can have long term repercussions for our health, including increasing the likelihood of developing digestive, inflammatory, and autoimmune diseases.


Now, this is not to say that we should live dirty lives- cleanliness is incredibly important, but we should allow our bodies to be exposed to diverse conditions: the simple act of going into nature seems to have a positive effect on our gut microbiome.


Being in nature helps support our gut bacteria!
Being in nature helps to support our gut bacteria!


It is also known that our early life has a big influence on the gut microbiome. Several factors influence the development of our microbiome. Positive influencers include good maternal health during pregnancy, being born by vaginal delivery, being breast fed, and having pets. Negative influencers include poor maternal health during pregnancy, being born by c-section, perinatal antibiotics, formula feeding, and any kind of ️early life adversity or trauma.


Some of these factors may leave us feeling a little discouraged, especially as we may not always have a choice in some of these things, but there are many things that we can control that have a positive effect on our gut microbiome.


There are many general changes one can make to our lifestyle to improve our microbiome, from getting adequate sleep, to going out into nature and engaging in physical activity regularly. However, one of the most powerful drivers of our microbiome is our diet.


Studies show that a diet high in animal protein quickly led to the intestinal flora changing to bile tolerant microorganisms, such as Bacteroides & Bilophila (the bad kind). In this animal based diet, an increase in Bilophila wadsworthia was seen, which supports the link between an increase in bile acids, dietary fat and growth of organisms capable of triggering inflammation in the gut. The standard Western diet, which is rich in animal proteins, processed foods, and sugars, helps to proliferate disease causing bacteria. The takeaway is that, by over feeding our gut microbes with processed foods and animal fats, and not feeding them enough fiber-rich whole plant foods, we are creating a hostile environment within our gut, and a breeding ground for inflammatory and disease causing microbes. Our gut microbes thrive on fiber; it is their food source, and in our industrialized societies, we are simply not getting enough of this power food that is only found in plants!


Changing our diets can have dramatic effects on our gut health, often within a matter of days. A Harvard study published in the Journal Nature in 2014 showed that a change in one’s diet was quickly reflected in that person’s gut microbiome. By changing to a plant-based diet, beneficial microbiota increased and reversed the inflammatory process brought on by the Western Diet.


So, what steps can we take to optimize our gut microbiome?

  • First and foremost, eat a diversity of whole-plant foods, like fruits, vegetables, legumes, whole grains, nuts and seeds every week.

  • Cut out processed meats and avoid animal proteins, especially red meat and dairy.

  • Get 7-8 hours of restful sleep every night.

  • Get at least 30 mins of exercise or natural movement daily.

  • Be mindful of your stress, and actively do things to reduce it.

  • Dig those hands into your environment and get out into nature!


The body is resilient, and our gut microbiota even more so! Because their individual life spans are so short, small, daily changes to our lifestyle can lead to rapid and noticeable changes in our gut microbiome, even within a few days! In a way, our past does not define us and we can start fresh today. Each day is an opportunity to make the right choices and start anew, reset ourselves and make wholesome choices.


Eat well, and Love yourself!




To optimize your Gut Health, download Dr Mendez Gut Health Guide! If you are looking for support to help improve your diet and boost your gut microbiome, then get in touch today or register to make an appointment to discover how Doctor Méndez can help you to optimize your health.



Hills RD Jr, Pontefract BA, Mishcon HR, Black CA, Sutton SC, Theberge CR. Gut Microbiome: Profound Implications for Diet and Disease. Nutrients. 2019;11(7):1613. Published 2019 Jul 16. doi:10.3390/nu11071613


Phillips ML. Gut reaction: environmental effects on the human microbiota. Environ Health Perspect. 2009;117(5):A198‐A205. doi:10.1289/ehp.117-a198

Deng F, Li Y, Zhao J. The gut microbiome of healthy long-living people. Aging (Albany NY). 2019;11(2):289‐290. doi:10.18632/aging.101771


Tasnim N, Abulizi N, Pither J, Hart MM, Gibson DL. Linking the Gut Microbial Ecosystem with the Environment: Does Gut Health Depend on Where We Live?. Front Microbiol. 2017;8:1935. Published 2017 Oct 6. doi:10.3389/fmicb.2017.01935


Derrien, M., Alvarez, A.-S., & Vos, W. M. D. (2019). The Gut Microbiota in the First Decade of Life. Trends in Microbiology, 27(12), 997–1010. doi: 10.1016/j.tim.2019.08.001


David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559‐563. doi:10.1038/nature12820


Desai MS, Seekatz AM, Koropatkin NM, et al. A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility. Cell. 2016;167(5):1339‐1353.e21. doi:10.1016/j.cell.2016.10.043

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