How the Modern Diet Is Affecting Our Gut Microbiota

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While the ratio is close, ​there are more microbial cells than human cells in our body. We provide a home to trillions of microorganisms in exchange for their life-sustaining services, such as helping absorb essential nutrients and regulating our immune, metabolic, and nervous systems. Like all healthy relationships, though, our relationship with our gut microbiome must be reciprocal to thrive. 

The microorganisms in our gut ask for very simple things in exchange for very complex services. However, our relationship (and, in turn, health) is suffering because we are not providing the simple things our gut community needs, the right kind of diet being one of those basic requirements. One of the biggest problems with our modern diet is that it is causing a loss of microbiota diversity, which you will soon learn has some serious health repercussions. 

Why is gut microbiome diversity so important?

Similarly, to a macro-ecosystem like a rainforest or coral reef, the micro-ecosystem in our gut is comprised of an abundance of species interconnected through one of five different types of relationships: mutualism, amensalism (one organism is inhibited or destroyed while the other is unaffected), commensalism (one organism gets an advantage with no effect to another), competition, and predation and parasitism. 1 Loss of diversity on a macro and micro scale directly impacts an ecosystem’s balance and resilience. 

For example, when sea otter populations were decimated due to the unregulated fur trade along the Pacific Northwest in the 18th and 19th centuries, sea urchins (a favorite food of sea otters) abounded with no limitations. Sea urchins love munching on the holdfasts of sea kelp. Because there was no top predator to control sea urchin numbers, giant sea kelp forests virtually disappeared where they once thrived. Without the sea otters, the kelp forest ecosystem entered a state of disharmony and eventual demise, taking down with it the countless species that depend on the kelp for survival. Fast-forwarding decades, though, once sea otters gained protection and were reintroduced, kelp forests returned as did the diversity of that ecosystem. 

Every living organism, from the tiniest microbe to the adorable sea otter, plays an integral role in the ecosystem it belongs to. Every species has a job, and the same holds true in our gut microbial community. 

Somewhere between 500 and 1,000 bacteria species and an undetermined number of viruses, fungi, and other microbes reside in our gut. 2 What’s interesting, though, is that no two gut ecosystems are the same. Your gut community profile is completely unique to you! And “considering the characteristics of gut microbiota such as the large diversity, the stability and resilience, and the symbiotic interaction with the host [you], we can define the host and the microorganisms inhabiting it [you] as a superorganism.’’ 3

There is a strong relationship between gut microbiota diversity and health, which makes sense given the variety of jobs our gut microbiome is responsible for: 3

  • Regulating digestion

  • Extracting, synthesizing, and absorbing nutrients 

  • Preventing bacteria invasion and pathogenic colonization 

  • Controlling the development, balance, and function of innate and adaptive immune cells (80% of your immune system resides in the lining of your gut)

What are some health consequences associated with a lack of gut microbial diversity? 

Most health concerns affecting westernized countries correlate with dysbiosis (an unbalanced microbiota) and the loss of microbial diversity in the gut microbiota. When analyzing the gut microbiota of individuals with non-communicable conditions such as those affecting cellular health, metabolic health, and cardiovascular and immune systems, a common thread is often a poorly diversified gut microbiota. 4 A lack of microbial diversity means that certain jobs are not being done or are not being done efficiently because of a shortage of “workers.” A diverse gut community has also been linked to longevity. 5

How does our modern diet impact our gut ecosystem?

Our diet and way of life have changed drastically over the past 12,000 years, starting when agriculture replaced our traditional hunter-gatherer way of life. In just the last hundred or so years, though, the widespread use of antibiotics, cesarean sections as a birthing option, fast and processed food becoming the norm, the proliferation of urbanization, and an increasingly sedentary lifestyle has caused a sustained global health catastrophe impacting the lives of approximately 40% of Americans

The human body is an evolutionary masterpiece. It is a self-regulating, self-healing, multi-dimensional network of human and microbial cells working together in perfect harmony; that is when conditions are conducive for homeostasis (proper nutrients, sufficient water, sunlight, consistent sleep cycle, regular physical activity, etc.). As we’ve become a widely industrialized and urbanized society, we now face exposure to all sorts of environmental pollutants and toxins that can affect our health. Not to mention, many of us have unchecked stress levels, poor sleep habits, spend way too much time indoors, and don’t move around enough. Some factors seem (and sometimes are) out of our control, but what you eat is something you do have control over and a decision that can be monumentally impactful (positively or negatively). 

The trillions of microorganisms working around the clock in our gut love fiber. The modern diet, unfortunately, is low in fiber and high in fat and protein from animal sources, pretty much the opposite of what our gut needs. A diet high in saturated fat, sugar, preservatives, and artificial ingredients is very different from what our (homo sapien) guts have evolved to require over hundreds of thousands of years. While some species of microorganisms have proliferated under these modern conditions, many species are dying off and disappearing as conditions are no longer suitable for their survival. 6 Quantity in terms of gut microbes is not enough; diversity is essential. 

To understand who exactly is living in your gut (and who is missing), a health test that analyzes your gut microbiome can provide valuable insight that can help you make the right choices for your unique biology. The best diet, though, for all of our guts is a predominantly plant-based diet, as fruits, vegetables, legumes, and grains are high in fiber. 

But that’s a bit more to it than that, as you are about to learn from the Hadza. 

What we can learn from the Hadza and their traditional diet  

The Hadza are a small group of hunter-gatherers in Tanzania who have maintained their ancestral way of life. This particular group has sparked numerous studies and discussions about what constitutes a healthy gut microbiome and how to support diversity. Research has shown a stark contrast between the microbiota of urban populations and Indigenous populations that maintain hunter-gatherer or traditional agrarian lifestyles, which is linked to diet among other lifestyle factors. 3

For 40,000 years, the Hadza tribe has been eating a diverse and fiber-rich diet sourced directly from the wild land. While they hunt and eat as many as 30 different species of game, the core of their diet is plant-based. On any given day, a Hadza individual can consume upwards of 100 grams of fiber; the average American adult only eats 10 to 15 grams of fiber a day. 2 They eat a lot of tubers, berries, and honey, but the specifics of their diet change with the seasons and what’s available. 

Interestingly, their gut microbiome profile also changes with the seasons and includes microbes that aren’t found in the guts of individuals living in westernized nations. During the dry season, when they eat more meat, their microbiota profile is actually more similar to a Westerner’s gut. But once the wet season comes back around and their diet becomes more diversified again, microbes that were undetectable during the dry season return. This is a promising discovery as it suggests that the loss of diversity in the microbiomes of industrialized nations isn’t necessarily permanent if the right foods are reintroduced back into the diet to support the return of missing or diminished species. 7

Adhering to a hunter-gatherer way of life ensures food diversity on a daily basis, as what you eat is solely based on what you find. This is another aspect of the western diet that is causing a loss of microbial diversity. Data from the American Gut Project suggests that you should consume at least 30 different plant-based foods weekly to support a widely diverse gut microbiota. How many different plants are you eating every week? 

The take-away from the Hadza, who have one of the richest and more diverse gut microbiomes, is not only to enrich your diet with a lot more fiber but to source that fiber from a wide variety of plants. 

Diversity supports diversity! 


1 Mosca, A., Leclerc, M., & Hugot, J. P. (2016, March 31). Frontiers in microbiology. Retrieved June 15, 2022, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815357/ 

2 Eisenstein, M. (2020, January 29). Nature News. Retrieved June 15, 2022, from https://www.nature.com/articles/d41586-020-00193-3 

3 Rinninella, E., Raoul, P., Cintoni, M., Franceschi, F., Miggiano, G. A. D., Gasbarrini, A., & Mele, M. C. (2019, January 10). Microorganisms. Retrieved June 15, 2022, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6351938/ 

4 GMFH Editing Team GMFH Editing Team. (2020, November 30). Gut Microbiota for Health. Retrieved June 15, 2022, from https://www.gutmicrobiotaforhealth.com/worldmicrobiomeday-2020-defending-gut-microbiota-diversity-for-better-health/ 

5 Deng, F., Li, Y., & Zhao, J. (2019, January 15). Aging. Retrieved June 15, 2022, from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6366966/ 

6 Segata, N. (2015, July 20). Current Biology. Retrieved June 15, 2022, from https://www.sciencedirect.com/science/article/pii/S0960982215006144 

7 Doucleff, M. (2017, August 24). NPR. Retrieved June 15, 2022, from https://www.npr.org/sections/goatsandsoda/2017/08/24/545631521/is-the-secret-to-a-healthier-microbiome-hidden-in-the-hadza-diet