What is the Microbiome?

The human microbiome refers to the vast community of trillions of microorganisms residing in and on our bodies, playing crucial roles akin to an organ’s function. These microorganisms, which include bacteria, fungi, viruses, and parasites, are predominantly found in the intestines but are distributed throughout the body. Each person’s microbiome is unique, heavily influenced by their DNA, and first established from exposure to microbes in the birth canal and breast milk. The balance between symbiotic and potentially harmful microbes is vital for health; disruptions in this balance can lead to dysbiosis, increasing disease susceptibility. Diet, environment, and medications like antibiotics can significantly influence the microbiome’s composition and function.

The microbiome is influenced by various factors that can either maintain its health or disrupt its balance. Positive influences include a balanced diet rich in fiber, fruits, and vegetables, which promote beneficial bacteria growth. Probiotic foods like yogurt and fermented products also support microbiome health. Conversely, negative impacts stem from excessive use of antibiotics, which can kill off beneficial bacteria, leading to dysbiosis. Poor dietary choices, high in processed foods and sugars, also negatively affect the microbiome by fostering harmful bacteria overgrowth, increasing the risk of diseases.

The microbiome and environmental factors

Humans acquire microbiomes in two ways: vertically (from our parents) and horizontally (from our environment, including food). The process of populating our microbiome likely begins in the womb and definitely at birth, when newborns receive bacteria from their mothers that help prevent harmful and opportunistic bacteria. As we age, environmental factors, especially nutrition and antibiotics, play an increasingly important role in the composition of our microbiome.

Nutrition

Nutrition plays a key role in affecting the microbiome

Nutrition profoundly impacts the human microbiome, influencing both its composition and functionality, which in turn affects overall health. Specific dietary patterns and macronutrient intake play crucial roles in shaping the gut microbial community. For instance, high-fiber diets are associated with greater microbial diversity and the production of beneficial short-chain fatty acids (SCFAs) like butyrate, which have anti-inflammatory properties and support gut health. These diets promote the growth of fiber-digesting bacteria, contributing to a balanced and robust gut ecosystem. Conversely, low-fiber, high-fat diets, often characteristic of Western dietary patterns, can lead to a reduction in microbial diversity and an increase in pathogenic bacteria, contributing to obesity and metabolic disorders (BMJ) (BMJ Gut).

The interplay between diet and the microbiome is further illustrated by the effects of specific dietary components. For example, artificial sweeteners such as sucralose and aspartame can disrupt the balance and diversity of gut bacteria, potentially leading to metabolic issues. Similarly, food additives like emulsifiers have been shown to reduce microbial diversity and promote inflammation in animal models. On the other hand, personalized nutrition approaches, which tailor dietary recommendations based on individual microbiome profiles, have shown promise in improving metabolic health outcomes by optimizing the composition and functionality of the gut microbiota (BMJ) (BMJ Gut).

Overall, maintaining a diet rich in diverse, fiber-containing foods while minimizing processed foods and additives is crucial for fostering a healthy gut microbiome. This, in turn, supports overall health and can help mitigate the risk of chronic diseases such as obesity and type 2 diabetes.

Antibiotics

Antibiotics, which first came into mass production in the 1940s, are responsible for curing millions of infections and saving countless lives. However, the widespread use of antibiotics is also directly responsible for a growing number of superbug infections and a rise in all diseases. According to the CDC, antibiotic resistance is responsible for 23,000 annual deaths in the U.S. and as many as 2 million U.S. citizens develop a drug-resistant infection each year. Moreover, some researchers have predicted that by the year 2050 antibiotic resistance will cause 10 million deaths every year – surpassing cancer as the leading cause of mortality worldwide.

Many of the rapidly growing diseases today – such as autism and autoimmune disorders – have been linked with microbiome health, something that can suffer from the overuse or indiscriminate use of antibiotics. The risks of antibiotics are not limited to direct usage in humans, however, as agricultural and farming practices that rely on antibiotics may have a harmful downstream effect on the food chain and ultimately impact human health (https://bmcvetres.biomedcentral.com/articles/10.1186/s12917-017-1131-3 & https://www.mdpi.com/1420-3049/23/4/795).

Herbicides (Glyphosate)

Herbicides and pesticides have been widely used since the mid-20th century for boosting agricultural productivity and food security. However, mounting evidence suggests that these chemicals also contribute to chronic disease by disrupting the gut microbiome. Studies indicate that glyphosate, the active ingredient in many herbicides, alters gut bacterial composition, with nearly 54% of core human gut bacterial species showing sensitivity to it (PMC). Occupational exposure to pesticides has been linked to reduced gut microbiome diversity, a factor associated with inflammatory and autoimmune conditions (Frontiers). Moreover, pesticide residues in food and water may lead to chronic, low-dose exposure in the general population, compounding these health risks over time.

The long-term consequences of pesticide exposure extend beyond gut health, with research demonstrating a connection to certain chronic illnesses such as metabolic disorders, neurological diseases, and immune dysfunction (Nature). Pesticides can also disrupt the gut-brain axis, potentially contributing to conditions such as autism and neurodevelopmental disorders (EHP).

How it relates to chronic illness

The intricate relationship between the gut microbiome and chronic illness is a growing field of study with profound implications for health management. Variations in the composition and function of gut microbiota have been linked to a spectrum of chronic conditions, from metabolic diseases like diabetes to inflammatory and cardiovascular diseases, and even neurological disorders. This association primarily stems from the microbiome’s influence on the body’s metabolic processes, immune function, and inflammation pathways.

Diet plays a critical role in shaping the microbiome, with certain dietary patterns promoting a healthier gut flora that can mitigate disease risk. Diets rich in high-fiber vegetables, nuts, healthy fats, and proteins such as fish and eggs are associated with a more diverse and beneficial microbial population. These beneficial microbes contribute to lower inflammation and better overall health. Conversely, diets high in processed foods and unhealthy fats favor the growth of harmful bacteria that are linked to higher risks of serious health conditions, including obesity, heart disease, and type 2 diabetes.

Emerging research underscores the potential of microbiota modulation in treating and preventing these diseases. For instance, the introduction of specific probiotic strains and fecal microbiota transplantation (FMT) are being explored for their therapeutic benefits in resetting harmful imbalances in the gut flora. These interventions have shown promise in managing conditions like Clostridioides difficile infections and inflammatory bowel disease, and they continue to be investigated for broader applications in other chronic conditions.

Understanding and intentionally influencing the microbiome offers a promising avenue for not only enhancing disease treatment but also for preventive health care, potentially shifting the paradigm from disease treatment to disease prevention. The ongoing research into the gut-brain axis, immune modulation, and colonization resistance further illustrates the extensive impact of microbiota on health and disease. As research progresses, it is anticipated that new microbiota-based therapies will become integral components of clinical practice, offering new hope for patients suffering from chronic conditions.

What can you do?

Recent findings emphasize the importance of dietary choices in fostering a healthy gut microbiome, which can significantly impact overall health and help prevent heart disease, diabetes, metabolic conditions, autoimmune disease and more. The most important rule in gut health is prioritising nutrient-rich, unprocessed, low carbohydrate, healthy fats and ideally organic foods. This helps prevent the colonization of unfriendly gut species.

Generally speaking, a diet rich in a range of beneficial animal foods, unprocessed plant foods such as fruits, vegetables, nuts, seeds, and whole grains helps to cultivate beneficial gut flora. If, however, the microbiome is compromised, certain plant foods may be hard to metabolise. A range of genetic and metabolic issues can also make certain plant chemicals problematic including oxalates, salicylates, amines and lectins. It’s advised to see an Integrative practitioner if you suspect food sensitivities.

Probiotics/Prebiotics

Probiotics and prebiotics, both from food and supplements, are key to a healthy microbiome. One should consult with a practitioner as to which testing (usually a stool sample) would be best to measure their current microbiome and dependent on those results which pre or probiotics might benefit them.