Imagine a bustling cityscape, teeming with life. But instead of skyscrapers and bustling avenues, this city is built of microscopic citizens: the trillions of bacteria, fungi, and archaea that reside within our bodies, collectively known as the microbiome. This internal ecosystem plays a critical role in our health, influencing everything from digestion and immunity to mood and brain function.
You are no longer merely a human; you are now a holobiont. The term “holobiont” refers to an organism that operates as a collective of multiple mutually beneficial species. You embody a holobiont because your body isn’t a singular entity but rather an intricately complex ecosystem comprising 39 trillion bacteria, primarily beneficial, thriving inside and on the surface of your body. These bacteria are abundant, with their quantity roughly matching that of your own cells (approximately 37 trillion), and together, they weigh around three pounds, equivalent to the weight of your brain. Remarkably resilient, they withstand stomach acid and the chemical environment of your intestines.
However, just like any city, the microbiome can fall into disarray. This imbalance, known as microbiome dysbiosis, is increasingly linked to a wide range of chronic diseases, including:
Inflammatory bowel disease (IBD)
Studies have shown that people with IBD, such as Crohn’s disease and ulcerative colitis, often have distinct microbiome profiles compared to healthy individuals. These profiles are characterised by a decrease in beneficial bacteria and an increase in potentially harmful ones.
Obesity
Research suggests that gut bacteria may play a role in weight management by influencing how efficiently we extract energy from food and store fat. People with obesity tend to have lower levels of certain gut bacteria associated with leanness and higher levels of bacteria linked to weight gain.
Type 2 diabetes
The gut microbiome is thought to influence insulin sensitivity and glucose metabolism. Some studies suggest that imbalances in gut bacteria may contribute to the development of type 2 diabetes.
Neurological disorders
The gut-brain axis, a complex communication pathway between the gut microbiome and the central nervous system, is being increasingly implicated in neurological disorders such as Parkinson’s disease, Alzheimer’s disease, and depression.
Understanding the Causes of Dysbiosis:
Several factors can contribute to microbiome dysbiosis, including:
Diet: A diet high in processed foods, sugar, and unhealthy fats can disrupt the delicate balance of gut bacteria. Conversely, a diet rich in fruits, and vegetables, can promote the growth of beneficial bacteria.
Antibiotics: Antibiotics can wipe out beneficial gut bacteria, leading to dysbiosis.
Stress: Chronic stress can negatively impact the gut microbiome by altering the production of stress hormones, such as cortisol, which can disrupt the gut barrier and increase inflammation.
Environmental factors: Exposure to environmental toxins, such as pesticides and herbicides, can also harm the gut microbiome.
By understanding the importance of the microbiome and taking steps to nurture its health, we can empower our clients to prevent and manage chronic diseases and cultivate a foundation for lifelong well-being.
The microbiome comprises an intricate community of microbes, including bacteria, archaea, fungi, algae, and protists, along with their biomolecules. These microorganisms inhabit a well-defined habitat either within or on a living or non-living entity. The exposed surfaces of the human body, facing the environment, host trillions of microbes from the three major domains of life – bacteria, archaea, and microscopic eukaryotes.
Nevertheless, the diversity, abundance, and functional potency of microbial taxa in distinct parts of the human body differ significantly. The occurrence of shared microbial taxa across different body habitats is quite rare. Recent advancements in next-generation sequencing technologies have revealed that the indigenous microbial community within the human body, along with their functional attributes in specific body habitats, undergo variations over time, among ethnic groups, and depending on the health status of the host.
Disruptions to the community structures or functions due to external factors can disturb the harmonious interactions between the host and microbes, potentially leading to diseases. Furthermore, the microbiome’s dysbiosis state can influence the effectiveness of treatments, prolong the duration of therapy, and result in undesirable treatment outcomes.
The gastrointestinal tract exhibits the highest microbial diversity in terms of community membership, while the vaginal milieu displays minimal compositional diversity at the species level. Nevertheless, the richness of indigenous microbial communities and the functional potency of the microbiome across various body sites are not static. Over time, the composition of microbial communities undergoes variations, with the oral cavity demonstrating the highest heterogeneity, while the indigenous microbial taxa remain stable in the vagina and gastrointestinal tract.
Structural and functional changes in the microbial community in different body sites are influenced by factors such as diet, environmental exposure, host genetics, age, gender, health status, and lifestyle. The diversity of microbiomes in any ecosystem, including a specific body habitat in a healthy human, is characterised by the total number of specific microbes and their relative abundance distribution compared to other microbes in the same or a different habitat.
Microbial diversity, the functional potency of microbiota, and the intricate interactions between microbiota and humans are directly correlated with health and human diseases. For instance, a decrease in microbial diversity in the digestive tract may result in a lower abundance of metabolic functions, an elevated level of pro-inflammatory molecules, and a reduced capacity for xenobiotic degradation. These alterations can lead to conditions like malnutrition, inflammatory bowel disease, and metabolic diseases, while also diminishing the efficacy of various therapeutics.
However, the diversity index and its association with health status are not uniform across all body habitats, and increased microbial diversity can sometimes lead to diseases such as bacterial vaginosis. In a specific body site, the microbial taxa or its genome (genes), proteins, and metabolites may potentially serve as biomarkers for the early prediction of health disorders and also for forecasting the therapeutic potency of drugs commonly used to treat infectious or metabolic diseases.
The primary determinant in shaping microbial composition and selecting gut microbiota within the gastrointestinal tract is diet. Research indicates that dietary choices such as following a vegan lifestyle, consuming unique plant species, adopting a gluten-free diet, eliminating dairy or incorporating milk/cheese, consuming fibre-rich vegetables, opting for whole grains, choosing antibiotic-treated animal products, including poultry, red meat, high-fat red meat, eggs, salted snacks, sugary sweets, ready-to-eat meals, sugar-sweetened drinks, and regularly consuming seafood have significant impacts on altering the gut microbial community compositions and the functional potency of the bacterial genome.
Specifically, a consistent consumption of an animal-based diet tends to elevate the relative abundance of Alistipes, Bilophila, and Bacteroides, which are bile-tolerant microorganisms.
Simultaneously, it reduces the levels of Roseburia, Eubacterium rectale, and Ruminococcus bromii, belonging to the Firmicutes category. These microorganisms encode a substantial number of Carbohydrate-Active enZymes and efficiently metabolise dietary plant polysaccharides.
Enterotypes
Enterotypes refer to distinct microbial ecosystems that inhabit the human gut, playing a pivotal role in influencing various aspects of our physiological and metabolic functions.
These enterotypes are primarily characterised by the dominance of specific bacterial species within the gut microbiota. The three main enterotypes identified in scientific research are Bacteroides, Prevotella, and Ruminococcus. Each enterotype is associated with unique microbial compositions and metabolic activities, contributing to the intricate balance that maintains gut health.
The prevalence of a particular enterotype in an individual can be influenced by various factors, including diet, genetics, and environmental exposures. For instance, a diet rich in fibre may promote the dominance of Prevotella, while a diet high in animal fats could favour the proliferation of Bacteroides.
The impact of enterotypes on human health extends beyond digestion, affecting immune function, metabolism, and even mental well-being. Imbalances in enterotype composition have been linked to various health conditions, including inflammatory disorders and metabolic diseases.
Bacteroides Enterotype:
Dietary Preferences: Bacteroides-dominated enterotypes are associated with diets rich in animal fats and proteins.
Metabolism: Bacteroides bacteria excel in breaking down complex carbohydrates, contributing to the digestion of dietary fibre and the production of short-chain fatty acids (SCFAs).
Health Implications: In a balanced state, Bacteroides play a crucial role in gut health. However, imbalances in this enterotype have been linked to conditions such as metabolic disorders and inflammation.
Prevotella Enterotype:
Dietary Preferences: Prevotella-dominated enterotypes thrive on diets rich in plant-based fibres, including fruits, vegetables, and whole grains.
Metabolism: Prevotella bacteria specialise in breaking down complex carbohydrates from plant sources, leading to the production of SCFAs with anti-inflammatory properties.
Health Implications: Prevotella-dominated ecosystems are generally associated with positive health outcomes, supporting optimal digestion and a balanced gut environment.
Ruminococcus Enterotype:
Dietary Preferences: Ruminococcus enterotypes are associated with diets high in resistant starch and complex carbohydrates.
Metabolism: Ruminococcus bacteria are known for their ability to break down resistant starches, contributing to the production of SCFAs and promoting gut health.
Health Implications: While less studied than the other enterotypes, a balanced Ruminococcus enterotype is believed to play a role in maintaining a healthy gut environment.
Xenobiotics
Xenobiotics are substances that are not naturally produced in the body, like medications, pesticides, additives in food, certain elements in our diet, chemicals from industries, and pollutants in the environment. Our gut microbiota, which is the community of microorganisms in our digestive system, often breaks down these substances. This breakdown process helps control how harmful they are, how easily our body can use them, and how they are removed through urine. The usual changes include reducing and breaking down these substances. Some medications, called pro-drugs, have a particular type of bond (azo bonds) in their structure that needs to be reduced for them to work effectively.
The antibiotic prontosil doesn’t show activity against bacteria in a lab setting (in vitro), but it does inhibit the growth of gut bacteria inside the body (in vivo). The difference in how prontosil works between these two conditions is due to its transformation in the gut by a microbiota-encoded enzyme called azoreductase. This enzyme changes prontosil into triaminobenzene and sulfanilamide. Azoreductase enzymes are common in various gut microbial communities and can work on a wide range of substances.
More than 50 oral medications depend on their interactions with gut microbial and liver enzymes to be effective in the bloodstream. Enzymes from gut bacteria, like β-glucuronidases, can also affect how certain oral medications used in cancer and inflammation treatment work and their potential side effects. Some bacteria that process bile acids can produce substances that prevent the growth of harmful bacteria like Clostridium difficile in the gut.
Clostridium difficile, often abbreviated as C. difficile, is a bacterium that can cause infection in the colon and lead to a range of symptoms, from mild diarrhoea to severe inflammation of the colon. This bacterium is commonly associated with healthcare settings, where individuals are often exposed to antibiotics, which can disrupt the normal balance of the gut microbiota.
Enzymes
Enzymes from different groups of bacteria can decrease how much of a medication our body can use. For example, patients taking the medication digoxin for heart issues may have reduced effectiveness if their gut contains specific bacterial species. About 10% of these patients rapidly break down more than half of the administered digoxin, leading to its quick removal from the body and lower concentrations in the bloodstream. The transformation of digoxin involves specific enzymes in these bacterial strains, influenced by protein-rich diets and other gut bacteria.
Enterococcus faecalis is a Gram-positive bacterium found in the human and animal gastrointestinal tracts, playing a role in carbohydrate fermentation and lactic acid production within the gut microbiota.
Enterococcus faecalis is generally a normal inhabitant. However, it can become an opportunistic pathogen causing infections, especially in individuals with compromised immune systems.
Its resilience and ability to survive in various environments raise concerns, particularly in healthcare, where it is associated with infections like urinary tract infections and endocarditis.
One type of bacteria found in the human colon, Enterococcus faecalis, can produce an enzyme that affects the availability of L-dopa, a medication for Parkinson’s disease. This enzyme converts L-dopa to dopamine, limiting its effectiveness and contributing to potential side effects. Another enzyme, produced by a different bacterium, Eggerthella lenta, transforms dopamine into m-tyramine. The different responses of Parkinson’s patients to dopamine may be linked to variations in their gut microbiome.
Eggerthella lenta is a Gram-positive anaerobic bacterium that inhabits the human colon. It is a part of the normal gut microbiota and plays a role in the fermentation of carbohydrates. Like many bacteria in the gut, its functions are intertwined with maintaining a healthy balance in the microbial community.
Prebiotics
Over the course of your lifetime, sixty tons of food will pass through your digestive tract. What you eat also feeds your bacteria. Prebiotic foods can improve bacterial function. We can also introduce new bacteria into our ecosystem by eating foods that naturally contain healthy microbes. These are probiotic foods. Other foods modify the environment of the gut, making growth of some bacteria more favourable.
Throughout our lives, we are constantly introducing new bacteria into our body.
Even exchanging bacteria with friends and family, which then becomes part of our microbiome. A kiss can introduce as many as 80 million bacteria per smooch. But the most common entry point is through eating. Foods that affect the microbiome are either probiotics or prebiotics.
The human digestive system incompletely breaks down carbohydrates, allowing complex forms to pass into the colon undigested. Survival for colonic bacteria depends on these undigested food substrates originating from the upper digestive system. Typically, bacterial fermentation of saccharolytic carbohydrates produces beneficial metabolites.
In low carbohydrate conditions, bacteria shift to alternative energy sources. This leads to the production of metabolites that may be harmful to the host. After the fermentation of dietary carbohydrates, the primary bacterial fermentation products include short-chain fatty acids and gases.
Saccharolytic carbohydrates are those that can be broken down into sugars through fermentation by bacteria in the digestive system. These carbohydrates are often found in plant-based foods.
Here are some examples of foods that contain saccharolytic carbohydrates:
Fruits: Many fruits contain saccharolytic carbohydrates, such as apples, pears, bananas, and berries.
Vegetables: Fibrous vegetables like broccoli, Brussels sprouts, cabbage, and leafy greens are good sources of saccharolytic carbohydrates.
Quinoa: contains complex carbohydrates that can be broken down through fermentation.
Nuts and Seeds:
These are more fatty than other plant-based foods, but they also contain some saccharolytic carbohydrates.
High-Fibre Foods:
Broccoli, Brussels sprouts, Carrots, Spinach, Sweet potatoes, Fruits, Apples, Pears, Berries (such as raspberries, blackberries, and strawberries), Avocado, Kiwi
The extent to which these carbohydrates are fermented can vary among individuals based on their gut microbiota. The fermentation process can produce beneficial compounds and gases but may also cause digestive symptoms in some people.
Microbiota-accessible carbohydrates in the human diet primarily come from fibre. However, in energy-dense diets, dietary fibres are often limited.
This deficiency is referred to as the fibre gap or low-fibre diet. This can lead to a significant reduction in the diversity of gut microbiota and the loss of beneficial metabolites.
This may contribute to various health issues and illnesses, including:
- metabolic syndrome
- diabetes related to obesity
- inflammatory bowel disease (IBD)
- liver disease
- colon cancer
Probiotics
Probiotics come from processed food so that it is fermenting before it gets into the body. This is unnatural as the body has its own fermentation process that occurs much lower in the gut.
The EU recently declared that probiotic foods cannot be labelled as having health benefits due to the distinct lack of evidence.
It is best to avoid these foods as they can confuse the gut:
Fermented Vegetables
Traditional Yoghourt, Kefir
Sourdough Bread
Fermented Soy Products
Raw Apple Cider Vinegar
That concludes our look at the microbiome. Eating a diet with a lower amount of animal products and processed foods is highly beneficial to human health. The human body is an intricate ecosystem, and the health of our microbiome is deeply intertwined with our overall health. By nurturing this invisible orchestra within us, we can create a symphony of well-being that resonates throughout our lives.
Below is a list of known issues caused by problems with the microbiome. Almost all disease starts with a poor gut microbiome along with acidosis / toxicosis.
Conditions of Dysbiosis of the Microbiome
- Alzheimer’s disease
- Asthma
- Atherosclerosis
- Autism
- Bipolar disorder
- Breast cancer
- Celiac disease
- Chronic fatigue syndrome
- Chronic obstructive pulmonary disease
- Colorectal cancer
- Crohn’s disease
- Depression
- Diabetes
- Esophageal cancer
- Food allergies
- Gallbladder cancer
- Heart failure
- Irritable bowel syndrome
- Leaky gut syndrome
- Liver disease
- Metabolic syndrome
- Multiple sclerosis
- Obesity
- Pancreatic cancer
- Parkinson’s disease
- Psoriasis
- Rheumatoid arthritis
- Schizophrenia
- Stomach cancer
- Ulcerative colitis