Heath, Disease and the Human Microbiome

by | Jul 25, 2021 | Investigations

The gut ‘microbiome’ refers to the collective genomic content of microbes that inhabit the human gastrointestinal tract. The Microbiome is largely composed of different species of bacteria, with a smaller population of non-bacterial microbes such as fungi. The majority of the gut flora reside in the large intestine (especially the colon) with a much smaller population present in the small intestine.

Recent research has revealed that environmental factors, including diet, have the biggest influence on the composition and health of the gut microbiome (Rothschild et al, 2018). The ancient Greek physician, Hippocrates, after whom the Hippocratic oath is named, is quoted as saying that “all disease begins in the gut.” Traditional naturopaths have long maintained this belief and continue to stress the importance of gut health.

With the discovery of the microbiome, it has become apparent that what Hippocrates said all those years ago has some semblance of truth. Medical and biological research has taken a renewed interest in the gastrointestinal tract due to its recently discovered role in the genesis and development of many diseases. In fact, it is now accepted that the gut microbiome affects nearly all aspects of human health (Mohareji et al, 2018).

This essay will focus on the importance of maintaining a healthy gut, how dysbiosis contributes to ill health, and the different treatments that are available for correcting a toxic bowel. First, a brief overview of the naturopathic view concerning microbiome imbalance is given and then more recent research is explored regarding the bowel and its role in various health disorders.

Naturopaths distinguish between two groups of bowel bacteria: acid-producing and alki-producing (putrefactive). The naturopathic model maintains that acid-producing bacteria, which include Bifidobacterium and Lactobacillus, are required to maintain an optimum bowel pH (slightly acidic). On the other hand, an alkaline bowel promotes the growth of putrefactive bacteria that cause toxicity and ultimately, disease. “Good” bacteria fulfill several important functions. These include:

Regulating bowel pH: Beneficial bacteria help maintain an ideal bowel pH (slightly acidic) due to the production of metabolic acids.

The production of vitamins: Vitamin K, B12, and folic acid are all produced by the bowel flora. Vitamins B1, B2, and B6 are also produced in smaller amounts.

Maintaining mucosal integrity: Metabolites produced by good bacteria, such as butyrate, support the integrity of the intestinal mucosa (Vasquez, 2016).

Protection against pathogens: Beneficial bacteria produce anti-microbial substances which help eliminate pathogenic bacteria. They also promote mucosal immunity by shaping the host’s immune response to pathogens (Perez-Lopez et al, 2016).

Regulating immune function: Lactobacillus bulgaricus exert an immunological effect by upregulating the number of white cells (leucocytes) and activating the thymus gland and spleen. Furthermore, good bacteria promote anti-inflammatory benefits. (Vasquez, 2016)

Short-chain fatty acid (SCFA) production: Beneficial bacteria in the colon ferment complex carbohydrates that are inaccessible to human digestion. This process produces SCFAs, such as butyrate – a major source of energy for the colonocytes (Roy, Lawrence and Levy, 2006).

Putrefactive bacteria have a damaging effect on the integrity of the intestine and promote toxicity. An overgrowth of pathogenic microbes is associated with a number of diseases. Specific adverse effects of putrefactive bacteria include:

Production of toxins: The bowel flora produce various metabolites, some of which can be toxic. For example, amines produced via the decarboxylation of amino acids must be detoxified in the liver. Gram-negative bacteria have a membrane comprised of lipopolysaccharide (LPS). Because LPS is a mediator of toxic inflammatory responses, it is known as an endotoxin, exposure to which is associated with a variety of physiological symptoms.

Cause “leaky gut”: Healthy gut flora is required to maintain the integrity of the intestinal barrier. An overgrowth of putrefactive bacteria can result in translocation of harmful bacterial metabolites across the intestinal membrane, also called “leaky gut”.

Changes in bowel pH: An overgrowth of pathogenic bacteria can cause unfavourable changes to the bowel pH. This can alter the microenvironment and upregulate the proliferation of harmful bacterial species.

Defining ‘dysbiosis’

Dysbiosis is broadly defined as a change in the composition of the microbiota relative to the composition found in healthy individuals (Petersen, 2014). ‘Dysbiosis’ may be characterised as a state of imbalance – a suboptimal composition of microbes in the gut which has consequences for health and disease.

Although each person has a unique microbiome composition, we know from research done on individuals with no signs of disease what a healthy microbiota architecture should look like. Recent research has found marked changes in the structure of the microbiome (including a decrease in bacterial diversity) in patients suffering from inflammatory bowel disease and other disorders (Murtaza, Cuiv and Morrison, 2016).

Microbial diversity is an important characteristic of a healthy microbiome. Evidence suggests that members of the microbiota have different contributions to host health including the ability to induce protective anti-inflammatory responses (Petersen, 2014). The link between low microbial diversity and illness indicates that a wide variety of bacterial species is important for the maintenance of good health. The bowel flora can become imbalanced due to a poor diet, immunosuppressive drugs, antibiotics, or consumption of contaminated food or water (Vasquez, 2016).

The naturopathic position

The naturopathic definition of dysbiosis is slightly more simplified. It states that dysbiosis is the overgrowth of putrefactive, alkali-producing bacteria in the gut. Naturopaths maintain that an alkali condition in the bowel is conducive to an unhealthy bowel environment and leads to ill health. It is thought that alkali conditions inhibit the proliferation of “good” acid-producing bacteria.

Naturopaths point to overconsumption of protein as a key factor that can lead to dysbiosis and unhealthy bowel conditions. It is thought that putrefactive bacteria feed on undigested protein in the colon, which results in the proliferation of these species and increased production of toxins. If protein consumption is high and there is a lack of protein-digesting enzymes in the stomach, this can lead to the passage of undigested protein into the large intestine, providing food for the “bad” bacteria.


Oral medications, especially antibiotic drugs, the use of which has become more aggressive in recent years (Ramachandran et al, 2019), can cause dysbiosis in the gut. Research has shown that the administration of these powerful drugs can result in rapid changes to the gut microbiome (Lewis et al, 2015). A cause for great concern is that antibiotics are one of the most common types of medications prescribed to children and infants. Researchers have correlated antibiotic administration in early life with long-lasting health complications including obesity, allergies, autoimmune disease, and behavioral disorders (Neuman et al, 2018).

The overall consequences of antibiotics extend beyond their effects on the microbiota. Many antibiotics are known liver toxins and can also affect the immune system. In all studies on drug-induced liver injury, antibiotics were the most common culprit (Bjornsson, 2017). It is deeply concerning that orthodox practitioners minimize the adverse effects of antibiotics and often prescribe them without hesitation, especially considering there are much safer, more holistic alternatives, some of which will be explored later in this essay.

Candida Albicans

A common feature of microbiome dysbiosis is an overgrowth of the fungi known as Candida Albicans, the predominant fungal species present in the human gut. An overgrowth of Candida is linked to carbohydrate consumption. While many orthodox physicians do not recognise Candida overgrowth as a significant health concern, naturopaths view Candida infection as the end result in a long process of health deterioration.

Candida can also spread due to a very abrupt “attack” on the gut; this could be due to antibiotics or other influences that affect the microbiota. Studies done on stool samples have found Candida present in 63% of individuals; 11% of these showed Candida overgrowth (Otasevic et al, 2018).

Fungi are also known to produce mycotoxins that can be damaging to health. Candida produce a mycotoxin that suppresses the immune system (Shah, 1998). Candida infection can cause a wide range of unpleasant symptoms – according to Chaitow and Trenev (1990) this can include thrush, allergies, bloating, diarrhoea, constipation, fatigue, muscular aches, depression, erratic vision, craving for sugary foods, upper respiratory tract infections (including postnasal drip) and chronic acne.

The link between dysbiosis and ill health

Treating dysbiosis is essential for the reinstitution of a state of health in patients with chronic inflammatory disorders including autoimmunity and fibromyalgia (Vasquez, 2016). Many orthodox doctors only recognise microbes as they relate to ‘infections’ and fail to take into account the diverse microbe-host interactions that can contribute to health and disease.

Fendler et al (2001) found that 56% of patients suffering from inflammatory arthritis have some form of dysbiosis. Furthermore, intestinal permeability (also known as “leaky gut”) has been identified as a danger signal for what are known as “autoimmune” diseases (Mu et al, 2017). A leaky gut can allow toxins to enter the body and trigger the genesis and development of a so-called “autoimmune” condition. New research has implicated the microbiome in several (if not all) chronic diseases (Hills et al, 2019).

Inflammatory bowel disease (IBD)

Inflammatory bowel disease is a complex disorder caused by a number of factors, including environmental and lifestyle choices such as diet (particularly lack of dietary fibre in the form of fruits and vegetables), and smoking (Ananthakrishnan, 2015). The global incidence of IBD is increasing. It is widely believed that changes to the structure of the microbiome play a role in the precipitation of the disease and therefore microbiota restoration and rebalancing may offer a curative effect. Indeed, a meta-analysis conducted by Ganji-Arjenaki and Rafieian-Kopaei (2018) found probiotics to be beneficial for IBD.

Irritable bowel syndrome (IBS)

Unlike IBD, irritable bowel syndrome is classified as a ‘functional’ disorder of the gastrointestinal tract. Staggeringly, 10-15% of the population suffer from the symptoms of IBS (Hills, 2019). IBS is divided into three subtypes: IBS-C (constipation), IBS-D (diarrhoea) and mixed (both constipation and diarrhoea). Orthodox physicians often consider IBS to be somewhat of a mysterious and perplexing disorder, which is puzzling considering there is much evidence to suggest that IBS is simply a manifestation of small intestine bacterial overgrowth (SIBO). The mechanism tying IBS to SIBO is explained by Lin (2004), who writes that:

“The gastrointestinal and immune effects of SIBO provide a possible unifying framework for understanding frequent observations in IBS.”

In other words, IBS is directly linked with gut dysbiosis.

Cardiovascular disease (CVD)

The microbiome may also play a role in atherosclerosis and heart disease. Adherence to a Mediterranean (and for that matter, paleo-Mediterranean) diet is associated with a marked decrease in the likelihood of CVD mortality (Grosso, 2017). This diet, with its emphasis on healthy whole vegetables and fruits, also promotes beneficial changes to the microbiome.

One study found adherence to a Mediterranean diet was associated with lower urine levels of TMAO (De Filippis et al, 2016), which is a predictor of CVD events (Wang et al, 2011). TMAO is synthesized by the liver from trimethylamine (TMA) which is produced by gut microbes during the metabolism of choline. Choline (lecithin) is a metabolite of phosphatidylcholine, a lipid present in high amounts in animal fats.

Type 2 diabetes

Endotoxemia caused by bacterial LPS may play a role in the cause of insulin resistance (Cani et al, 2007), suggesting a relationship between gut health and diabetes. Elevated LPS occurs in those with increased intestinal permeability, which in turn can be caused by adverse changes to the microbiome (dysbiosis). Increased concentrations of gram-negative bacteria that promote LPS may also be considered a type of dysbiosis. Therefore, normalising the microbiome and healing the intestinal mucosa may help heal type 2 diabetes.

Deficiency of short-chain fatty acids is also associated with type 2 diabetes and therefore increasing the concentration of SCFS-producing gut bacteria (which can be done through increased dietary fibre consumption) may help alleviate the disease (Zhao, 2018).


Toxic microbe metabolites that remain in circulation may contribute to the onset or progression of cancer (Rajagopala et al, 2017). In fact, increased fibre intake may be associated with a lower risk of colorectal cancer. Indeed, a risk assessment study estimated that 38% of colorectal cancer cases are caused by poor diet (Zhang et al, 2019). Studies have also found that specific bacterial strains may be potentiators of tumorigenesis, including Fusobacterium nucleatum (Brennan and Garrett, 2016).

The gut-brain connection

Recent advances in physiology have revealed a profound link between the enteric and central nervous systems, called the gut-brain axis. This complex interaction between the gut and the brain is heavily influenced by the microbiota (Carabotti et al, 2015). Microbiome dysbiosis including small intestine bacterial overgrowth (SIBO) and leaky gut may produce central nervous system inflammation (Galland, 2014). It is therefore not surprising that common mental health disorders, including depression and anxiety, have been directly linked with microbiota dysbiosis. Peirce and Alvina (2019) state that:

“Overall, a picture of the gut microbiome playing a facilitating role between stress response, inflammation, and depression, and anxiety is emerging.”

Supporting these findings is a meta-analysis conducted by Huang, Wang and Hu (2016) which found probiotics to be associated with a significant reduction in depression.

Reshaping the microbiome for improved health

The microbiome is directly associated with health and disease. It stands to reason that correcting dysbiosis and engaging in activities that improve the microbiota is crucial for improving and maintaining long-term health. While not recognised by mainstream physicians, naturopaths stress the importance of detoxification for correcting illness.

There are toxins in our food and our environment, and yet more toxins produced by microbes in the bowel. Therefore, a holistic detoxification regimen should take the microbiome into account. Optimising diet and reducing the intake of protein (especially meat) can, according to naturopaths, help reduce the number of putrefactive bacteria in the bowel. If this is not enough, supplemental probiotics (acid-producing Lactobacillus and Bifidobacterium strains) may need to be administered. Vasquez (2016) stresses the importance of a holistic approach to microbiome correction:

“Exclusive therapeutic focus on the eradication of microbes is fraught with inefficacy if it fails to address the intrinsic patient-specific imbalances that allowed that individual patient to be susceptible to microbe-induced inflammation and dysmetabolism.”

He suggests a three-part treatment protocol that consists of 1. Treating pathogenic microbes using antibiotics/herbals, 2. Restoring immune function through vitamin/mineral supplementation and 3. Optimizing nutrition through dietary manipulation.

Herbal/botanical therapies

There are a number of powerful herbal remedies for removing pathogenic bowel flora and correcting dysbiosis. Aloe vera has been shown to be effective at modulating the conditions of the gut. In fact, a meta-analysis conducted by Hong (2018) found aloe vera to be a safe and effective treatment for IBS.

Berberine, an alkaloid extract from the plant Berberis vulgaris has potent antimicrobial properties and has been used for centuries as a remedy for infectious diseases. According to Vasquez (2016) many clinicians use berberine to treat gut dysbiosis due to fungi, bacteria or other microbes.

Oregano oil is also an effective treatment for gastrointestinal parasites, including candida albicans. In fact, essential oils (including oregano) have been shown to inhibit the growth and activity of candida yeast more efficiently than antifungal drugs (Bona, 2016). Herbal therapy in the treatment of IBD is also increasing worldwide and studies show positive results for a number of substances including aloe vera, wormwood, and curcumin (Triantafyllidi, 2015). There are also several other botanicals/herbals that have shown to be effective in the treatment of bowel disorders and dysbiosis.

Bowel cleanses

Severe dysbiosis often cannot be corrected by herbal and probiotic supplements alone. In this case, bowel cleanses may be necessary. The use of bowel enemas, colemas or colonic irrigation has long been advocated for by naturopaths in the treatment of disease. Enemas clean out the colon, whereas colonic irrigation cleans the entire large bowel. The colema, as utilized by Jensen (1981), is an intermediate between the enema and irrigation techniques. It was Jensen who claimed to have washed much old, hard, encrusted material out of patients’ bowels. If this is true, then bowel cleansing may be an important treatment for many people who suffer from gastrointestinal symptoms.

Vitamin C, in high doses, can also be used as a bowel cleanse. Vasquez (2016) advocates using 20-60 grams of vitamin C dissolved in 1 little of water, together with two cups of coffee to induce a rapid, laxative effect. This can be used to correct dysbiosis by reducing the overall load of gastrointestinal microbes.

Diet and lifestyle

Dietary habits play a key role in the health and composition of the gut microbiome. Naturopaths maintain that a diet high in animal protein may increase putrefactive activity in the gut. Too many alkaline-producing bacteria can alter the pH of the bowel which then leads to the further development of pathogenic flora.

Studies have shown distinct differences in microbiota composition in people who consume a standard Western diet compared to those who consume diets rich in fibre (Bibbo, 2016). A metagenomic analysis found that microbial diversity decreased with higher carbohydrate intake, while diversity increased with fruit, vegetable, coffee and red wine intake (Zhernakova, 2016). High fermentation carbohydrates including grains, breads, pasta, pastries, potatoes and refined sugar promote the overgrowth of bacteria and Candida in the intestines (Vasquez, 2016), which can lead to the development of SIBO. Indeed, low FODMAP (fermentable oligosaccharides) diets have been shown to ease the symptoms of IBS.

However, these kinds of diets are not advised for long-term adherence due to the restriction of healthy fruits and vegetables, which serve as prebiotics that support the growth of beneficial flora (Hills at al, 2019). Ketogenic diets have also become ‘trendy’ lately for their weight loss benefits. However, because fibre and prebiotics are required to maintain a healthy flora, restricting plant-based carbohydrates long-term can have a negative impact on the microbiota (Reddel, et al, 2019).

Other lifestyle factors may play a role in shaping a healthy microbiome. Due to the influence of the microbiome on the gut-brain connection, it is hypothesized that the microbiota may also affect sleep. For example, a review published by Wagner-Skacel et al (2020) found that the prevalence of Faecalibacterium was significantly associated with improved sleep scores in patients with bipolar. Vasquez (2016) explains that negative stress can promote microbial pathogenicity through microbial reception of stress-related hormones and neurotransmitters, including norepinephrine.


Probiotics are supplements containing live microorganisms. The most commonly administered probiotics are the acid-producing Lactobacillus and Bifidobacterium. Naturopaths use probiotics to restore the good bacteria in the gut and promote a more balanced microbiome. Probiotics have shown to be effective in treating numerous conditions. Probiotic bacteria provide health benefits by correcting dysbiosis, normalising gut motility and reducing pathogens (Hills et al, 2019). Cultured food products and beverages such as natural yoghurt, kefir and kombucha are natural probiotics.


Prebiotics provide food for healthy gut bacteria. Prebiotics are carbohydrates that are not digested in the small intestine. These carbohydrates travel through the gut and enter the large bowel unchanged. Here, they are fermented by the microbiota and promote the growth and diversity of “good” bacteria. The fructo-oligosaccharide, inulin, is a well-known prebiotic found in Jerusalem artichokes, asparagus, chicory root, onions and garlic. Other prebiotics include lactulose (a disaccharide composed of galactose and fructose) and raw starch sources such as uncooked potatoes. Prebiotics have been shown to improve microbiome composition by increasing Bifidobacteria and decreasing E. coli (Musilova, 2015).


The human gastrointestinal microbiome has important consequences for health and disease. Furthermore, the discovery of the gut-brain axis extends the importance of the microbiome to mental and emotional wellbeing. Maintaining a healthy gut microbiota involves adhering to a healthy diet that contains plenty of plant foods, prohibiting overconsumption of starchy carbohydrates and animal protein, reducing stress, and improving sleep. Healing a damaged microbiome may require the use of herbal/botanical therapies, bowel cleanses, and the consumption of pre- and/or probiotics.

Although he lived more than 2,000 years ago, the Greek physician Hippocrates was truly ‘ahead of the game’ when he said that “All disease begins in the gut”.


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