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Health Protocols

Maintaining a Healthy Microbiome

Diet and Lifestyle Strategies for Supporting a Healthy Microbiome

The fundamental link between the gut microbiome, diet, and physiology has become increasingly apparent (Amato 2015), and underscores the power of diet as a means to maintain a healthy microbiome—and thus a healthy body. The gut microbiota is in constant evolution, varies greatly among individuals, and modulates metabolism, opening the possibility to predict individual responses to particular foods as part of personalized medicine interventions (Xu 2015; Vanamala 2015; Davenport 2017).

Western versus High-Fiber Diet

A high-fat diet, especially one including large amounts of saturated fatty acids, has been shown to induce gut dysbiosis, intestinal permeability, and inflammation (Araujo 2017; Yang 2017; Silva Figueiredo 2017). A diet high in complex carbohydrates and fiber, on the other hand, supports the growth of microbial populations that are efficient carbohydrate fermenters. These bacteria produce short-chain fatty acids and other fermentation products that support the health of the intestinal lining and have positive effects on immune and metabolic functions (Montemurno 2014; Yang 2017).

A Western-type diet in particular—high in animal proteins and fat and low in fiber—selects for bacteria that metabolize proteins efficiently and those that can best tolerate bile acids secreted in response to high-fat meals. Microbial metabolism of proteins and certain bile acids creates byproducts that appear to contribute to the development of diseases known to be closely connected to a Western diet, including colon cancer, cardiovascular disease, and metabolic disorders (Montemurno 2014; Ridlon 2014). Conversely, in one study, a Mediterranean-style diet with 35% of calories from fat, and a low-fat diet (<30% total fat), each improved gut microbial communities in subjects with obesity and metabolic dysfunction after two years (Haro 2017).

Prebiotics are carbohydrates that are completely or partially indigestible and that promote the growth of beneficial bacterial populations. These include small carbohydrates called pectin-oligosaccharides, large and small fructose-based carbohydrates known as inulins, and resistant starch (Ferrario 2017; Kelly 2008). Legumes, fruits and vegetables, nuts, and whole grains are especially high in prebiotic fibers (Vinke 2017; Dahl 2015; Slavin 2013; Lamuel-Raventos 2017). These foods have long been recognized as the cornerstones of a healthy, high-fiber diet, including the Mediterranean diet, known to show benefits regarding a number of metabolic and inflammatory health problems (Fabbiano 2017; Montemurno 2014).

Omega-3 Polyunsaturated Fatty Acids

Although high-fat diets are generally associated with negative changes in the gut microbiome, different types of fats may have different effects. For example, omega-3 polyunsaturated fatty acids such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) appear to improve the microbial balance and increase anti-inflammatory immune activity in the gut and throughout the body (Watson 2017; Costantini 2017; Silva Figueiredo 2017). This may be due to increased positive interactions between the immune system and gut microbes, resulting in higher microbial diversity, increased short-chain fatty acid production, and improved intestinal barrier function (Candido 2017; Menni 2017; Costantini 2017).

Fermented Foods

Fermentation, mainly by lactic acid bacteria, has been used to preserve food and enhance flavor for thousands of years, and fermented foods are recognized for their probiotic and health-promoting nature (Hill 2017). Fermented foods are a source of vitamins, minerals, enzymes, and a range of biologically active, health-promoting peptides produced by microbes during fermentation. Fermented food consumption has been associated with health benefits such as improvements in: high blood pressure, high cholesterol levels, insulin resistance, certain digestive disorders, cognitive function, and immune function, and may lower risks of cardiovascular disease, diabetes, osteoporosis, and certain cancers (Tamang, Shin 2016). In addition, the living microbes present in fermented foods may act as probiotics when ingested (Sanlier 2017; Stanton 2005; Tamang, Shin 2016).

Table 1. Examples of microorganisms commonly used in food fermentation

Fermentation Microorganisms

Foods in Which They Are Typically Used



Acetobacter species

A. aceti subspecies aceti
A. pasteurianus
A. peroxydans
A. syzygii
A. okinawensis
A. malorum
A. tropicalis
A. pomorum

Used in fruit fermentation and are important in making many vinegars. They produce acetic acid, and are also present in kombucha, cocoa, and some wines.

Streptococcus species

S. thermophilus
S. faecalis
S. bovis

Widely used in dairy fermentation to produce such foods as yogurt and cheeses. They produce lactic acid and are also found in some vegetable ferments.

Lactobacillus species

L. delbrueckii
L. plantarum
L. lactis
L. acidophilus
L. brevis
L. fermentum
L. buchneri
L. nagelii

Widely used in dairy, vegetable, fruit, grain, and meat fermentations to produce cheeses, kefir, yogurt, cocoa, wine, sourdough, sausages, cucumbers, kimchi, olives, sauerkraut, kombucha, and many other foods.

Bifidobaterium species

B. longum
B. animalis subspecies lactis
B. breve

Added during dairy fermentation to boost probiotic content. They are found in some cheeses and yogurt.

Bacillus species

B. coagulans
B. subtilis

Used in soybean fermentation to produce natto and soybean pastes. B. subtilis is well known for producing the enzyme nattokinase.

Yeasts and Molds:


Saccharomyces species

S. cerevisiae
S. cerevisiae subspecies boulardii
S. uvarum

Used in grain fermentation to make beer, wine, and sourdough. They can also be found in kombucha, and some species are used as probiotics.

Aspergillus species

A. oryzae
A. sojae

Used to ferment soybeans and rice. A. oryzae (a.k.a. koji) in particular is important in the production of sake, miso, soy sauce, rice vinegar, and rice wine.

Rhizopus species

R. oligosporus
R. oryzae

Used to ferment soybeans and produce tempe and soy sauce.

Penicillium species

P. camemberti
P. roqueforti

Used to make white mold cheeses (eg, Camembert) and blue mold cheeses (eg, Roquefort)

Zygosaccharomyces species

Z. rouxii
Z. bailii

Used in soybean fermentation to produce miso and soy sauce. Also found in kombucha.

(Battcock 1998; Fernandez 2015; Tamang, Shin 2016; Tamang, Watanabe 2016; Pokusaeva 2011; Coton 2017; Mamlouk 2013; Suezawa 2008; Oliveira 2017; Laich 2002; Guenther 2011; Ropars 2017; Swain 2014; Londono-Hernandez 2017; Kitamoto 2015; Fijan 2014; Kawarai 2007; Kim 2017; Marongiu 2015; Gallone 2016; Krogerus 2017; Kelesidis 2012; Wang 2009; Mayo 2008; Lefeber 2011; Vogel 1993)

Alcohol (Ethanol)

Abuse and dependence on alcoholic beverages has been associated with dysbiosis leading to inflammation and increased permeability of the intestinal mucosa. Absorption of bacteria, microbial products, and other intestinal contents through the damaged mucosa may trigger inflammation in the liver and contribute to alcohol-related liver disease (Capurso 2017; Dubinkina 2017). Furthermore, some evidence suggests certain people with alcohol dependence may have increased gut permeability and higher scores for depression, anxiety, and cravings. Changes in microbiome composition found in this group of people pointed towards the possibility that the microbiome might be a potential target to reduce the risk of relapse in some people with alcohol dependence (Capurso 2017; Leclercq 2014).

Stress and Sleep

Stress and sleep disruption are closely connected and have been correlated with disturbances in the healthy balance of gut microbes (Weljie 2015; Galland 2014; Poroyko 2016; Benedict 2016). Dramatic reductions in gut microbial abundance and function have been noted following sudden acute stress events, such as a heart attack, trauma, or burn injury (Alverdy 2017). It is thought that high psychological stress conditions in the body trigger changes in the gut microbiome, which may lead to changes in the regulation of some neurotransmitters (Househam 2017). In addition, due to the bidirectional communication along the gut-brain axis, dysbiosis in turn can trigger dysfunctional activation of the stress response (Alverdy 2017; Bermon 2015; Rogers 2016; Clapp 2017).

Stress reduction may be one way to improve the health of the microbiome. Meditation has been shown to reduce activation of the stress pathways and suppress chronic inflammation, which may support beneficial gut microbial populations (Househam 2017). Furthermore, getting enough sleep and observing normal sleep/wake rhythms may both be important for supporting a healthy microbiome (Thaiss 2014; Parekh 2018; Anderson 2017).

More information is available in the Stress Management and Insomnia protocols.

The Gut-Brain Axis

The digestive tract has its own nervous tissue, called the enteric nervous system, that senses and responds to the gut environment and regulates gut activity. While the enteric nervous system can function independently, it also communicates closely with the body’s central nervous system through a network referred to as the gut-brain axis. The bidirectional nature of this communication explains not only how stress may affect digestion, but also how events in the digestive tract may influence the brain (Quigley 2018; Zhou 2015; Mayer 2014; Carabotti 2015). 

The gut microbiome is emerging as a key player influencing communication along the gut-brain axis. Gut microbes produce an array of neuroactive chemicals, help control intestinal barrier function, and modulate immune and inflammatory signaling, all of which influence signaling along nerve pathways (Carabotti 2015). Disturbances in the gut microbial community are now thought to be involved in neurological disorders such as Parkinson disease, Alzheimer disease, autism spectrum disorders, and in depression, anxiety, and chronic pain. Findings from animal research suggest that, most likely via the gut-brain axis, the intestinal microbiome may even shape appetite, feeding behavior, and taste preferences (Mayer 2015; Mayer 2014; Hu 2016). In a remarkable experiment, researchers transplanted fecal microbes from human Parkinson disease patients into genetically susceptible mice. This triggered manifestations of the disease, such as impaired movement, in the exposed mice, while the same genetically predisposed mice transplanted with fecal microbes from healthy people did not develop these symptoms (Sampson 2016).


Regular moderate-intensity exercise is well known to mitigate stress, reduce chronic inflammation, and improve metabolism (Lalanza 2015; Beavers 2010; Nicklas 2009; McGarrah 2016; Sato 2003; Colombo 2013). Findings from several studies suggest physically active and highly fit individuals have greater gut microbial diversity with more beneficial microbes than sedentary people (Clarke 2014; Estaki 2016; Bressa 2017; Barton 2017; Petersen 2017). The observed benefits of exercise on immune response, metabolism, and overall health might be mediated in part by its beneficial effects on the gut microbiome (Bermon 2015; Monda 2017). In addition, some researchers have proposed that microbial byproducts may play a role in preserving skeletal muscle structure and function, particularly in the elderly, a cross-talk that is becoming known as the “gut-muscle axis” (Ticinesi 2017; Grosicki 2017).