Gut Microbiome Guide
What is the gut microbiome?
The gut microbiome is made up of bacteria living in your large intestine. There are trillions of bacteria residing here, and they have a profound effect on your health, both physical and mental.
Understanding the layers of the digestive tract:
The large intestine has four main layers. The inner most layer is the mucosa. The lumen is the space within the gut which contains remnants of foods, liquids, and whatever else your body is trying to eliminate through faecal matter. The bacteria in your large intestine are hanging out in the outer layer of the mucosa.
What are the functions of the gut microbiome?
Digestion and nutrient metabolism: food breakdown continues all the way into the large intestine. The gut microbes produce digestive enzymes, which help breakdown food particles, so that nutrients can be absorbed.
Fermentation: gut microbes ferment fibre and indigestible carbohydrates. The product of this fermentation process are compounds called short chain fatty acids (SCFAs), which have many positive effects on the gut health and more. Find out more.
Immune regulation: the gut microbes support the immune system by regulating immune cell function (via SCFAs) and helping the body to differentiate harmless and harmful substances (immune tolerance).
Protection against bad bacteria (pathogens): there is a delicate balance between beneficial bacteria and harmful (pathogenic) bacteria within the microbiome. The growth of the beneficial bacteria keep the pathogenic bacteria from becoming too abundant, which can cause disease.
Production of vitamins: the gut microbiome synthesize some key vitamins, including vitamin K, biotin (B7), and folate (B9).
Production of neurotransmitters: the gut microbiome also synthesize neurotransmitters, including GABA, serotonin, glutamate, and dopamine. Therefore, gut health must be considered as a key aspect to mental health.
Metabolism and weight regulation: the relationship between the gut and metabolism is complex and multilayered. The gut microbiome can influence appetite and fullness (satiety) and regulate fat storage. Imbalances in the microbiome are associated with insulin resistance, type II diabetes, high cholesterol, and inflammation.
Maintaining the health of the digestive tract: the gut microbiome support the integrity of the gut lining to prevent “intestinal permeability” (or “leaky-gut”). Read on to find out more.
What is dysbiosis?
Dysbiosis is the imbalance of bacteria within the gut microbiome. In the instance of dysbiosis, there may be not enough beneficial bacteria and an overgrowth of bad or pathogenic bacteria. A wider array of organisms can also be out of balance, including parasites, viruses, and yeasts.
What causes dysbiosis?
A diet high in ultra-processed foods, refined sugars, and low in fibre and wholefoods.
Antibiotics can wipe out the beneficial bacteria, and leave the microbiome vulnerable to the overgrowth of bad bacteria.
Over the counter medications including antacids/ PPIs (Nexium, Gaviscon, Mylanta, QuickEze, etc) and NSAIDs (Neurofen, Naprogesic, Ponstan, Voltaren).
Prescription medications including anti-psychotics, immunosuppressants (corticosteroids), and chemotherapy agents.
Chronic psychological and physical stress has been known to negatively impact the gut microbiome.
Lifestyle factors, including smoking, alcohol consumption, lack of exercise, and poor sleep.
What is “Leaky-Gut”?
“Leaky gut”, or more appropriately known as intestinal permeability, is significantly intertwined with the gut microbiome. Often dysbiosis and intestinal permeability occur simultaneously, with similar causative factors.
Above I described the first layer of the gut lining, the mucosa. The epithelial layer is part of the mucosa, and is made up of cells, connected by tight junctions. In the instance of leaky gut, these tightly knit cells making up the epithelial lining become permeable, or leaky.
When the epithelial lining is compromised, larger particles such as foods compounds, bacteria, toxins, and other substances from the gut can sneak through to the blood stream. The consequences of this include inflammation and immune dysregulation, which are the underlying drivers of most disease.
What causes intestinal permeability?
The factors that contribute to intestinal permeability are very similar to those that cause dysbiosis. These include chronic stress, poor diet, alcohol consumption, NSAIDs, antibiotics, and gastrointestinal infections.
Some other causes include prolonged high intensity exercise and gluten consumption.
Certain health conditions are associated with intestinal permeability, including inflammatory bowel disease (Crohn’s disease and ulcerative colitis), irritable bowel syndrome (IBS), diverticular disease, coeliac disease, and many (if not all) autoimmune conditions.
Symptoms of intestinal permeability:
Gastrointestinal symptoms may include bloating, diarrhea, constipation, abdominal pain/ discomfort, IBS, food intolerance, and allergies.
Non-gastrointestinal symptoms may include fatigue, joint pain, muscle aches, headaches, migraines, skin rashes, eczema, psoriasis, allergies, asthma, mood disturbance, depression, brain fog, difficulty concentrating, auto-immunity, and chronic inflammation.
Prevention of intestinal permeability & dysbiosis:
Eat a primarily wholefood based diet, with a diverse range of fibres from fruits, vegetables, legumes, nuts, and seeds.
Include fermented foods in the diet such as sauerkraut, Kim Chi, kefir, unsweetened yogurt, kombucha, and miso.
Include gut-healing foods in the diet such as bone broth, slow cooked meats, and collagen powders or gelatin.
Limit medications use where possible, by finding natural alternatives, and visiting a naturopath or nutritionist to address the underlying cause of illness and disease.
Reduce or eliminate alcohol, soft drinks, fruit juices, energy drinks, flavoured milks, and other high-sugar beverages.
Treatments of intestinal permeability & dysbiosis:
The treatment of these conditions will vary from person to person, depending on their symptoms and other health conditions. A consult with your naturopath or nutritionist can help to determine what treatments are indicated.
Some common treatments of dysbiosis, especially if there is an overgrowth of bad bacteria, include herbal antimicrobial tonics. Probiotics are also utilised, particularly the strain Saccharomyces boulardii. Prebiotic fibre supplements can be very useful in some people, including partially hydrolyzed guar gum (PHGG).
In the case of intestinal permeability, gut healing powders are often very useful. They will contain ingredients which heal the “leaky” areas of the gut lining. These include glutamine, zinc carnosine, vitamin A, and vitamin D. Anti-inflammatory compounds such as slippery elm, turmeric, licorice, chamomile, aloe vera, marshmallow, and quercetin, can help to relieve symptoms and resolve permeability.
