The Gut Microbiome and its role in Human Health

Written May 2018 by Phoebe Wynne-Lewis, BHSc, Dip Nat Med, Dip Herb Med – FxMed Technical Support

The human microbiota is the entire collection of microorganisms living on the surface and inside our body. These communities are important for human physiology, immune system development, digestion, mood and detoxification reactions.

Some of these microorganisms residing in the gut encode proteins for functions including; metabolizing dietary nutrients (ie fatty acids, glucose and bile acids) and drugs, digesting complex indigestible polysaccharides and synthesizing vitamins and bioactive molecules. Consequently, we have two genomes, one inherited from our parents and the other acquired, i.e., the microbiome. The most important difference between these two genomes is that, while the inherited genome remains almost stable during our lifetime, the microbiome is extremely dynamic and can be influenced by a number of factors, including age, diet, hormonal cycles, travel, therapies and illness.

The “Gut Microbiome” is a complex community of bacteria living in our intestines. This community is comprised of an estimated 100 trillion microorganisms, containing up to 1000 different species, with a few dominant bacterial species being the major inhabitants. The microbiome also harbours some yeast, viruses and pathogens. All of these organisms perform a multitude of functions, and need to be properly balanced in order to maintain good health.

There are no good or bad bacteria per se. Potentially harmful microbes only become dangerous once they start to take up too much real estate, outnumbering the more beneficial ones. A microbiome containing too many so-called ‘bad’ bacteria and not enough (or the right combinations) of ‘good’ bacteria has been connected with an increasing number of common diseases, including; colorectal and gastro-intestinal cancers, immune-based inflammatory diseases such as inflammatory bowel disease, crohns disease, rheumatoid arthritis and multiple sclerosis; cardio-metabolic disease including obesity, type II diabetes and hypertension; and depression, brain diseases, autism, and allergies.

Studies suggest that a more diverse group of gastrointestinal microorganisms is associated with improved health while a community of bugs that is less diverse is seen in conditions of illness.  Many micoorganisms are beneficial; for example, they produce digestive enzymes, lactic acid, and other protective compounds that keep the bowels, and the body functioning well. Scientists are striving to understand how the specific species, their abundance and/or the interplay of microorganisms within a community, can influence health. What is clear is that the gut microbiome and its human host can work together, symbiotically, to avoid microbial imbalance, and the more diverse an individual’s gut microflora are, the better for that person’s wellbeing.

Microbial Imbalance
Dysbiosis is defined as a microbial overgrowth or imbalance that results in detrimental symptoms for the patient. Other definitions of dysbiosis include: poor microbial diversity, reduced levels of beneficial bacteria, and a shift in the composition of the microbiota, resulting in negative symptoms for the host. An imbalance of microflora leading to symptoms may be due to colonisation with pathogenic bacteria, fungus, and/or parasites. Typical symptoms may include diarrhoea, gas, bloating, constipation, reflux, gastritis or abdominal pain. Dysbiosis can be the cause of these pathologies or simply an exacerbating factor.

How to restore a healthy Gut Microbiome:

1) Diet

When we regularly eat a variety of healthy, fibre rich, non-processed foods, our microbiome becomes programmed to work for us. And the more varied our diet, the more flexible and diverse the microbiome becomes. Refined carbohydrates, sugar and processed foods get absorbed quickly into our small intestine without any help from microbes. This results in the gut microbes remaining hungry so they begin snacking on the cells that line our intestines, causing Leaky Gut. Our intestinal lining is meant to be a strong barrier between our gut and the rest of our body. When the intestinal wall becomes leaky, particles of food enter the bloodstream, causing our immune system to attack them, and ultimately our own tissues. This leads to inflammation and a whole cascade of conditions, including autoimmunity. Sugar also feeds organisms like Candida albicans, which attacks our intestinal wall and can lead to a systemic Candida infection.

When we consume raw, organic fruits and plant foods, we acquire a dose of prebiotics, simple carbohydrates, micronutrients, and phytochemicals. Additionally, we ingest food-borne microorganisms, some of which may take up residence in our gut and/or transfer genes to bacteria living in gut biofilms, therefore potentially increasing the biodiversity of our gut microbiota.

Fermented vegetables help to increase the biodiversity of our microbiota. For example sauerkraut, pickles, kimchi, kefir, yogurt (not processed) and kombucha. These probiotic foods are a rich source of healthy bacteria which can colonize our gut and transfer genetic material to microbes that are already established in our intestine.
Prebiotics include types of dietary fibres found in foods like legumes, onions, cabbage, garlic, asparagus, oats, barley and beans. Prebiotics are what fuels the bacteria and creates the environment they thrive in.

2) Adapt a new diet gradually

An inconsistent diet, can wreak havoc on the gut microbiota. The gut microbiome needs time to properly adapt to new foods and so it is better to gradually change our diet by the seasons, than to change it day-by-day.

3) Limit conventional drugs, and bodycare products that negatively impact the microbiome

  • Antibiotics damage the cell membranes of gut microbiota cells, disrupt the normal, protective flora and can also allow for the colonisation of pathogens. Antibiotics decrease microbial diversity in the gut promoting a range of adverse health effects. Some sources suggest that the host’s GI flora is permanently impacted after just one course of antibiotics. If antibiotics are required, it is important to take steps to rebuild the microbiota after the antibiotic treatment is completed. Many other pharmaceutical drugs elicit similar effects.
  • Antibacterial lotions / hand sanitizers and excessive use of liquid soaps or body washes can decrease the microbial diversity of the skin microbiota and may impair the skin’s protective barrier, decreasing our exposure to beneficial microorganisms.

4) Increase time spent in nature

  • By walking in a park, gardening, or simply spending more time in natural environments exposes us to a range of microorganisms. Matter in the air such as pollen carries a load of bacteria. Many airborne particles will therefore be deposited in the upper airways, so that after being carried up the trachea by the action of cilia, they will be swallowed. Therefore, airborne microorganisms end up on the skin, in the airways, and in the gut where they modulate the immune system.

5) Improve the microbiome of your home

  • Traditionally, homes were constructed with timber, mud, animal dung, thatch, and other natural products and were ventilated by outside air. By contrast, modern buildings are constructed with synthetic materials, plastics, and concrete, and the timber is treated with adhesives and biocides, while the buildings are ventilated by air conditioning systems.
  • When these modern structures degrade, become damp, or accumulate condensation in cavity walls, they become habitats for unusual strains some of which synthesize toxic molecules that we are unable to inactivate, ie toxic mould.
  • Chronic exposure to mould-produced mycotoxins can result in a range of health problems, including chronic fatigue, depression, brain fog, sugar cravings, low libido, and muscle weakness.
    Some ways to improve our home’s microbiome is to place plants around the house, replace harsh cleaning products with natural alternatives, and regularly open windows to bring natural light and fresh air into the building.

6) Natural Births and Breastfeeding

  • Evidence has shown that children who are born via caesarean section have a different microbiota than those who are vaginally delivered, and are more likely to develop health problems such as obesity, asthma, allergic disorders, and type-1 diabetes when they get older. These children aren’t exposed to the acid-producing bacteria found in the human vagina.
  • Babies are born with nearly sterile and bacteria-free intestines. Breast milk helps to colonize a baby’s gut flora and nourishes the bacteria to allow it to become established. It also contains an important mix of microorganisms and prebiotic oligosaccharides.

7) Manage stress levels

  • It’s well established in the scientific literature that the bacteria in our gut affect our brain function, stress levels, and behaviour. Conversely, human studies have shown that chronic psychological stress can disrupt the balance of the microbiota, triggering unfavourable shifts in bacterial composition and diversity affecting gut motility, epithelial barrier function, and inflammatory states.
  • Our gut is our second brain. If the microbiome is out of balance, we may feel anxious, depressed, tired and suffer from memory problems or brain fog. In addition to eating the right foods, it is important to remove stressors prior to eating and be relaxed.

8) Exercise in moderate amounts

  • Human studies have suggested that exercise seems to have positive effects on the microbiome, as long as it’s not excessive.
  • A balanced training routine that consists of regular strength training, plenty of low-moderate intensity activities (e.g. walking), contributes to a healthy microbiome.
  • Extreme forms of training, on the other hand, can have detrimental effects on health. Prolonged, high intensity endurance training may induce leaky gut and gastrointestinal distress in many people.