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The Tiny World Within

The essential yet invisible microbiome


The Tiny World Within

The microbiome, the collective term for the dense, interconnected bacterial community in our digestive tract, is not simply history’s most successful hitchhiker. Far from being a passive parasite, this living web is an active and dynamic player in our overall health.

The first seeds of bacterial life are sown long before birth. From that point forward, our microbiome evolves with the influences of environment, diet, medications, and even stress. Age, sex, body weight, and genetics all shape the vast biological world within us.


Why does flora matter?

Dr. Jordan Sokoloski, a naturopathic doctor in Thunder Bay, Ontario, sees many patients with digestive issues. “The microbiome is so critical to digestive health overall,” he says. While our food is initially broken down by teeth, muscles, and enzymes, bacteria complete the transformation to absorbable nutrients, even adding in some self-made vitamins along the way.


Magical metabolites

Our microbiome performs vital functions beyond simply processing our kale salad. When our bacteria break down food, tiny nutrient-derived compounds called metabolites are formed that act both within the gut and throughout the rest of the body.

Short-chain fatty acids (SCFAs) are produced when we digest fibre. SCFAs feed and reinforce the walls of our intestines, blocking the passage of food and bacteria into our circulation. This tight barrier is a gatekeeper, preventing inflammation and infection from developing in the body.

The impact of SCFAs and other metabolites goes far beyond the confines of the intestines. The cells of our body are in constant communication with the microbiome through messages transmitted by compounds such as SCFAs.

Cellular dialogue between our gut and immune system shapes our response to dietary and environmental triggers, helping to prevent the onset of allergies and autoimmune disease. Metabolites have equally important effects on our metabolism, our hormonal production, and our inflammatory responses.


The microbiome and the mind

Our guts have earned the moniker “the second brain” owing to the digestive arousal accompanying a big presentation, a transatlantic flight, or a marriage proposal. Neurological ties to the digestive tract, or perhaps more specifically, to the microbiome, may be quite binding indeed.

Digestive disturbances exist alongside brain-related conditions such as Parkinson’s disease, autism, and anxiety. This coexistence of digestive and neurologic concerns is not just a coincidence. Bacterial metabolites may explain this connection.

Lipopolysaccharides (LPS) are brain-damaging substances made by certain gut bacteria. These toxins have been found in the brain tissue of people with Alzheimer’s disease. LPS are also present in people with inflammatory bowel diseases who, coincidentally, are themselves at higher risk of developing Alzheimer’s disease. Could our gut flora be making us sick?


Cardiovascular connections

Heart disease is another forum where bacterial activity may be important. Trimethylamine-N-oxide (TMAO) is produced when we eat meat. People with higher levels of TMAO may be at higher risk of atherosclerosis and of cardiovascular disease in general.

Other metabolites are much more co-operative. “Why is a high-fibre diet so important for decreasing cardiovascular risk?” asks Sokoloski. He points to the cardiovascular benefits of SCFAs—the intestinal defenders described above.

Dietary fibre is known to mop up excess cholesterol in the blood, but the SCFAs produced through fibre digestion may provide extra help, suppressing inflammation, improving cholesterol numbers, and decreasing the risk of atherosclerosis. These metabolites are another link in our understanding of diet and disease.


Feed the bugs (and try not to kill them)

If the microbiome is so vital to health, what can we do to protect it? Factors such as genetics and age are beyond our control, but dietary choices can modify the microbiome in as little as 24 hours. However, these shifts are quickly reversed if diet changes are not maintained.

Our flora may be as individual as our fingerprints, meaning there is no single optimal bacterial composition suitable for everyone. Much like a streetwise tomcat, a genetically unique and diverse microbiome is the most resilient. A flexible and complex digestive community is created and sustained by eating a wide variety of foods.

Sokoloski emphasizes feeding beneficial flora with inulin-containing foods such as garlic, onions, artichokes, and oats. These high-fibre foods drive the production of anti-inflammatory SCFAs while reducing harmful LPS levels. Fermented foods such as kefir, sauerkraut, and kimchi are naturally nourishing for the microbiome.

It’s equally important to avoid negative influences. Limiting use of antibiotics, antacid medications, and laxatives can preserve bacterial populations. Being proactive in our efforts to reduce stress, sedentary living, and environmental exposures can prevent further harm to our precious microbial cargo.


Supplemental support

To help the gut through periods of challenge, supplemental probiotics could be considered. Although probiotic supplementation can cause measurable changes in the composition of our microbiome, these changes do not seem to be permanent.

While the strains themselves may not persist, improvements to symptoms such as bowel disruption or psoriasis may last for many months after stopping probiotics. One strategy for probiotic use may be to take them in periods of stress or medication use, or when symptoms re-emerge.

Digestive bacteria and their metabolites communicate with every system in our bodies, influencing and even directing the workings of our cellular processes. This interplay of flora and function may lead to new insights and creative options for optimizing our health.

When should I take my probiotics?

Some bacterial species seem to have slightly higher survival odds when paired with food, but this may not affect how they work in your body. Take your probiotics any time of the day and help them survive their digestive journey by choosing products with an acidity-shielding enteric coating.

Fighting bugs with bugs

Salmonella enterica Serovar Typhimurium, a harmful strain of digestive bacteria, needs iron to survive. Researchers have found the beneficial strain, Escherichia coli Nissle 1917, can gobble up iron in the digestive tract faster than S. enterica. Scientists have exploited this iron-grabbing tendency by giving extra E. coli to mice, shutting down the growth of the harmful bacteria.

Flora facts

  • Over 8,000 strains of bacteria have been identified in the human digestive system.

  • We have as many bacterial cells as cells in our body. The total weight of flora in a 154 lb (70 kg) person is about 1/2 lb (225 g).

  • There are about 1 trillion bacteria for every millimetre of our colon.



No Proof

No Proof

Matthew Kadey, MSc, RDMatthew Kadey, MSc, RD