A Depleted Microbiome May Be the Source of Your Ailments – 10 tips to improve it

Jun 29, 2024

I’ve been talking about bugs a lot lately. Not the kind with wings or that you might find crawling under a rock but the teeny tiny kind that we can’t see without a microscope. Maybe because they are so small we don’t think of them very often but it turns out these microscopic organisms may hold the key to health or sickness in all of us.

My recent conversations have been as varied as asthma in a toddler, diabetes in a friend, diarrhea after a bout of pneumonia, recurring colds, high cholesterol, Crohn’s disease in a pre-teen, high blood pressure, Parkinson’s, Alzheimer’s and autism. What do all these seemingly diverse issues have in common? There is evidence showing a depleted microbiome plays a role.

What is the Microbiome?

Taking a bit of a step back in case this is new to you, the microbiome is simply all the bacteria, fungi, viruses and other microorganisms that live in and on you. Ever since Louis Pasteur introduced the germ theory of disease back in the 19^th century we have been focused on all out war against these bugs. However we now know that reality is far more complex.

Estimates vary widely but the most recent accurate assessments show while there are about 30 trillion human cells in a typical adult, there are probably nearer 40 trillion cells that belong to various microorganisms living symbiotically with us. Original estimates stated there were probably 10 times as many non-human cells in our body but we now have more accurate calculations providing this 4:3 ratio.

It might be mind-boggling to you to think our bodies are more non-human than human but I would have you zoom out from your body for a minute and take a look at the world around you. Take a walk outside particularly in a park or garden area and see how many of those flying and crawling bugs there are in nature compared to plants, trees and animals, also living symbiotically with each other. Our attitude to bugs really needs to change.

While we’ve identified many pathogenic bugs over the years (those that cause illness) there are many thousands more that are not only beneficial to our bodies but essential to their healthy functioning

The study of the microbiome is one of the hottest specialties in medicine right now but it is still in its relative infancy. In fact it’s estimated that we have no idea what 95% of the microorganisms that make up the microbiome do. We do know that a fraction of 1% is likely to be pathogenic and even then it’s the balance and the diversity of all the different organisms that seems to lead to health versus illness.

Those bugs that have been identified and studied have been shown to be involved in a huge range of bodily processes such as immunity, metabolism, hormone regulation and neurological function. One major role of the largest colony that inhabits us, those in our gut, is to create Short Chain Fatty Acids (SCFAs) which are anti-inflammatory and needed to control the fires that burn within us as we deal with everyday toxins and pathogens. But SCFAs are only created if we feed our bugs well. They like plenty of fiber from plants.

Many diagnosed diseases are now being tied to a depleted microbiome. A single course of antibiotics is enough to wipe out up to 1/3 of your flora and it is not easily restored. Serial antibiotics for ailments like acne, ear infections, or recurring urinary-tract infections are particularly detrimental to overall health.

The malleability of your microbiome is tremendously complex and not yet well understood. What we do know is that it builds from birth and is impacted greatly by what type of birth you had and whether or not you were breast-fed as to how much flora you accumulated from your mother. From there your own personal experiences will influence its development in terms of what you eat, your social interactions (how many other microbiomes you interact with), how much time you spend in nature and what insults you encounter like antibiotics as well as pesticides and preservatives found in food. Remember preservatives are made to stop food spoiling through bacterial growth and sugar is a key preservative.

Your microbiome can be manipulated over weeks or months if your circumstances or lifestyle changes. There’s no “silver bullet” though and even the promise of precision medicine is unlikely to find instant cures for a body out of balance as it is the highly complex interaction of your human genome with the diversity of your microbial genome (collectively at least 200 times bigger) and your personal lifestyle that make the difference.

10 Tips to Improve Your Microbiome

Eat more fiber. You know you’re supposed to eat more plants but it’s not just to absorb all those vitamins, minerals and polyphenols they contain. It’s to feed your microbiome so your bugs can work to keep you healthy.
Avoid taking antibiotics or other prescription drugs. Try natural antimicrobials first like raw honey, oregano oil, garlic, tea tree oil, unrefined coconut oil or for respiratory infections nebulized hydrogen peroxide. These natural substances are “smart” enough to work with the body and kill only the pathogenic bugs.
Limit your intake of processed food. Shelf-stable food is full of preservatives to stop bugs growing and that is exactly what they do in your body. Sugar is a natural preservative and will kill off the good guys letting pathogenic bugs thrive.
Eat only organic food that has not been dosed with pesticides or other antimicrobials. Glyphosate is a major culprit used widely in the US (but banned in many other countries). Originally developed as an antibiotic it is used extensively in farming and sprayed on wheat just before harvesting to kill it so it dries better for storage. Implicated in the rise of Celiac disease and gluten sensitivity but also detrimental to our microbiome.
Take a high-quality probiotic daily. One that is certified to contain a minimum of 30 billion organisms with 10+ different strains by the time you ingest them. More may be needed if depletion is severe. Not a silver bullet and questionable how effective it is at making permanent changes to your microbiome but a useful strategy nonetheless.
Add fermented foods to your diet such as sauerkraut, pickles, olives, kefir and unsweetened yogurt. This is how traditional cultures have eaten for gut health with the added bonus of preserving food. Just about anything can be fermented but make sure a salt-brine is used with no pasteurization. The Fermentation Association has great information to get you started.
Get more sleep. While not yet fully understood it is clear that poor sleep patterns disrupt your microbiome. It is a bidirectional relationship such that a healthy microbiome can improve your sleep. Aim for 7-9hrs a night for most people in a cool, dark, quiet room.
Manage your stress. Physical and emotional stress has been shown to deplete your microbiome. Consider meditation, tapping (EFT), yoga or other practices known to reduce stress and encourage your microbiome to flourish thus reducing inflammation.
Exercise regularly. Studies have shown interesting codependences between the microbiome and exercise such that exercise causes your microbes to make more butyrate (a SCFA critical to digestion, insulin sensitivity and mood regulation) but the microbes also stimulate your nervous system to promote the desire to exercise more. So just get started with something you enjoy.
Embrace nature. Useful to incorporate in #8 and #9 but also think about playing in the dirt and getting sunshine on your skin. Even in itself just being out in nature supports a healthy and diverse microbiome.

This is a rapidly evolving area of medicine. Here’s a couple of recent journal articles for those who want to dig further.12

The Healthy Human

Discussion about this post