how to improve your mircobiome

What is Microbiome and How You Can Strengthen Your Mircobiome

There is an organ in our body that is essential for life but invisible. It is not visible on x-rays or MRIs and can only be seen through a microscope.

Introducing… your microbiome.

Your microbiome is a massive collection of 100 trillion microorganisms that live in, and on, our bodies. To give you some perspective on this, you only have around 10 trillion human cells.

We’re outnumbered ten to one!

They work synergistically amongst themselves, and with us, playing an integral role in the way our bodies function. They’re everywhere; on our skin, in our nose, mouth, eyes, ears, literally everywhere with the largest numbers found in the large and small intestines. Because of its many roles in supporting the smooth running of the human body, the microbiome is also labelled as supporting organ.

They are essential for our health, and it is not an exaggeration to state that

They do all sorts of things you’d never expect. They stimulate immune response, help in breaking down large food compounds and even synthesize vitamins and amino acids. Some of their lesser known functions include helping you manufacture vitamins, helping to regulate your blood pressure, making all the chemicals that float around in your blood, as well as being involved in the control of many features of pregnancy.

A healthy person’s microbiome will protect them from pathogenic organisms, such as those that have been introduced to their bodies through ingestion of contaminated water or food. Without them we’d get very sick, and may not even survive.

You’ll hear these microorganisms (bacteria, and yeasts for example) referred to collectively as your “microbiome”, “inner ecosystem”, or “micro flora”.

Regardless, hopefully you can agree, that it’s no exaggeration to say they’re essential to our health.

Even if the thought makes you squirm, the fact is, we need them, and they need us. Which begs the question, maybe we should be actively taking care of them?

Get a daily dose of fermented foods

This allows you to inoculate your body with beneficial bacteria daily. It helps you cope with everyday stresses that can have a negative effect on your beneficial bacterial population. There are hundreds of strains in our digestive tracts so a probiotic is not enough. You need to learn how to make kombucha, water kefir, sauerkraut, as well as how to ferment almost any vegetable out there. The benefit of consuming a wide variety of ferments is you get a wide variety of strains that your digestive tract in particular just loves!

Avoid anything “anti-bacterial” like the plague

You’ll often see these labels on hand soaps, cleaners, and detergents. Look out for ingredients like Triclosan, Triclocarban/Trichlorocarbamide and PCMX/Chloroxylenol on labels. Really though, the term “anti-bacterial” tells you everything you need to know.

Save antibiotic use for emergencies

Use antibiotics only when there is no other choice. Broad-spectrum antibiotics such as amoxicillin can inadvertently kill large parts of the microbiome. Some beneficial bacterial species simply never recover.

If you find yourself facing a round of antibiotics, follow the protocol that will help reduce (but not eliminate) the negative impact these medications have on all your beneficial bacteria.

Exposure to just one course of antibiotics under the age of one, can have lifelong consequences

Likewise, if you have kids, don’t race to the doctors demanding antibiotics when your kids get sick with things like sore throats, ear infections, and bronchitis. Here’s some food for thought from Dr. Martin Blaser, Director of the Human Biome Project at NYU, and author of the book “Missing Microbes”:

60-80 percent of kids who currently are taken to the doctor by their parents complaining of bad sore throats or ear pain walk out with an antibiotic. And most of the time the doctors have no idea if the illness is caused by bacteria or a virus.”


Upper respiratory tract infections are mainly caused by viruses. More than 80% of them can be traced to microbes with exotic names like rhinovirus, astrovirus, metapneumovirus, and parainfluenza.”

Exposure to just one course of antibiotics under the age of one, can have lifelong consequences. This is scary, but knowledge is power. If you’d like to read more on this, check out Dr. Blaser’s book “Missing Microbes”. I highly recommend it!

Avoid conventionally raised meat, poultry, eggs

70-80% of antibiotics are used to fatten up animals for slaughter, and residual amounts of these can be passed onto you. This is why I recommend you avoid conventionally raised meat, poultry, and eggs.

Avoid farmed fish

Unfortunately the same is true here, as with conventionally raised meat, poultry, and eggs. I recommend choosing wild, sustainable caught fish to avoid this potential antibiotic exposure.

Read also: Eat Real Food That Is Good For You

Don’t be so clean!

Our crazy cleanliness has been connected to the demise of our microbiome. Let your hands get dirty, and let your kids play in the dirt. It’s also recommended to spend time in contact with pets, as well as other animals (like you might on a farm).

Eat organic fruits and vegetables

Eat organic vegetables, and wash them in water, rather than sanitizer. The main principle behind the organic farming system is to look after the health of the soil, and surprisingly this soil is an excellent source of bacterial exposure for us. If you’re on a budget, I suggest you follow the Environmental Working Groups Shopper’s Guide to Pesticides in Produce (also known as the “Clean Fifteen, and the Dirty Dozen”) to help you to prioritize your organic purchases.

Eat a wide variety of fruits and vegetables

Eat a variety of fruits and vegetables as they have fermentable fibres. These are found mainly in soluble fibre, but also somewhat in insoluble fibre. These fermentable fibres are food for the beneficial bacteria in your digestive tract, and we all need food! A wide variety of fruits and vegetables will help you get an equally wide variety of different kinds of fibres (even beyond soluble and insoluble), that all bring unique health benefits.

Read also: Fibre – What You Need To Know About It

Avoid consuming too much sugar

I’ve been talking a lot about all the good bacteria up until now. Well, of our bacterial population, about 80% is considered “good”, and 20% “not so good”. We can never get rid of the bad guys entirely, but that’s ok so long as we keep them in check. As much as loosing bad bacteria to antibiotic use is bad, a shift in a balance in our bacteria can have negative consequences too. Sugar is the ideal food for those bad bacteria, so a diet high in processed sugars can encourage them to increase in population, causing health problems.

Be wary of some natural anti-microbial supplements

Don’t over-do the natural anti-microbial supplements

Don’t get me wrong, I’m all about the natural solutions for things, but there’s a BUT. Be wary of some natural anti-microbial supplements like the incredibly potent oil of oregano. While it’s very effective in acute situations (like a cold), it should never be taken long term for prevention as it can be detrimental to your gut flora. If you already know you have an imbalance in your gut flora, you should be extra cautious and probably avoid it entirely.

Avoid long-term medication use

While this may not always be in your control, it’s always worth considering the root cause of your health issues, and addressing those in the hopes you can reduce, or eliminate a chronic reliance on medication. All long-term medication use will have a negative impact on your gut flora in particular. If this applies to you, pay particular attention to your gut flora, and digestion in general.

Wherever possible, avoid the use of c-section

This is for future generations. Your baby is sterile in the womb, but its first inoculation of beneficial bacteria comes through exposure to fluids during a traditional vaginal birth. We literally pass our microbiome onto our kids, and this is the first step in the process. If you have a c-section however, your baby’s first bacterial inoculation comes from the hospital surroundings.  How you avoid a c-section is far beyond my scope of practice, but I do love the book “Gentle Birth, Gentle Mothering” by Dr. Sarah Buckley, if you’re interested in reading up on it.

Wherever possible, breastfeed your kids

Breast milk is an important transport system for beneficial bacteria from mother to baby. This simple act can have a lifelong impact on your child. Again, the book “Gentle Birth, Gentle Mothering” by Dr. Sarah Buckley, is a great book to introduce you to this concept. Remember that when your kids are on solid foods, fermented foods are great for them too! Start them on this good habit while they’re young.

The moral of the story? Being healthy, means you have to take care of your microbiome as well as yourself.