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The microbiome


Our gift to them.


The good guys and bad guys.


Their gift to us.

Doctor's orders

My plant prescriptions for a glorious flora.

The microbiome 


The gut microbiome represents the total genes that are represented by our diverse and abundant gut micro-organisms.  The microbiota is a term used to describe the microorganisms themselves.  The two terms are often used interchangeably, but we'll use microbiome for simplicity's sake.

The gut microbiome includes the bacteria, the yeasts, the viruses and archaea that reside in our colon.  Although it has been ignored for the last thousands of years, it's now that we recognize that our gut lining, and the bugs it contains, is by far our largest point of contact with the outside world.  We carry over 2 kilograms in bacteria, which is heavier than most organs.  The large quantity of genes in our gut bugs explains why we have delegated the digestion of over 300000 edible plant's fibers to our gut bugs.  We simply don't have enough genes to code for all the enzymes necessary to digest all those different types of plants which all contain multiple different types of fibers.

We have a pitiful 16 Glycoside Hydrolases, the enzymes that break down fiber.  Sixteen!  There are over 60000 bacterial Glycoside enzymes in our microbiome that help us digest fiber.  The genome of our gut ecosystem is 150 times bigger than ours, and we absolutely rely on our gut bugs to do most of our food processing.  

In the last 4 years only, over 13000 studies have been done on our gut microbiome, which makes up for over 80% of the research that has been published since 1977.  We are only now discovering how a healthy gut flora can improve health in general.  On the flip side, we are also learning more and more about Dysbiosis.  This refers to the state of our microbiome where there is loss of the beneficial or good bugs, at the expense of an increased proportion of bad bugs.  Where there is dysbiosis, there is loss of the beneficial compounds produced by our gut bugs that feed on fiber.  Then, while feeding on unhealthy food we consume, the bad bugs release noxious chemicals that create gut inflammation and make the gut lining more permeable (thus the term "leaky gut").  This hyperpermeable, or leaky, state creates openings where inflammatory compounds can enter the bloodstream, contributing to inflammatory, auto-immune, allergic and other chronic diseases.

Diseases like IBD (inflammatory bowel disease), Crohn's or ulcerative colitis, asthma and allergies have all been traced back to dysbiosis in the gut.  We also have lots of research linking dysbiosis with the following conditions:

  • Obesity

  • Diabetes

  • Metabolic syndrome

  • Anxiety, stress, ADHA

  • Cardiovascular disease

  • Allergies

  • IBD, IBS (irritable bowel syndrome)

  • Cancer

The connection between our gut bugs and our health is simple.  Our bugs (let's call them probiotics), eat food (called prebiotics: fiber, resistant starches, polyphenols and omega-3s) and in return produce compounds (let's call them postbiotics) that either benefit us or harm us.  If we feed them good food (fiber filled plants), they produce beneficial compounds, like short-chain fatty acids and anti-inflammatory cytokines, and if we give them CRAP (calorie rich and processed) foods or animal products, they produce harmful compounds, like TMAO and pro-inflammatory cytokines, that contribute to chronic disease, food intolerance, allergies, and loss of the integrity of the intestinal lining.

So this equation represents very well what's going on in our microbiome:

Prebiotics (food) + Probiotics (bacteria) = Postbiotics (beneficial compounds)

In the next sections, we'll break down these three elements so you can really grasp the impact that our microbiome has on our health, and how we can nourish it.



Prebiotics are the gut bug's food.  In more technical terms, they're chemical compounds that promote reproduction and activity of our gut microorganisms.  Our gut bugs mainly feast on fiber from our foods, but they also like to chow down on resistant starches, phytochemicals from plants, phenols and omega-3s.  When we feed them good food, they feed us with great postbiotics that enter the bloodstream, reach distant organs and even cross the blood-brain barrier.  In this section, we'll review the different prebiotics that our gut bugs like to feast on.


For an in-depth look at fiber, jump to the For Nerds' section on Carbs.  They exist solely in plants.  No animal products contain them.  The fiber's polysaccharide links are hydrolysed by an enzyme called Glycoside Hydrolases.  The human genome has 16, while there are many hundreds of thousands of different types of dietary fibers.  Gut bugs to the rescue.  They contain over 60000 of these enzymes and help us digest fiber.  Although we likely evolved from eating over 100 grams of fiber per day, the RDI is a small 30 grams per day, and most people (over 95%) don't even make it to that amount.  We are starving our microbial self.  Good gut bugs disappear with the beneficial postbiotics they produce, and soon follow the chronic health conditions associated with dysbiosis.  The conclusion, the more plants there are, the more fiber there is, and the healthiest we'll be.

Resistant starches

Although fiber is the microbiome's preferred fuel source, resistant starches can still be used.  They behave like soluble fibers and provide a food source for our good bacteria.  They can be found in green bananas before they ripen, in potatoes, sweet potatoes, beans, chickpeas, oats, peas, lentils, nuts and whole grains.  Basically from plants.  They're not found in abundance in any animal product.


These compounds confer some of the plant's colours and most make their way to the colon untouched.  They're metabolized by gut bacteria and the chemical compounds they produce in return are highly beneficial to our health.


Nuts and seeds provide lots of nutrition.  Even after chewing, microscopic pieces find their way to our colon where they nourish the good bugs, the ones capable of producing beneficial postbiotics.  The whole food versions feed our gut, but processed versions such as nut butters or oils, are already processed to a point where they are already fully absorbed by the time they make it to our colon.


When talking about probiotics, we are talking about the bugs themselves, the producers of the biotics.  We have three large species, or enterotypes, of gut bugs:

  • Firmiticutes (the grain lover)

  • Prevotella (the veggie muncher)

  • Bacteroides (the western gourmand)

The good gut bacteria are always competing with the bad ones for colon real estate.  The good bug species, Firmiticutes and Prevotella, produce beneficial compounds called postbiotics.  The bad bugs in the Bacteroides family produce TMAO, biliary salts and other pro-inflammatory compounds after feasting on our processed and animal-product containing western diet.  As you may have already guessed, the good bacteria thrive on a plant-based diet, while the bad thrive on a fiber depleted animal based diet and CRAP diet (calorie rich and processed).  The goal should always be to have as many different species of good bacteria as possible, since different species produce different postbiotics, all with different metabolic advantages.

Probiotics are also often seen as part of oral supplements and can help supplement and provide a headstart to your depleted microbiome.  The thing is, even if probiotics sound like a good idea, supplements only contain a small number of species, often bifidobacterium and lactobacillus, compared to the innumerable species in your gut.  Also, these new probiotics will only survive the digestion process in small numbers, and then must be fed a fiber rich diet to thrive and survive.  So taking a probiotic and then eating an animal based diet is a waste of time and money, and the bacteria will quickly die off.  Probiotics aren't a silver bullet.  You won't see any major health changes immediately.  Keep in mind that it takes at least 1-2 months before the new populations of bacteria can self-sustain, and they'll require a healthy fiber rich diet to do so.  The amount of postbiotics getting produced will then increase, and only then will most notice the benefits.

If you are gonna take probiotics, here are a few of my suggestions to choose the right ones:

  • Make sure they contain at leaset 25-50 billion CFU (colony forming units)

  • Refrigerated ones are more reliable

  • Use those with many different bacterial species

  • Delayed-release capsules may help more bugs survive the trip to your colon

  • They have a limited life span, so use before they expire




Postbiotics are the beneficial compounds produced by bacteria that feed on prebiotics.  The most popular and studied group of postbiotics are the SCFA (short-chain fatty acids).  Three SCFA, acetate, propionate, butyrate, are released by probiotic bacteria, then these beneficial compounds play major roles in decreasing gut inflammation, maintaining gut lining integrity by increasing thickness of the gut wall mucus layer, while others pass through to the bloodstream where they find target organs at a distances and exert their beneficial and health promoting effects.  In the next section, I'll elaborate more on how the SCFA affect individual target organs everywhere in our bodies.

The digestive system

Inside our gut, SFCA produced by probiotic bacteria will:

  • Increase colic pH, making its environment safer for good bugs, while suppressing the growth of the bad ones

  • Butyrate, one of the 3 SCFA, provides 70% of the energy used by colonocytes, the gut wall's cell lining

  • Increase gap junction protein synthesis, increasing wall integrity and making it less "leaky"

  • Decrease endotoxin entrance in the bloodstream 

  • Increase intestinal motility

Cardiovascular system

SCFA will have direct and indirect effects on the cardiovascular system through many mechanisms:

  • They provide a second meal effect, where they decrease subsequent calorie intake at the following meal, and protect against obesity

  • The increase ileal brake, by slowing down gut motility and making you feel fuller longer

  • They increase insulin sensitivity

  • They decrease liver and peripheral fatty acids

  • They decrease cholesterol synthesis

  • They increase secretion of cholesterol in bile

  • They promote leptin (decreases appetite) and inhibit ghrelin release (increases appetite)

  • Decreased production of pro-inflammatory TMAO

  • Decrease intestinal hypersensitivity and pain


SCFA will cross the blood-brain barrier and:

  • Slow the production of toxic amyloid

  • Potentially slow down the appearance of Parkinson's disease (currently being studied)

  • Potentially help ADHD management


SCFA have multiple effects on our immune system, like:

  • Decreased production and release of pro-inflammatory cytokine production, including passage from gut lumen to blood stream

  • Decreased food intolerance

  • Decreased food allergies

In summary, there's a lot of great information on SCFA.  We know of lots of its benefits, but there's even more we don't know.  Huge corporations are already trying to bottle SCFA in pill form, to be sold to the masses, but Mother Nature already figured all of that out for us.  It's in our plants.  Eat fiber rich plants and the bacteria in our gut will give them to us for free!  The plant-based diet is the ideal and evidence-based diet to feed our friendly flora, increasing their output of health promoting SCFA postbiotics.

A word on fermented foods

Fermented foods are all the rage lately. Kombucha has gained popularity as a healthy way of populating your microbiome.  All fermented foods have beneficial bacteria and yeasts that produce powerful nutrients in return for the sugars they ferment.  Fermented foods contain not only beneficial bugs in them, but also have vitamins, antioxidants, beneficial acids, like vinegar, and have a great combination of synbiotics (combination of prebiotics and probiotics in one).  Here are examples of fermented foods that you included in your plant-based transition:

  • Sauerkraut

  • Sourdough

  • Kimchi

  • Kombucha

  • Tempeh

  • Miso

By now you should be well aware that to have a high-end microbiome, you have to eat a fiber rich plant filled diet.  The probiotic bugs in your colon will feast on the prebiotics in your diet, then reward you with beneficial postbiotics, primarily the beneficial SCFA that will reach every single nook and cranny of your body.  If your diet is great, your microbiome will be great, and your poops will be awesome!

Doctor's orders

doctor's orders

At this point, you know that the secret to a great disease fighting and health promoting microbiome is your diet.  A diet rich in fiber, resistant starches, plant polyphenols and omegas from nuts is the evidence based way to take your poops to the next level.  The good bacteria will feed and reward you with healthy SCFA.  These powerful compounds will pass through to the bloodstream and even cross the elusive blood-brain barrier to help prevent and reverse chronic disease.  The best marker of a healthy microbiome is gut bug variety, and the best predictor of a healthy microbiome is plant variety.  Read that again.  Not plant quantity, but plant variety.  Experts recommend that people wanting a top level microbiome eat at least 30 different types of plants per week.  Each plant has a different and distinct type of fiber, which in turn feeds a different and specific type of bacteria.  Variety is the spice of life, and the maker of a great microbiome.

Organic food is also a great way to adopt the plant's microbiome as your own.  Yup that's right, even plants have their own microbiome.  Pesticides, while increasing crop yields by decreasing pest invasion, kill off the beneficial bacteria in the plants.  Some of these pesticides, like glyphosate (Round Up), act as an antibiotic that decreases the beneficial bugs on the food we eat.  Studies have also shown that these pesticides find themselves in our food chain, are ingested, and wreak havoc on our gut microbiomes.  So try to eat organic when you can, and your gut bugs will thank you.

Fermented foods are also a great way to bump up beneficial bacterial counts.  Check out kombucha, tempeh, kimchi and other cultural food staples, and see how you can add them regularly to your diet.

The plant-based diet, the diet we evolved with for millions of years, just so happens to be the one that will provide optimal health for us, our kids, our planet, our microbiome, our values and animal ethics.  Coincidence?  I think not...

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