The Microbiome and Your Health

Some of you reading will see the title and think “This is going to be interesting”.  Others will see the title and think “What on earth is a microbiome?”

Let’s start with the basics. The microbiome refers to the collection of micro-organisms that travel around with you 24/7/365.  What kind of micro-organisms you might ask?  Well  . . . bacteria, virus, molds, yeasts, parasites.  And, there are a lot of them!  Different interpretations have been made about the number or volume of micro-organisms that reside in or on the body and this is a bit of an academic argument – however it has been postulated by some that an average human body has about 10 trillion cells.  The amazing thing is that the number of micro-organisms are greater by 10 times! Yes, 100 trillion micro-organisms living in us or on us.  Furthermore, these micro-organisms have their own genes, and the total “genetic pool” of these organisms represents 99% of the genes that we carry around.  That is, your own genes represent only 1% of the total genes that are looking at this article.  This astounding information has led some science editorial writers to ask the question, “Who is in charge here?”  Well, the answer may very well be “the bugs”.  The influence that the microbiome has on health and physiology is constantly being re-evaluated – thousands of peer-reviewed articles are published every year on the relationships that exist between “good” microbiota and “good” health, as well as “bad” microbiota and “bad” health. And when I say health, I mean the health of the heart, lungs, gastro-intestinal tract, immune system, skin, and the brain – really, there are not any tissues in the body that are not affected by the collective influence of the microbiome.

These “bugs” inhabit every square centimetre of our skin, but the bulk of the awareness of the microbiota are toward those bugs that exist in our gastro-intestinal tract. (Note:  Some academics in this field refer to the bugs as being the “microbiota” and the gene pool of the bugs being the “microbiome”.  This is correct from a terminology perspective, and yet most people use these terms interchangeably – you may find me going back and forth – for the purpose of this blog, both terms are being used to describe the bugs and not the genes, unless stated).  The bugs in our GI tract perform all kinds of functions – from producing enzymes and vitamins, to aiding in the digestion of food, to being the “gatekeepers” of the intestinal tract, to stimulating the immune system and a host of other functions.  Now, this is when the bugs that exist are “good guys”.  When the bugs that we have are “bad guys” there are a host of bad things that they contribute to including inflammatory bowel disease, irritable bowel syndrome, poor digestion, food intolerances, food allergies, autoimmune disease, skin disease, hypersensitivity reactions, and brain disease – particularly mood disorders as well as Alzheimer’s and other forms of dementia.  The “take-home” message is that the microbiome has a very significant influence on whether we live healthy or sick lives.

Another interesting point is that every single person on earth has a unique microbiome.  The microbiome is as individual as we are. It has been determined that there are in the range of 1000 different species of bacteria that can inhabit the human GI tract, and each one of us houses 200 to 600 of these species.  Even members of your own family have different microbial flora than you.  The science in this field has been moving at an accelerated pace for 10-20 years and yet there is still a great deal to learn.  One of the more recent findings has been in the area of what makes the microbiota function poorly and what makes it thrive.  What has been known for quite a while is that the use of antibiotic medications wreaks havoc on the flora.  Using antibiotics when they are truly necessary is still an important thing – in some cases, lifesaving.  However, the over-utilization of these drugs is a major issue.  Frustratingly, many people are unaware of the volume of antibiotic medication that is used in food production (animals) and ultimately gets into our food supply, ultimately causing issues with our microbiota.  The simple message is that antibiotics are non-discriminatory – they kill the bad bugs that make us sick and they kill the good bugs that keep us healthy.  With the increasing knowledge about the importance of our intestinal bugs, we are starting to seriously question the use of antibiotics in circumstances other than infectious emergencies.  Other chemicals also have negative effects on the GI flora – these include the non-steroidal anti-inflammatory drugs, herbicides, pesticides, food preservatives, and the list goes on.

What can we do to preserve or improve the microbiota in our gut?  Certainly the utilization of “probiotics” or good bacteria has been a strategy in place for a few decades.  Recently, there has been some debate in the scientific circles about just how much benefit is derived from the consumption of probiotics.  The uniqueness of our flora suggests that there should not be a “one size fits all” probiotic strategy.  This being said, what, then, is the right probiotic for you? Quite honestly we don’t know. What we do know (or at least what the current consensus is) is that we need to promote diversity of the flora. This can be achieved through probiotics by ensuring that you consume as many different species of bugs as you can. Most notably, this includes the consumption of fermented foods.  The other way to create diversity in your microbiome is to consume large volumes of plant material and as many different types as you can.  You see, the best bugs love to eat plants – so, when we eat plants, they (the bugs) eat plants.  When we eat ice cream, the bugs eat ice cream.  Bottom line is this – we have the capacity to influence our own microbiome and therefore to influence our own health.  The microbiome has remarkable effects on how well (or poorly) our body functions and what we put in our mouths has an enormous influence on what type of microbiome we carry around with us.

Dr. Michael Breen is the co-owner of the Chiropractic Family Care Centre and has been in Private Practice in Calgary, Alberta for over three decades.  Dr. Breen graduated from the University of Calgary Faculty of Kinesiology in 1981 (Honours) and from Palmer College of Chiropractic – West in San Jose, California in 1986.  His foundational clinical work is in the field of Health Optimization.  He uses his background in athletics and chiropractic to aid his patients in recovering physical capacity and uses his background in nutrition and functional medicine to aid his patients in the recovery from chronic illness.  He is the co-founder of the Healthy Transformations program.  Dr. Breen can be reached at

The Anti-Inflammatory Food Model

The nutrition model used in the Healthy Transformations Program is called the Anti-Inflammatory Diet.  In a previous blog I outlined the confusion that exists in what appears to be competing nutritional approaches.  It is discouraging for many consumers to be caught in what seems to be a “war of words” between these approaches.  All too often, consumers fall into a phenomenon of “believing” that what they are doing is correct instead of “knowing” that what they are doing is correct.  Please read the blog titled Confused About What To Eat – You’re Not Alone! to come to an understanding of how we ended up where we are.

The Anti-Inflammatory Diet is driven by recent advances in the field of biochemistry, particularly as it relates to how food influences the chemical and genetic function of our body.  It has been known for a number of decades that inflammation is the underlying basis of disease.  What has recently been discovered is the extent to which these inflammatory influences are environmental – meaning, they are the consequence of how we live and how we eat.  There are four primary environmental influences – they are 1) what we eat 2) cellular toxicity 3) overweightness and obesity and 4) free radical influence.  I will make a few comments about items 2, 3, and 4 before we tackle the food influence.

We live in a toxic environment.  The best level of environmental science and toxicology has identified the ubiquitous presence of toxins outside and inside our bodies.  Many of these toxins exist in our homes, where we work and where we go to school.  It is a truly sad state of affairs and yet there is no value in denying the presence nor the influence of toxicity that resides in all of us.  What must be understood is that these toxins have deleterious influences on our health.  The mechanism by which this happens is complex, but fundamentally, cellular toxicity drives the activation of inflammatory cytokines.  The “up-regulation” of these chemicals causes adverse cellular function including adverse signalling to the nucleus of cells ultimately affecting genetic expression.  Reducing toxic burden by effective detoxification processes is a critical step in reducing inflammatory influences.

We also live in a world where the levels of overweightness and obesity have reached epidemic proportions.  So much so, in many countries of the developed world, the number of overweight and obese individuals outnumbers those that are of normal weight.  Think about that.  If you are normal weight in these countries, you would be in the minority as it relates to body fat.  As it relates to inflammation, there are two problems connected to our overweight cultures.  First, because the majority of toxic substances are fat soluble (meaning the toxins will set up shop in the fat cells of our bodies), those with more fat tend to store more toxins.  This is referred to as toxic burden.  Bottom line – more toxins mean more inflammation and overweight people store more toxins.  Second, fat cells produce their own chemistry.  And, much like the influence of toxins, the general effect of fat-based chemistry is to drive inflammation through the action of various inflammatory cytokines.  Therefore, on two fronts, fat accumulation drives inflammatory influences.

Free radicals are the by-product of metabolism.  That is, the basic functions of things like breathing and heart-rate cause the production of free radicals as does exercise and exposure to the sun.  So, what’s the problem?  Well, nothing actually, as long as we have adequate amounts of anti-oxidants to “absorb” the free radicals that are being produced.  So, the problem comes from both sides – if we are producing too many free radicals, or if we don’t have enough anti-oxidants, then the presence of “non-absorbed” free radicals is (you guessed it) a driver of inflammatory biochemistry.  Interestingly, ill-health and disease create metabolic changes that produce increased volumes of free-radicals.  That is, sickness begets sickness.  And, adding fuel to the fire, is the reality that toxic burden drives free radical production.  In a Functional Medicine model, things often go wrong from a number of different (but connected) factors.  In the end, managing free radical production is critical to reducing cellular inflammatory responses.

So, now we get to food and the Anti-Inflammatory dietary model.  I am regularly asked the question “What is an anti-inflammatory diet?” “Is it the same as a Keto diet?”  No, but an anti-inflam diet is somewhat ketogenic.  “Is it Paleo?”  Not exactly, but there are elements of the Paleolithic diet that are consistent with the anti-inflam diet.  “Is it a Low Carb diet?”  Definitely not – in fact it is a high carb diet, but the type of carbohydrates consumed are very well defined.  Is it a Gluten free diet?  Kind of – by default, but not by primary intent. “Well, how would you define it?”  It’s not easy but let me put it this way – The Anti-Inflammatory diet is a high carbohydrate, low sugar, mildly ketogenic, moderate protein, high nutrient density diet.  It doesn’t fit neatly into the diet compartments that we seek or what I call the “Moniker” diets.  I like to say that it is a thinking persons’ diet because there is a requirement to learn about what food truly represents to our physiology.

So let’s look at this one piece at a time.  Why would we want to eat a high carbohydrate diet when the rest of the dietary world is on the low-carb craze?  Well, because over the last 40 years, the scientific world has repeatedly demonstrated that those people who consume plant-based diets are healthier and live longer than those people who do not.  Plain and simple – plants (to the very greatest extent) are carbohydrates and we should eat a lot of them.  Advocates of the low-carb diet will commonly consume as little as 25 grams of carbohydrates per day, and even if this volume were plant based, it is not nearly enough to provide the benefit that plants contribute to our health.  In the anti-inflammatory diet, our patients will consume 140 grams per day of green leafy vegetables and an additional 3+ cups – more than 450 grams – of other vegetables.  This total of 600 grams of plant based carbohydrate is more than most people ever consume per day, but it is foundational to health.  The anti-inflammatory diet is also a low-sugar diet.  Wait a second – I though high carb diets were high in sugar?  Not true if the carbs you eat are low on the Glycemic Index.  This is a VERY important point.  There is a remarkable difference in sugar concentrations between different types of carbohydrates – plants included.  We generally think of sugar in the form of “refined” sugar such as candy and soft-drinks.  However, some carbohydrates such as grains and starches have a Glycemic Index that is nearly as high, and occasionally higher, than glucose.  We guide patients to not fall into the trap of assuming that all plants are OK to eat – this is most certainly not true.  Learning what plants are low on the Glycemic Index is a critical element of the proper application of the anti-inflammatory diet.  Therefore, eating a high carbohydrate, low-sugar diet provides the essential benefits of plants (particularly, high nutrient density and high fibre) without the devastating effects of high sugar.  And here’s the big point – persistently high blood sugar levels have been directly implicated in the production of inflammatory biochemistry that drives disease processes in the body.  Therefore, keeping blood sugar levels low reduces cellular inflammation.

The Anti-Inflammatory Diet is also a Ketogenic Diet, although the effect is what we call “Mildly Ketogenic”.  A full ketogenic diet may have up to 70% of dietary calories provided in the form of fats.  Now, there are a lot of very good reasons to have more calories provided by fats – the big oops in the Keto Diet is that most proponents do not get enough low G.I. carbohydrates with all the benefits that they provide (which was described in the previous paragraph).  So, the most aggressive keto diet will have 70% fats, 20% protein, and 10% carbohydrate.  The Anti-Inflammatory diet will drop the fat volume to around 50% fat, with 20% protein, and 30% carbohydrate – but remember, all of those carbs are green leafy, and other low G.I. vegetables.  The data on the Keto influence is growing rapidly.  Certainly, fats are more energy efficient – we need less of them to provide the same caloric value.  Fats (when converted to Ketones in the liver) burn more efficiently and therefore produce fewer free-radicals in the energy production aspect of our physiology.  It has been demonstrated that our central nervous system (brain and spinal cord) are better adapted to burn ketones for energy than previously thought.  This is big news – because higher blood sugar levels in the brain (from high sugar diets) is now being seen as the initiator of cellular inflammation in the brain which drives dementia and Alzheimer’s.  In fact, it has been demonstrated that aggressive Ketogenic Diets may be a contributory factor in the recovery from concussion.  The overall message is that we must eat more fats than we have been told in the last 50 years.  Eating fats do not make you fat.  And, eating fats do not cause cardiovascular disease.  Sugars make you fat, and sugars cause cardiovascular disease (and a whole bunch of other bad things).

The body needs proteins for growth and cellular repair.  How much protein is required for this function has been under debate for a long while and there are many “camps” in the debate.  The very best science has come to the conclusion that in almost all circumstances (including athletes), the volume of protein in the diet does not need to be more than 20%.  There have been a lot of interpretations on how much this means, but the consensus is that we do not need more than 1 gram of protein per kilogram of body weight per day.  This is where the “Paleo Diet Gone Amuck” comes into play.  The biggest mistake of the Paleo diet is that some of the proponents have come to incorrectly assume that the diet encourages sky-high volumes of protein.  This is not true.  One of the reasons that we should be mindful to not eat too much protein is that high levels can contribute to pulling us out of a ketogenic state (which I just described as being very beneficial).  Fats and proteins commonly co-exist in foods – particularly in animal products.  If the attempt to become ketogenic is through the consumption of large volumes of flesh, you may not be getting the effect you are looking for.  The best way to become ketogenic is to stick with the model of 20% protein in the diet and to increase the plant sources of fats such as olive oil, coconut oil, and other medium-chain triglycerides.

Nutrient density is not a common term these days when it comes to the lexicon of diets.  However, high nutrient density is fundamental to health.  In the overall diet debate, too much time has been spent talking about calories from food.  To the body, having lots of calories in food without high nutrient content is like a car having lots of gasoline but no wheels or tires.  It looks like a car and sounds like a car but when you hit the gas, it doesn’t perform too well.  We need to be much more attentive to the nutrient value that we get from food.  The nutrients are the “language” of food – they speak to our cells.  So much so, that if the language of food is clear, we have the capacity to influence positive genetic expression.  Did you hear that?  Getting higher volumes of high nutrient dense foods allows our genes to keep us healthy!  This is very big stuff and is a fundamental emphasis of the field of epigenetics.  Now, where do we find the foods with the highest nutrient density?  You guessed it – vegetables and fruits that are low on the glycemic index.

At this point, I hope you can now see how it all comes together with the Anti-Inflammatory diet.  It stands alone as a dietary model, and yet it has components of other “popular” contemporary models.  In my opinion and when applied correctly, these other models are helpful and will improve the health of their devotees.  However, the Anti-Inflammatory diet considers the best of each of them and is consistent with the current best knowledge in dietary science.

Dr. Michael Breen is the co-owner of the Chiropractic Family Care Centre and has been in Private Practice in Calgary, Alberta for over three decades.  Dr. Breen graduated from the University of Calgary Faculty of Kinesiology in 1981 (Honours) and from Palmer College of Chiropractic – West in San Jose, California in 1986.  His foundational clinical work is in the field of Health Optimization.  He uses his background in athletics and chiropractic to aid his patients in recovering physical capacity and uses his background in nutrition and functional medicine to aid his patients in the recovery from chronic illness.  He is the co-founder of the Healthy Transformations program.  Dr. Breen can be reached at