The Human Microbiota

I’ve always wondered why if humans are so similar in our genome, we are so different when in comes to our biological manifestation.  For example, our differences in food tolerances, allergies, metabolism, etc.  The Human Genome Project found that humans are 99.9% identical in terms of genes.  That means the genetic difference between you and the person standing next to you in the grocery line, gas station, bookstore or at work is a mere tenth of a percent.  And our nearest genetic relative, the chimpanzee, has a 96% similarity to us genetically.  I don’t know about you but I find that fascinating.

What are we made of?

So again, I’m wondering how we can be so alike, and yet so different.  Let’s put this in perspective by looking at the humane microbiota.  First, let’s define a microbiota.  The medical definition of a microbiota, or microbiome, is “the microorganisms that typically inhabit a particular environment, such as the soil, a body of water, or a site on or in an organism, considered as a group.1

Microbes are single-celled organisms often times found in a colony of cells.  The five main groups of microbes are bacteria, viruses, fungi, algae and protozoa.  Our gut is mostly bacteria, along with viruses and fungi.  When we look at the human ecosystem – our human cells combined with the microbes we play host to – the microbe cells outnumber human cells by a count of 10:1.  When we take this to the gene level, human genes are outnumbered by microbe genes by a count of 100:1.  Every human is made up of 10 trillion human cells and 100 trillion microbial cells.  That means 90% of the cells in or on our bodies belong to microbes.

Why does this matter?

What is the significance of being only 10% human?  Well, the world is mostly microbial.  We could not function, or survive, without this microbial community – be it the ones living on our skin, in our ears, mouth or gut.  Microbes evolve much more rapidly than humans and perform many tasks we cannot or would take us generations.  They can quickly turn genes on and off, including ours.  If you’ve ever heard the term epigenetics, microbes play a big part.  Epigenetics is the study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself.  What?!?!?!  In layman’s terms, epigenetics looks at how, without changing our genetics, we can change whether or not we express what’s in our genes.

Let’s say you are genetically predisposed to heart disease.  By making diet and lifestyle alterations, you can have an impact on whether or not those genes are turned on or off.  And because microbes can adapt quicker, they help us to adapt quicker.  We’ll get more into epigenetics later.

Back to digestion

When we talked about the large intestine last time, I said the large intestine is where bacteria step in and make sure nothing goes to waste.  The large intestine is home to the majority of our gut bacteria, and thus the majority of our microbiome.  This gut bacteria is the major contributor to the metabolic process, the development of the immune system, and regulates inflammation – a major player in chronic diseases and autoimmune disorders.

How do they do all of this?  Well, these bacteria in our large intestine need to eat too.  I’m sure you’ve heard of probiotics.  Probiotics are the good bacteria in our gut.  But they need to eat to do their job for us.  We need to feed them properly.  Probiotics need what are called prebiotics.  Prebiotics come from indigestible fiber in the foods we eat.  When properly fed, bacteria can go to work for us by producing vitamins we cannot, like vitamin K.  They can create amino acids and regulate the uptake of amino acids.  They create short-chain fatty acids that help to reduce inflammation.  They create neurotransmitters like serotonin and enzymes that can assist in the breakdown of food. The microbiome also influences how food affects our blood sugar levels.  By feeding the good bacteria, they remain strong and can help kill off the bad bacteria living in our gut.

Even the balance of types of bacteria in the gut affects how well we digest food.  For example, there are bacteria that are proficient at digesting carbs.  If these are abundant, your digestion of carbs may be optimal.  If they have been wiped out or decreased, you may find yourself less able to digest carbs.

Due to diet, lifestyle, medications, toxins and pollutants we all have a different microbiome, meaning we all have a different manifestation of the effects of our distinct microbiome.  The difference in our imbalance contributes to the differences I puzzled about earlier.

The good news is we can change the microbiome by making changes to our diet, lifestyle and environment.  Some things that have been found to damage the microbiome?  NSAIDS, antibiotics, proton pump inhibitors, and emulsifiers (binders) in processed foods to name a few.  Just as these little bacteria help us from a nutritional standpoint, when out of balance, they are not able to help protect us from bad stuff that can be harmful.  For example, microbes in the gut can determine which painkillers are toxic to your liver.  We need these guys in so many ways to keep us in balance and healthy.

Healing the microbiome

What can you do to start rebuilding and protecting your microbiome?  You need to weed the garden to reduce bad bacteria overgrowth, and start fertilizing.  Here are five ways you can start doing both:

Limit the use of NSAIDS - they can significantly impact your microbiome and gut liningEat lots of fiber (both soluble and insoluble) - feed the microbiome and help them do their job.
Reduce the use of antibiotics - overuse can wipe out populations or strains of good bacteria.Eat whole grains or sprouted grains - if you eat grains, these are the most beneficial as they are higher in fiber.
Stop using antibacterial products - we need exposure, rather than creating superbugs.Eat fermented foods - like probiotics, they are filled with good bacteria.
Keep meat consumption down and limit to "clean" meat - this will help to keep down inflammation.Eat healthy fats - we have been trained to avoid fat, and this may have ultimately helped to create our health problems.
Avoid artificial sweeteners - they induce glucose intolerance (insulin resistance) which can lead to diabetes.Buy local - local, organic foods are the best way to feed our gut with good bacteria from the ground.

To sum up, the microbiome is 90% of our cells.  What we feed our microbiome determines how well it works for us, including digestion, the expression of genes, and how well our immune system works.  If these morsels have left you hungry for more, keep tuning in.  We’ll cover more of the microbiome puzzle, and get into the weeds as we go.

Yours in Wellness,


Previous post: The Gut and Nutrient Absorption

Next post: The Human Microbiome Project




    I quite like looking through an article that can make men and women think.

    Also, thank you for allowing me to comment!

Leave a Reply