What I’m Learning: The Human Microbiome

Among the most interesting topics that were mentioned in my anatomy and physiology class was that of the human microbiome; the trillions of microscopic organisms living in and on us. Hearing of the topic left me with a sense of wonder. How could we live with so many trillions of foreign organisms in and on us? This class was naturally followed by a frenzy of research on the topic. I was quickly blown away by the incredible ability of these microbes to both literally sustain our lives, yet also sometimes cause us disease.

It turns out that whether they help or harm you largely depends on the composition of your microbial populations, and we have an incredible amount of control over what this composition is.

In order to fully understand that, let’s get a better understanding of what the microbiome is.

We may be less human than we think we are… that is, scientists estimate that there are at least as many foreign microbial cells living in and on us as there are of our own cells, most of which live in our large intestine.1

Ok, that’s kind of gross. Just wait until you hear how we get them:

Although our first exposure to microbes likely begins inside the womb, 2 our first major exposure begins from the moment we pass through the birth canal, when we are smeared in microbes which begin to populate our skin. 3 One way our guts are first populated by microbes is by our mother’s milk, which contains natural probiotics: microbes transported into the mother’s milk by immune cells from her gut.4

As we begin our lives touching surfaces and eating in this unsanitary world covered in microscopic life, every surface of epithelium (the cell barriers between our true insides and the outside world), including the inner lining of our digestive tract, begin to be populated by microbes.5

These processes begin to develop our natural populations of symbiotic microbes, or microbiota, and the term for their collective genetic material is the microbiome. Our microbiomes include organisms such as bacteria, fungus, and parasites, as well as viruses!6 With these microbes growing and populating our bodies, how do we all not get infections and die?

To start, we need to know that not all microbes are created equal. Some help us while others, called pathogens, harm us. What we know as an infection may just be an influx in the population of harmful microbes or a more extreme version of what is called dysbiosis, an imbalance in our microbial populations.

One important way this imbalance is prevented in infants is that when we are breastfed by our mothers, we consume special sugars which feed only the beneficial microbes in our gut, starving out everything else.7 Antibodies such as secretory immunoglobin A (sIgA), supplied by our mothers’ breast milk, bind to unwanted microbes or viruses in the gut and tell the immune system to attack it.8

Now that we know what the microbiome is and how we get it, how do our over 30 trillion microbial body-mates impact our health?

Let’s begin with some of the early effects our microbiomes have on us as infants. The good bacteria supplied to us by our mothers begin to train the immune system to recognize good microbes from bad. How this happens is unknown.9 Children who don’t have these microbes have immune systems with less recognition of friend or foe, resulting in more immune diseases such as asthma, allergies or type I diabetes, in which the immune system attacks something unnecessarily, such as the body.10 Scientists theorize that this protective effect offered by microbes we’re exposed to may exist not only as a result of them crowding out pathogens, but also by secreting Immunoglobulin A (IgA), which I previously mentioned binds to pathogens and signals to the immune system to attack them.11 

The microbes in our GI tract are some of the most essential because they harvest nutrients and energy out of food that we cannot digest. Fiber, or non-digestible carbohydrates from plants, reach our colons (our most densely populated region) undigested, and from there our microbes get the job done. They ferment this fiber, releasing nutrients we couldn’t extract with our digestive enzymes.12 

When our microbes ferment what is in our colons, they release chemicals. These chemicals, called metabolites, can be both essential for health and a major cause of disease. Fiber fermentation creates short-chain fatty acids (SCFAs). SCFAs have many functions, such as being the primary energy source for the cells lining our gut, being anti-inflammatory, and enhancing our body’s capability to absorb nutrients by creating a more acidic environment13 (they are SCF”Acids”). SCFA’s also play a role in the regulation of our immune cells.14 Fiber may be one of the most important nutrients humans can get, yet it also happens to be the one Western society is the most deficient in. People living in places like West Africa may consume 5-10 times as much fiber as African Americans do, and have 50 times less colon cancer as well as significantly lower levels of secondary bile acids.15

Secondary bile acids are a class of metabolites that are harmful to us, and are produced by bacteria that ferment the excess bile acids that make it to our colons. These metabolites are carcinogenic and pro-inflammatory,16 meaning they are a probable cause of colon cancer and create an inflammatory response in our bodies leading to low-grade inflammation, which plays a role in many today’s major diseases.17

Foods containing choline or L-carnitine produce a compound called Trimethylamine, which is oxidized by our liver to produce trimethylamine-N-oxide (TMAO) and is widely recognized as promoting the development of heart disease, fatty liver disease, and kidney failure.18

Our gut microbes likely have psychological effects on us as well. They secrete neurotransmitters which communicate with our brain via the vagus nerve.19 They may even manipulate human behavior by inducing cravings that favor foods that they benefit from,20 which has serious implications for making resisting bad foods even harder or making healthy foods more appealing.

With these incredible effects that our microbiome has on our health, are we simply subjected to the effects of whatever microbes we are exposed to and are sorted out by our immune system? Or are there things that we can do to ensure a health-promoting microbial population?

One of the most important things you can do to avoid an unhealthy microbiome is to avoid antibiotics unless they are totally necessary. Antibiotics kill not only harmful bacteria, but also the beneficial ones. This leaves only strains resistant to the antibiotics behind, and they usually aren’t the nice ones. This can lead to deadly infections of antibiotic-resistant bacteria such as C. diff, which can result in needing to remove the deceased portion of the colon.  At the very least, the diversity of your microbiome will be permanently decreased with each use of systemic antibiotics. 21 

Healthy behaviors such as getting exercise may have a positive effect on the health of your microbiome, as it has been shown to increase the diversity of our microbiomes, increase gut motility (our body’s ability to effectively transport food through our gastrointestinal tracts), and increase levels of certain short-chain fatty acids (SCFAs),22 our most essential metabolites.

Just like any ecosystem, the human gut microbiome is dynamic and its composition depends largely on the environment it inhabits. There are two main approaches to change this ecosystem. One is to plant organisms in the environment in the hopes that they flourish and become a larger part of the population. This is the approach taken by those using probiotics, which are live microorganisms (usually bacteria) introduced into the body for this purpose.

The other way to change the ecosystem is to change the environment in which the organisms live, therefore favoring certain organisms over others. This is the effect seen when we eat “pre” biotics. Prebiotics are the foods we eat that become the substrate our microbes live in and eat. What we eat changes the substrate in our gastrointestinal tracts, therefore determining what type of microbes survive there.23 If a type of microbe can’t eat, it won’t survive. Microbes with more food will flourish more. The key to this is knowing which foods feed beneficial microbes and which foods feed harmful ones.

As I mentioned, the microbes that produce some of the most vital metabolites, SCFAs, are fed by fiber.  Fiber is only found naturally in plant foods. Populations who eat the most fiber have the highest levels of SCFAs, and very low rates of inflammatory gut diseases and colon cancer.24

When we eat more high-fat foods, especially those from animal sources, our bodies produce more bile acids, which make it down to the colon when in excess, where certain bacteria ferment them into secondary bile acids.25 We just learned that these are carcinogenic and pro-inflammatory.

Another harmful metabolite previously discussed, trimethylamine (TMA), then oxidized by the liver into trimethylamine N-oxide (TMAO), is produced by the fermentation of choline, found mainly in eggs, and l-carnitine, found mainly in red meat.26

So… What does all this mean? What is research saying is the best thing you can do?

Probiotics may be effective in restoring healthy composition to a damaged microbiome (such as after antibiotic use), but not in improving or maintaining health in someone who is already healthy.27

The most powerful thing we can do to maintain, restore and improve the composition of our microbiota is to eat more of the foods that feed beneficial microbes, as food alone may drastically change our gut microbial population within days.28 Focus on including as many fiber-rich and minimally-processed plant foods as you can (beans, fruits, vegetables, whole grains, nuts and seeds), and avoid as many high-fat foods, especially animal-based foods, as possible.

5 thoughts on “What I’m Learning: The Human Microbiome

    1. Hey Katie,

      That is quite an incredible figure! I am assuming you are referring to this study: https://doi.org/10.1002/cncr.25507, in which there was a nearly 50% increase in colorectal adenomas when sleeping 6 or less compared to 7-9 hours.

      Fascinating! I wonder if changes in microbial diversity has an effect on this result, as sleep deprivation was recently correlated with decreased microbial diversity (https://doi.org/10.1371/journal.pone.0222394). Also, microbial diversity might affect sleep quality.


  1. Very true and interesting article. When I started researching into health and nutrition I was amazed at how much the body relies on a healthy gut. I think it’s also a part of the body a lot of people overlook when it comes to being healthy.

    Liked by 1 person

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