The Human Microbiome – part one

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June 25, 2021

Be good to it so it can be good to you!  

There is a huge village living inside of you. It is invisible to the naked eye, yet it plays a role in what  happens to the food you eat, the medications you take, the allergens you react to, how you react to  stress and much more. Research is expanding our knowledge daily about how microbiomes help determine long-term health. 

Since this is such an interesting and involved topic, I’ll present the basics about the microbiome today, and will follow it up with a separate post next week about how to try to optimize it.

What is a microbiome? 

You have heard of the Human Genome Project – the study of human DNA.  The microbiome we are talking about is the genome of the 100 trillion organisms living in your body. If  we consider the genes we carry, 99% of them don’t belong to us, they belong to those other organisms. Infants are born with few bacteria, but depending on the way they’re delivered, how they’re fed and who they’re exposed to, by about three years old they have a fairly developed microbiome. 

We have a special symbiotic relationship — mutualism – with the organisms. We feed the organisms,  and they do important work for us.  

How many microbiomes do we have? 

In the intestines, there are bacteria, viruses and fungi from the mouth to the anus, but the majority live in the colon, also  known as the large intestine. They also take up residence on the skin, in the eye and even in the lungs. 

Normal gut bacteria usually keep bad bugs like Salmonella at bay, keep C difficile from taking over, and are responsible for key chemical reactions. On the skin, the good staph keep the resistant staph (MRSA) from growing. In the eye, bacteria help  avoid eye infections.

We used to think of the lung as being sterile. Now we know bacteria live there as well, probably in a dynamic  system, changing as some bacteria enter and others leave. Different areas have different microbes based on the oxygen level present in the upper and lower parts of the lung. Pneumonia may represent one resident species of bacteria overtaking the others.  

The intestinal microbiome 

Simple carbs, like sugar and starch, are absorbed easily by humans. Shortly after eating something like  cookies or white pasta, our blood sugar goes up. However, we can’t digest more complex carbs like  fiber, so those pass through the many feet of small intestines and end up in the colon. There, the  microbes snip the fiber into simpler sugars and ferment them.  Next week, we’ll go into how that affects you.

When you eat Big Macs and fries instead of fruits and vegetables, two things happen. One, the less  beneficial species, which like to eat meat, predominate. Second, the fiber-starved microbes feed on the  mucus layer of the colon. In other words, YOU become their food source. They find odds and ends in the mucosal  layer, nibble away at it, and allow space for bad bacteria and compounds that cause inflammation to  pass into the bloodstream. 

Is our microbiome good or bad?  

Neither, and both. Think of it as a very complex system, mediating the balance between inflammation  and immunity. There’s constant competition going on among the organisms. We aim for a rich, flourishing microbiome with diversity and abundance. A poor microbiome is scant and bland. Picture a beautiful rainforest with rich waterfalls, animals, ground cover and canopy, versus a sandy desert with minimal plants.

Microbes flourish when you feed them their preferred foods. For instance, in Japan, where foods containing seaweed are more popular,  people often have bacteria that help digest it, whereas people who don’t usually eat those products do not harbor those bacteria. Similarly, people in developed countries have a different biome than  those in traditional societies. The microbiome is determined by what you eat, and also determines how  you process calories.  We’ll explore how microbes that thrive on fiber can supply us with healthy precursors to anti-inflammatory compounds and mood-related transmitters like dopamine and serotonin, and how those that thrive on meat can increase the risk of heart disease.

Do we get to decide what makes up our personal microbiome? 

Our microbiome is affected by food, medications (especially antibiotics), our local environment,emotional and physical stress, and more.  The most important day-to-day determinant is definitely food!

Next week, I’ll tell you about how animal products and plants affect your microbiome differently.  And we’ll talk all about what prebiotics, probiotics and postbiotics are and how you can use them to your advantage for your longterm health.  

Stay well and stay tuned! 


  1. Terri kivelowitz on June 25, 2021 at 11:53 pm

    Very interesting. How about subject like fodmaps and digestion.

  2. Terri kivelowitz on June 25, 2021 at 11:54 pm

    Very interesting

  3. Roberta Dickey on July 9, 2021 at 9:46 pm

    Very interesting and amazing information. Thanks