The Viome Microbiome Refresher Course

microbiome refresher course

There is no better way to imagine the human body's digestive system than a very, very long tube. 

And in a lot of ways, that is spot on. The average adult person has up to 30 feet of ‘tubing’ that makes up the digestive system, starting from the mouth and following through to the colon and anus. For a broader visual, as one scientist put it, the digestive system “... has a surface area… that of half a badminton court 1.” 

That is a lot of room for microbes to live on.

But, as the whole system includes several different organs, several different digestive processes, and well, a lot of different types of human cells - it can be a little hard to remember that it’s more connected than we think. Our digestive ‘tubing’ has various connection points that separate one organ from the next (like valves in a plumbing system). Through these sections, more than just our food passes from one section to the next: many microbes make it past as well.

The origins of the gut microbiome

The world is full of microorganisms - bacteria, archaea, fungi, viruses, and more. They live on every surface you can see, and on many surfaces you can’t see, like in deep trenches underwater, caves, and the highest mountain peaks. With microbial living organisms all around us, it is safe to say that the ones that live inside of us had to come from somewhere. It’s also important to note, that just like the vast environment around us, our ‘microbiome’ makes up more than just the microbes that live in our gut. We have a vast diversity of microbes that have colonized all through our body - from the mouth to the gut, but also in various other organs like the kidneys, liver, and sex organs 2

But for the most part - they have all started in some ways from the top of the tube: our mouth. The foods we eat, the liquid we drink, and even the air we breathe are all full of microscopic living creatures that get taken in and taken up from our mouths. Some immediately find a home, snuggled closely in between our teeth, gums, or even our tongue. Making up the oral microbiome, this ‘top of the tube’ ecosystem plays a significant role in the early start of digestion and our overall health 3. Many of the microbes that thrive inside our mouth are beneficial and actually provide us with benefits that range from supporting a healthy blood pressure, helping transmit necessary digestion signals to the gut, and even getting their hands dirty by directly breaking down hard to digest foods as we chew.

Furthermore, the colonies that thrive in our mouths directly influence the microbial populations in our gut. Every time we swallow, what’s living inside the oral microbiome gets transferred down the hatch, making its way through the tubal system from the esophagus, stomach, and onto the intestinal tract. Not all make it through this highly acidic cycle (thanks to the incredible amount of hypochlorous acid produced in our stomach), but many do. Fortunately, our stomach helps to take out some pathogenic microbes who might be traveling, but the rest are sent down to the land of milk and honey, where our intestines provide a safe, nutrient-rich haven for various microbes.

The Entire Tube

We didn’t always view the entire tube as a whole system, especially in regard to the microbiome. But as times have changed - and science often does - we have learned a lot about the connections that tie these two opposing sides together. And the longer we look, the less they look like they’re ‘opposing’ but really just two sides of the same coin. 

Although research on the oral microbiome is a little newer than scientific study on the gut microbiome, it’s becoming quite clear it still has a lot to do with our health.

Scientists have found links between oral health and the brain, cardiovascular system, and other organs like the kidneys 4. We also depend on our oral microbiome to contribute key microbial players to the health of our gut microbiome. And now - we’re learning how to influence the microbes in our mouth through our diet to better support beneficial organisms and activities for our whole body health.

Intro to the Oral Microbiome

Before, the only time we talked about bacteria was when our dentist was asking us if we flossed. For the better part of a century, the perception was that the bacteria living inside the mouth were a pesky and sometimes harmful fact of life. Unfortunately, there has been a lot of misunderstanding around the human microbiome. These days we know that the microbes that call us home do us a significant amount of good.

The oral microbiome is just now becoming a hot topic in the science world, showing us that the ‘top of the tube’ has a lot to offer when it comes to our health. 

And that’s just the tip of the iceberg.

Which by this time should be no surprise. There is something about underestimating how connected our health is to the environment around us, our diet, and even our entire microbiome. But as we learn more, this simply means we can add to the data for how optimal health is defined for each person. Which means we’re only a few steps away from digitizing and decoding the answers to each person’s biology - starting with you.


  1. Helander, H. F., & Fändriks, L. (2014). Surface area of the digestive tract - revisited. Scandinavian journal of gastroenterology, 49(6), 681–689. https://doi.org/10.3109/00365521.2014.898326

  2. Gilbert, J. A., Blaser, M. J., Caporaso, J. G., Jansson, J. K., Lynch, S. V., & Knight, R. (2018). Nature medicine, 24(4), 392–400. https://doi.org/10.1038/nm.4517

  3. Dewhirst, F. E., Chen, T., Izard, J., Paster, B. J., Tanner, A. C., Yu, W. H., Lakshmanan, A., & Wade, W. G. (2010). Journal of bacteriology, 192(19), 5002–5017. https://doi.org/10.1128/JB.00542-10Narengaowa, Kong, W., Lan, F., Awan, U. F., Qing, H., & Ni, J. (2021). Frontiers in cellular neuroscience, 15, 633735. https://doi.org/10.3389/fncel.2021.633735