• Steven Shuster, MS, CISSN

The Gut Microbiome: Part 1


The gut microbiome is mostly made up of bacteria.

There are loads of bacteria throughout our GI tract and they affect our health in a variety of ways.

Variation in the gut microbiome is evident both between individuals and between populations.

The gut microbiome is a very active area of study and our understanding is changing all the time.

Gut microbiome. Probiotics. Prebiotics. Synbiotics. Fermented foods. These are all buzzwords in the health and nutrition world today. What do they mean and how important are they? In this next series of posts we are going to explore those very things and see what sense we can make of it.


The gut microbiome is made up of all the tiny, microscopic organisms that live within our guts. It might sound gross, but a healthy gut microbiome is essential to our health — both physical and mental.

Bacteria are the most abundant and voluminous of our gut microbes. You may have heard that bacterial cells outnumber human cells on the order of 10 to 1, but that number was “a back of the envelope calculation” that appears to be way off. Today’s best estimates put those numbers closer to parity; bacteria out number our own cells with a number of approximately 3.8×10^13 while our human cells number about 3.0×10^13. For an average male this means that about 0.2 kilograms (about 0.44 pounds) of bodyweight is gut bacteria.1

These microbiota play many important roles in the body. Just a few of those roles include, but are not limited to, fermenting fiber to create short chain fatty acids, producing some vitamins, and providing protection from harmful pathogens. The health of our gut microbiota has even been tied to the function of our central nervous system (or CNS: our brain and spinal cord).

Just like our series on the nutrition basics, we are going to break this topic down into easily digestible (pun intended) pieces and help you understand and make sense of some of the other information out there. We will discuss what the gut microbiome is, what it does and various factors that may affect its health. What impact do antibiotics have on your gut microbiome? What about the foods you eat? How about artificial sweeteners? We will also talk about some of the different types of products that are marketed to help maintain or improve the microbiota in your gut and see what the research really has to say about them. Keep reading as we scope out the interesting and constantly evolving world of our gut microbiome.

The Gut Microbiome Part 1: What is it?

The gut microbiome includes all the microbiota, or microscopic life, that lives in our guts, or gastrointestinal tract (GI tract). The GI tract includes the mouth, esophagus, stomach, and the small and large intestines (terminating in the anus). The GI tract is the path that food takes from the time we first put it in our mouths and begin chewing to when we finally evacuate.

Note that the GI tract is not the entirety of the digestive system. That also includes other organs such as the pancreas, gallbladder, etc. The GI tract is the part of the digestive system ingested food travels along while be digested and voided.

The evolution of the GI tract (also called the alimentary canal) is pretty interesting; it evolved as a way for the body to keep food outside of the body while it digests.

This can sometimes be a hard concept to visualize, but think about it like this: your GI tract is a tube within your body that keeps the digesting food separate from the rest of you. The specialized cells that line parts of your GI tract do different things that include releasing digestive enzymes to break down your food and keeping what is in the GI tract out of your body while absorbing only what you should.

In a healthy, well-functioning digestive system only the parts of food that we want to absorb are. The rest is excreted.

Where do these microscopic organism live?

Most references to the gut microbiota are about the microorganisms that live in the large intestines. However, we have microorganisms in varying amounts throughout our GI tract. For example, we all have a passing familiarity with the oral bacteria that can cause cavities and are one of the reasons we brush our teeth.

Though the stomach is relatively devoid of microbiota due to the high acidity, H. pylori can make a home there and sometimes cause ulcers and/or gastritis.

The small intestine is also relatively clean of microbiota in healthy individuals. However, bacteria can grow in the small intestine in a condition called Small Intestinal Bacterial Overgrowth, or SIBO. This can occur for a variety of reasons, such as low stomach acid or reflux from the large intestine.

Most of our gut microbiota lives in our large intestine, also known as the colon. The colon is where water and minerals are reabsorbed into the blood and bacteria further breaks the food that we have eaten. These are going to be the organisms with which we are most concerned. They are also the focus of a lot of current research so our understanding is changing almost daily.

Ok, we know where they live, but what exactly are they? A majority of the gut microbiome is made up of bacteria; it is estimated that an adult human male has about 0.2 kilograms or 0.44 pounds of bacteria in their guts.2 That may not sound like too much, but when put in other terms the numbers become more impressive.

For example, because bacterial cells are so much smaller than our own, there are probably more bacterial cells in your gut than human cells in your entire body! It sounds a little far fetched, but our best estimates suggest that it is true: 3.8×10^13 bacteria vs. 3.0×10^13 human cells.

It gets even crazier sounding than that, though: because of the diversity of species of bacteria in our guts, it has been estimated that bacterial genes outnumber human genes by a factor of about 150:1. This same study found that there are 3.3 million non repeating bacterial genes across at least 160 different species of bacteria. For comparison, the human genome is estimated to include about 21,000 genes. 3

These numbers have been part of the reason that people have become so interested in studying the gut microbiota. If we can better understand what genes bacteria have, how they are expressed, and the effect that this can have on us as humans we may be able to create novel interventions to maintain health and resist disease. Part of the problem (or interest, depending on perspective) is that the gut microbiome varies from person to person and from population to population.

A second group of researchers looked at the variation in gut bacteria of individuals throughout three regions of India. They found that while there were some “core” bacteria that were present in a majority of individuals, there was also a great deal of variation both within each region and between regions.4

How this variation is dependent on diet and location is an active area of study. It has recently been reported that immigrants coming to the United States have a greater diversity of bacteria in their gut than people who have been living here and that over time they lose that diversity. How this impacts their health is not yet well understood, but it has been suggested that it impacts their susceptibility to metabolic disease.5

The gut microbiome is being investigated to answer questions about health, disease, obesity, and even mental illness. Bacteria and their genes interact with us in ways that we are only just beginning to illuminate. In future posts I will cover some of the ways that bacteria interact with us and why it is important to have a healthy gut microbiome.

1. Sender R., Fuchs S., Milo R. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol. 2016;14:e1002533 doi: 10.1371/journal.pbio.1002533. PMC free article

2. Sender R., Fuchs S., Milo R. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol. 2016;14:e1002533 doi: 10.1371/journal.pbio.1002533. PMC free article

3. Qin, J., et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464, 59-65. 2010.

4. Das, B., et al. Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas. Scientific Reports volume 8, Article number: 10104 (2018).

5. Vangay, P. et al. US Immigration Westernizes the Human Gut Microbiome. Cell 175, 692-672. 2018.

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