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The Gut Microbiome Part 2: What does it do?

November 30, 2018

The gut microbiome does a lot of good things for us and is essential for our health. We are going to focus on the beneficial bacteria that are found in the large intestine.

The large intestine is so named because it has a wider diameter than the small intestine. Conversely, the large intestine is much shorter than the small intestine (less than five feet vs about ten feet for the small intestine).

Despite the shorter length, a lot of important actions take place in the large intestine and many of them are related to the bacteria that reside there. One of the important functions of the large intestine is reabsorbing most of the water that is mixed with our digesting food (called chyme). About 90-95% of the water that enters our large intestine is reabsorbed into the body before it passes through us.

Typically, this chyme takes about 12 to 70 hours to pass through our large intestines and it is dehydrated along the way to becoming the feces that we excrete. Along with water, the colon is also responsible for absorbing sodium and vitamins that are generated by our gut bacteria. As mentioned in the previous post, the GI tract is also responsible for making sure that we do not absorb the things that we want to keep out. The colon is no exception and an important part of its job is to keep waste products and potentially harmful pathogens outside of the body.

In order to perform all these important functions the colon must be healthy. Our microbiota play an essential role in keeping the colon healthy. A healthy colon is full of bacteria that are mutualistic organisms. Mutualistic organisms are members of different species that cooperate for the benefit of both. For a long time it was thought that our gut microbes were neither good nor bad, that they lived with us but did not help or hinder us in any way. Now we know that is not the case and that our health is aided by maintaining a healthy community of gut microbiota.

One important function of our gut bacteria is fermenting carbohydrate that we otherwise could not break down (fiber). The primary product of this fermentation are short chain fatty acids (SCFAs) that have numerous health benefits.

These acids help with colon cell division and growth, lower the pH of the colon to improve nutrient absorption, keep an ideal environment for our beneficial bacteria (and a poor one for harmful pathogens), and provide energy for our colon cells.

Fermentation also results in the production of some of the B vitamins and vitamin K.[1][2] Though we can get these vitamins from other sources, our gut microbiome may play an important role in ensuring that we get enough.

Our understanding of the role that our gut bacteria play in our health and disease is ever expanding. Recent investigations have described differences between the gut microbiome of people who are healthy weight and those who are overweight or obese. Similar investigations have found some similarities among the most long lived peoples. It is too early to make any definitive claims about the gut and these issues, but it is an active area of research.

It is important to note that this does not suggest that simply supplementing with the ‘right’ bacteria will cause a person to return to a healthy weight. These are multifaceted issues and while the gut microbiome does exert some direct effects throughout the body, there are other factors that affect both the gut microbiome and weight that have to be addressed.

Another active area of research is how our gut microbiome may affect our mental health. The vagus nerve allows for two-way communication between the gut and the brain and it appears that the status of the gut microbiome can actually affect our brain and neurotransmitters in direct ways.

Though a lot more research has to be done to understand all the facets of how the gut microbiome can affect mental health, there have been some interesting observations. For example, patients with Major Depressive Disorder (MDD) have dysbiosis or a microbial imbalance.[3] This does not imply that a simple course of antibiotics will be the fix, rather it highlights how so many diseases are much more complicated than previously suspected.

In research on mice it has been found that a fecal microbiota transplant (FMT) can result in the transference of some of the donor mouse’s mental traits. More specifically, it appears that anxiety can be transferred, to an extent.

Fluctuations in our microbiome may even have an impact on our circadian rhythm and sleep cycles![4] We do not know the full function of the gut microbiome and how it affects not just our GI health, but immune system, mental health, and behavior. However, we are learning more every day.

1. https://www.tsn-ahp.com/single-post/2018/03/07/Nutrition-Basics-The-Water-Soluble-Vitamins


2. https://www.tsn-ahp.com/single-post/2018/03/05/Nutrition-Basics-The-Fat-Soluble-Vitamins


3. H. Jiang, Z. Ling, Y. Zhang et al., “Altered fecal microbiota composition in patients with major depressive disorder,” Brain, Behavior, and Immunity, vol. 48, pp. 186–194, 2015.


4. Leone, V. et al. Effects of diurnal variation of gut microbes and high-fat feeding on host circadian clock function and metabolism. Cell Host Microbe17, 681–689 (2015).

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