Why the Bacteria in Your Gut Matters

When I was younger, I used to enjoy feasting on gigantic double bacon cheeseburgers (preferably covered with jalapenos). After a hard day at work or school, it seemed to hit the spot… for a while. These foods may taste great, but we know what they can do to our stomach afterwards. ‘Gut bomb’ is the term we used for such foods. It is a bit ironic, but our tongue-in-cheek description was more accurate than we ever realized.

A study, recently published in Nature, demonstrated that changes in diet can quickly alter the type of bacteria populating the human gut.[1] This is an exciting discovery because type of bacteria contained in your gut plays an important role in health. It is even believed that ‘bad’ bacteria can contribute to chronic illnesses and obesity.

Where bacteria call home

For those of you who are new to the subject, let’s get a little background. Your gut, also called the digestive or GI tract, is home to a myriad of bacteria. It may sound odd, but the health of your gut has a lot to do with the kinds of bacteria it carries. Some are beneficial and healthy, while others interfere with the body’s processes or contribute to disease. Just how many bacteria call your body home? We recently received an answer to that question.

The Human Microbiome Project, which was funded by the U.S. National Institutes of Health, estimates that the average person is host to around 100 trillion bacteria.[2] That’s a lot of bacteria! In fact, the gut is so full of bacteria that the typical bowel movement is not only leftover food—about half is leftover microbial mass.[3]

The thought may make your skin crawl, but these guys are your friends.  The relationship between the body and gut bacteria is mutually beneficial (for the most part anyway). Gut bacteria aid in digestion, release nutrients from food, stimulate cell growth in the gut, reduce harmful substances in the body, and inhibit the growth of harmful bacteria. What the bacteria get in return is food—our food. Our large intestine is sort of like a bacteria cafeteria. As long as we are eating, our little friends are being supplied with food as well.

Which bacteria are you feeding?

This means the food we choose to eat has a direct influence on the type or balance of bacteria we host. The study in Nature found the abundance of different types of bacteria in participants’ guts quickly changed depending on their diets.

When participants in the study ate a diet based on meat, cheese, and eggs, their levels of bilophila (fat loving bacteria) increased dramatically.[4] This occured because meat and cheese contain high levels of fat and the bilophila are able to thrive. However, when the participants switched to a plant-based diet, consisting of granola, rice, vegetables, lentils, and fruit, their levels of bilophila were much lower. In a way, our diet regulates which types of bacteria will thrive.

What’s the big deal?

Several studies have suggested that certain gut microbes (including bilophila) are a factor for obesity.[5] The relationship works something like this: When you consume a western diet, containing high levels of fats and sugars, the types of bacteria that are needed to digest them thrive. These bacteria are able to break these foods down more efficiently. As a consequence, your body will absorb these calories and store them as fat more quickly.

Besides weight gain, obesity-related bacteria have other negative effects on the body. ‘Bad’ gut bacteria are known to cause inflammation in the colon. Scientists at the University of Iowa are now looking into the effects of inflammation, as they believe inflammation to be a connection between diabetes and ‘bad’ gut bacteria.[6]

Balancing Bacteria

As mentioned earlier, there is a balance between the bacteria in your gut. If one type increases in number, the other types will tend to decrease. Researchers studied overweight mice with obesity-related gut microbes. They observed that leanness-associated microbes would invade the mice’s guts when they were put on a diet high in fruits and vegetables and low in saturated fat.[7] They also found that following the plant-based diet prevented weight gain and the development of metabolic symptoms in these mice. Is it any coincidence that this type of plant-based diet is also known to benefit health in many other areas? Given the choice, which diet would you prefer?

What to eat:

So what can you do to encourage beneficial bacteria to thrive? The most important thing is to eat plenty of whole grains, fruits, and vegetables. There are two major reasons for this recommendation. First, dietary fiber serves as food for many types of bacteria in our guts. If we don’t eat enough, we may end up starving the bacteria. When this happens, they begin to eat the mucus lining of our large intestine.[8] By insuring adequate fiber intake, the bacteria will be well fed and actually release valuable nutrients in the process.

Secondly, fruits and vegetables are full of oligosaccharides (a type of sugar). Oligosaccharides set up an environment in which our good bacteria can thrive. Clinical studies have demonstrated that oligosaccharides increase the numbers of friendly bacteria in the colon.[9] At the same time, they work to suppress the growth of new harmful bacteria. Probiotics, such as those found in yogurts (both dairy and soy-based) can also promote a healthy gut. However, we recommend the soy-based variants, as they are much healthier than traditional yogurt.

Your diet affects your health in numerous ways. Aspects of health and wellness are not separate, but interconnected. Over time, the health of your gut will affect other parts of your body. If you haven’t done so yet, begin incorporating healthy, whole foods into your diet. Plant-based diets have been proven superior time and time again. You can change your diet and your body will thank you for it. Remember, that double cheeseburger really is a gut bomb.


[1] Lawrence, David. “Diet Rapidly and Reproducible Alters the Human Gut Microbiome.” Nature (December 11, 2013). http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12820.html.

[2] “100 Trillion Good Bacteria Call Human Body Home.” SFGate. http://www.sfgate.com/health/article/100-trillion-good-bacteria-call-human-body-home-3683153.php#src=fb.

[3] Kolata, Gina. “Human Microbiome Project Explores Our 100 Trillion Good Bacteria.” The New York Times, June 13, 2012, sec. Health. http://www.nytimes.com/2012/06/14/health/human-microbiome-project-decodes-our-100-trillion-good-bacteria.html.

[4] Doucleff, Michaeleen. “Chowing Down On Meat, Dairy Alters Gut Bacteria A Lot, And Quickly.” NPR.org. http://www.npr.org/blogs/thesalt/2013/12/10/250007042/chowing-down-on-meat-and-dairy-alters-gut-bacteria-a-lot-and-quickly.

[5] “Healthy Diet Discourages Obesity Microbes in Gut.” Medical News Today, September 7, 2013. http://www.medicalnewstoday.com/articles/265750.php.

[6] Vu, Bao G., Francoise A. Gourronc, David A. Bernlohr, Patrick M. Schlievert, and Aloysius J. Klingelhutz. “Staphylococcal Superantigens Stimulate Immortalized Human Adipocytes to Produce Chemokines.” Edited by J. Ross Fitzgerald. PLoS ONE 8, no. 10 (October 30, 2013): e77988. doi:10.1371/journal.pone.0077988.

[7] “Healthy Diet Discourages Obesity Microbes in Gut.” Medical News Today, September 7, 2013. http://www.medicalnewstoday.com/articles/265750.php.

[8] Singh, Maanvi. “Can We Eat Our Way To A Healthier Microbiome? It’s Complicated.” NPR.org. Accessed January 7, 2014. http://www.npr.org/blogs/thesalt/2013/11/08/243929866/can-we-eat-our-way-to-a-healthier-microbiome-its-complicated.

[9] Macfarlane, G.t., H. Steed, and S. Macfarlane. “Bacterial Metabolism and Health-related Effects of Galacto-oligosaccharides and Other Prebiotics.” Journal of Applied Microbiology 104, no. 2 (2008): 305–344. doi:10.1111/j.1365-2672.2007.03520.x.

Jon Ewald, MD

Jon Ewald grew up in Minnesota and has a love for the outdoors. He obtained his medical degree at Loma Linda University, graduating in 2020. He is currently completing his residency in Radiology at University of Pittsburgh.

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