Buffet for Bacteria: How Diet Can Affect Your Microbiome

By Victoria Silvis

From childhood we are taught to eat plenty of fruits and vegetables while taking it easy on the sweets. Everyone knows these healthy foods are rich in important vitamins and nutrients, whereas sugary foods are often labeled as “empty calories” as they have no nutritional benefit. I find that while most are familiar with this concept, many do not realize the impact their diet can play on their gut microbiome.

Photo Credit: https://www.health.harvard.edu/blog/diet-disease-and-the-microbiome-2021042122400 depicting healthy foods fueling your gut.

What is the gut microbiome?

First, let me explain what the gut microbiome is. From the moment you are born, microorganisms including bacteria, viruses, and archaea begin to colonize your gastrointestinal (GI) tract. To some, this may sound frightening, especially during a time where we wear masks, wash our hands constantly, and are mindful about the germs we interact with daily. However, these microbes are different from the germs we hear about on the news. The microbes in your gut form a mutualistic relationship with us, meaning both you and microbes benefit from the interaction. TRILLIONS of microbes comprise the gut microbiota, which is why the microbiota is sometimes referred to as an additional organ within the human body, expressing the sheer importance of these organisms1. The microbiota mainly consists of a few main bacterial phyla: Bacteroides, Firmicutes, and Proteobacteria2. In fact, within your body you have about 10x more bacterial cells than human cells3! While the vast majority of the bacteria in your gut are “friendly” and keep pathogens at bay, in some instances “bad” or opportunistic pathogen bacteria are able to colonize, causing a loss of homeostasis. The bacterial imbalance can cause numerous issues ranging from a bout of diarrhea to severe inflammatory bowel disease4. This is because our gut microbiota functions to consume and break down dietary fiber that humans cannot digest, produce many biomolecules from these carbohydrates, and modulate immune interactions within our bodies5. As such, it is necessary to keep your gut bacteria in homeostasis where beneficial microbes are more prevalent than harmful microbes.

What’s food got to do with it?

Bacteria are specialized to consume and break-down carbohydrates and fiber from your diet, or from the mucin layer that lines your GI tract. The mucin layer is generated by goblet cells in the gut and serves to maintain a barrier between your gut microbiota and your intestinal epithelial cells. But this mucin barrier also contains glycans which can be liberated by bacteria as a food source, in turn dictating alterations in the glycans decorating the mucin barrier6. Food components that serve to benefit microbial abundance are known as prebiotics whichare generally non-digestible dietary fibers. Not all bacteria process the same dietary components. Just like you and I, bacteria have food preferences7. If I showed you an apple and an orange, you could choose your favorite, however these two contain roughly equal amounts of dietary fiber and sugars (glucose, fructose, and sucrose). So, choosing one or the other would not have a drastic impact on the carbohydrates consumed. However, if given the choice between an apple, containing natural sugars and dietary fiber, and a chocolate bar, containing processed sugar and no dietary fiber, the story changes. Bacterial strains that are able to break down processed sugar will begin to outcompete other bacteria that either cannot consume the processed sugar, or find it less favorable7. In some cases, the organisms that prefer this processed sugar are able to colonize the gut, but may be harmful and trigger an immune response leading to inflammation in the GI tract4. In fact, a recent study showed that mice consuming a high amount of glucose had increased mucus degrading bacteria Akkermancia mucinophila and Bacteroides fragilis. The increased abundance of these two bacteria decreased the mucin barrier leading to an increased risk of intestinal inflammation8. Although eating sugar-rich foods will not radically alter your gut immediately, it is important to keep your consumption of these items at a minimum for the sake of not only your nutritional requirements but also your gut bacteria. While the vitamins and minerals contained in foods do not affect the abundance of bacteria, the opposite is true. The abundance of particular bacteria can affect vitamin levels in your body. Gut bacteria actually produce B vitamins, and up to half of the daily recommended vitamin K9! So be sure to feed your microbes and yourself beneficial food!

Figure 1: Sedimentation swirling in homemade kombucha made by Rebecca Fleeman. GIF created by Victoria Silvis using GIPHY.

Figure 2: Healthy SCOBY in homemade kombucha made by Rebecca Fleeman. GIF created by Victoria Silvis using GIPHY.

What about fermented food and drinks?

Fermented foods and drinks can serve a source of probiotics, or live organisms that generally improve or restore the gut microbiota10. If you have ever looked at a bottle of kombucha, you may have noticed a little sediment on the bottom (Figure 1). Did you know that sedimentation is actually the microorganisms used to ferment the kombucha? The sediment is known as a SCOBY (symbiotic culture of bacteria and yeast; Figure 2), which is specifically used in the production of kombucha11. Many other foods and drinks are fermented similarly, using microbes to break down sugars and generate acids or alcohol. When fermented products reach the market, some still contain live microbes, and should be clearly labeled. You will often see a label with bacteria such as Lactobacillus on items like yogurt or kefir and indicates a good source of probiotics. However, not all fermented items are a source of probiotics. Sorry, but that beer will not be benefiting your microbiota since most alcohol, although fermented, loses any probiotics it contained through the production process, as acid released from the hops kills any remaining live microbes. There are a few beer brands that stray from this by adding a second fermentation step allowing for live cultures to survive until you pop them open12. Always check labels to see what benefits you are truly getting from what you are consuming.

So, do I need to change my diet?

Well, that is for you to decide. Everyone has a different diet and a different resulting microbiome, making a “one size fits all” rule impossible. Next time you eat, think about the components that make up that particular food, and how your body is breaking it down. Remember, you are not only feeding yourself, but also the trillions of microbes that help you stay healthy! As Penn State College of Medicine students, we may work in the chocolate capital of the United States, but take it easy on the Hershey bars. Eat a balanced diet with plenty of fruits, vegetables, and legumes because a healthy gut makes for a happy body.


1.         Baquero F, Nombela C.2012. The microbiome as a human organ. Clin Microbiol Infect 18 Suppl 4:2-4.

2.         Liu W, Zhang R, Shu R, Yu J, Li H, Long H, Jin S, Li S, Hu Q, Yao F, Zhou C, Huang Q, Hu X, Chen M, Hu W, Wang Q, Fang S, Wu Q.2020. Study of the Relationship between Microbiome and Colorectal Cancer Susceptibility Using 16SrRNA Sequencing. Hindawi BioMed Research International 2020:17-17. PMCID: PMC7011317.

3.         Thursby E, Juge N.2017. Introduction to the human gut microbiota. Biochem J 474:1823-1836. PMC5433529.

4.         Albenberg LG, Lewis JD, Wu GD.2012. Food and the gut microbiota in inflammatory bowel diseases: a critical connection. Curr Opin Gastroenterol 28:314-20. PMC3822011.

5.         Schroeder BO, Backhed F.2016. Signals from the gut microbiota to distant organs in physiology and disease. Nat Med 22:1079-1089.

6.         Schroeder BO.2019. Fight them or feed them: how the intestinal mucus layer manages the gut microbiota. Gastroenterol Rep (Oxf) 7:3-12. PMC6375348.

7.         Pudlo NA, Urs K, Kumar SS, German JB, Mills DA, Martens EC.2015. Symbiotic human gut bacteria with variable metabolic priorities for host mucosal glycans. mBio 6:e01282-15. PMCID: PMC4659458.

8.         Shahanshah Khan SW, Victoria Godfrey, Md Abdul Wadud Khan,, Rajalaksmy A. Ramachandran BLC, Cassie Behrendt, Lan Peng, Lora V. Hooper, Hasan Zaki.2020. Dietary simple sugars alter microbial ecology in the gut and promote colitis in mice. Science Translational Medicine 12:1-15.

9.         Morowitz MJ, Carlisle EM, Alverdy JC.2011. Contributions of intestinal bacteria to nutrition and metabolism in the critically ill. Surg Clin North Am 91:771-85, viii. PMC3144392.

10.       Bourrie BCT, Willing BP, Cotter PD.2016. The microbiota and health promoting characteristics of the fermented beverage kefir. Frontiers in Microbiology 7:647-647.

11.       Villarreal-Soto SA, Beaufort S, Bouajila J, Souchard JP, Taillandier P.2018. Understanding Kombucha Tea Fermentation: A Review. J Food Sci 83:580-588.

12.       https://blog.insidetracker.com/beer-fermented-contain-probiotics

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