We often hear, "you are what you eat." However, we are feeding a lot more than just ourselves when we eat. Trillions of microbes live in our guts and help us digest our food. What’s more fascinating is that we influence each other.

The food type we consume modifies microbial diversity, and these microbial communities can further affect our health/diseases status.

Carbohydrates, fats, and proteins, all of these macronutrients influence the microbial composition in your gut. Furthermore, vegan, vegetarian, and western diets (characterized by a high intake of processed foods) can have profound consequences in maintaining good or bad microbial communities living in our guts and eventually lead to health or diseases profiles.

Through this article, I will explain how different macronutrients such as carbohydrates, fats, and proteins may affect your gut microbiome. Also, I will present the research in dietary patterns, including vegan, vegetarian and western diets, how these diets modify the microbial profile, and how they can be associated with healthy or sick lifestyles. Finally, I will provide reasons why a plant-based diet is usually recommended. A plant-based diet is not exclusively plants. Meat can be included; however, a plant based diet means you’re consuming a higher amount of plants compared to other food items.

The food journey through your body

What is the connection between food and the microbiome? To answer that, we need to understand aspects of the food journey as it travels through the body.

Most plants contain fibers. Fibers are complex carbohydrates such as polysaccharides and oligosaccharides. These fibers are not as easily digested and may travel lower to the large intestine. In the intestine, the microbiota helps to break down these compounds with their digestive enzymes into smaller sugars (e.g., glucose and fructose) that can be easily absorbed by the intestinal membrane.

gut microbiome breaks down the polysaccharides in fibers such as celery.

An effect of the microbes breaking down fibers is the production of essential metabolites -vitamins and short-chain fatty acids (SCFA), which play crucial roles in maintaining human health.

Therefore, food provides fermentable substrates that sustains the microbial ecosystem, which is most abundant in the colon.

Depending on what you eat, you may contribute to the balance of good microbial workers during the food journey, which keeps you healthy. Conversely, if you don't provide the appropriate substrates to keep these good microbes active, other pathogenic microbial communities may grow and lead to diseases.

In the gut microbiome, beneficial and pathogenic microbes live together.

A balance of both microbial communities within the intestine leads to a healthy status. Otherwise, the imbalance in these communities (known as dysbiosis) may lead to the overgrowth of pathogenic bacteria or a reduction in beneficial microbes, which can lead to illness. Again, the microbial diversity (good and bad microbes) and the balanced control of the microbial growth is the key to maintain a healthy gut. To learn about the association between diet and microbiome click on this link.

How macronutrients influence your gut microbiome

With modern lifestyles, quick food preparation has become a necessity. But that can come with a cost.

Microbiome researchers studied how macronutrients – fats, proteins and carbohydrates modify the microbial communities within our guts.

how modern diets impact our gut microbiome - image of reasons for busy life and compromised food choices


There are two types of carbohydrates: digestible and non-digestible.

Digestible carbohydrates include glucose, sucrose, and fructose. These are compounds easily absorbed by the intestinal membrane, and they have been shown to reduce pro-inflammatory Bacteroides and Clostridia (Tomova et al., 2019). Sources of digestible carbohydrates are commonly found in sugary fruits.

The non-digestible carbohydrates include resistant starch, polysaccharides, oligosaccharides, and fibers.

These non-digestible carbohydrates are found naturally and abundantly in plant foods like bananas, artichokes, potatoes and onions.

These complex sugars need to be broken down before crossing the intestinal membrane.

Microbes in the large intestine are responsible for breaking down these non-digestible sugars.

These complex sugars are also called "prebiotics" because they act like substrates for microbial fermentation and promote the growth of beneficial bacteria such as lactic acid bacteria, Ruminococcus, Eubacterium rectale, Roseburia, Bifidobacterium, Prevotella, Dorea and Roseburia.

Furthermore, the action of these microbes on fermentable sugars has been associated with protective functions against disorders of the cardiovascular system and central nervous system. They also reduce pro-inflammatory and cholesterol-promoting species from the genera Clostridium and Enterococcus.

A diet rich in processed sugars can make the good microbes lazy because they don't have the proper substrate to work and cannot grow.

This can lead to other pathogenic microbes growing and controlling the microbial community within the gut. This microbial imbalance can lead to disease appearance or exacerbate existing chronic issues.

In contrast, although some food ingredients such as certain low-calorie sweeteners have been reported to enhance beneficial Bifidobacterium spp. (Dahl et al., 2020), they still represent a dietary controversy (Singh et al., 2017).

The two protein sources, animal and plant-originated, can influence the overall shape of the gut microbiome.

For instance, a diet rich in animal protein is associated with lower abundances of beneficial bacteria.

This is because, in animal meat, there are no fermentable fibers. Consequently, pro-inflammatory bacteria (e.g., Bacteroides and Clostridia) commonly increase in animal protein diets.

Furthermore, the lack of beneficial bacterial growth reduces the production of metabolites such as SFA, heightening the risk of gut inflammation and colorectal cancer (Sheflin et al., 2006).

In contrast, plant-derived proteins like those derived from pea intake increase beneficial bacteria such as Bifidobacteria and Lactobacillus while decreasing pathogenic bacteria such as Bacteroides fragilis and Clostridium perfringens. Likewise, plant-derived proteins have been associated with lower mortality than animal-derived proteins (Singh et al., 2017).


Similar to carbohydrates and proteins, we can also find good and bad fats.

Sources of good fat include olive oil, avocado, and nuts while harmful fats come from processed, fast foods and animal sources containing a high saturated and trans fats content.

These harmful fats decrease beneficial microbes (Bifidobacteria, Lactobacillus, and Prevotella) and increase pathogenic microbes (species from Firmicutes, Bacteroides, and Bilophila).

Overall, harmful bacteria activate inflammatory processes and increase the risk of metabolic disorders and cardiovascular diseases (Tomova et al., 2019).

macronutrient chart with amont of calories per gram

macronutrients in the gut

Dietary patterns

Western diet

A high intake of saturated fats, red meat, added sugars, and processed grains together with a low intake of dietary fiber from plants are characteristic of a western diet.

Studies have deeply explored the microbiome profile of populations consuming the Western diet compared to non-Western diets.

For instance, it has been reported that the western diet is associated with a higher abundance of Alistipes, Anaerotruncus, Collinsella, Coprobacillus, Desulfovibrio Dorea and Ruminococcus species (Tomova et al., 2019).

Other studies report the Western diet led to a marked decrease in total bacteria and lowered beneficial Bifidobacterium and Eubacterium species (Singh et al. 2017). Furthermore, the consumption of Western foods has been associated with the production of nitrosamines, which are chemical compounds classified as probable human carcinogens on the basis of animal studies (Park et al., 2015).

Vegetarian/Vegan diet

The vegetarian and vegan diets differ from the Western diet in that their composition is mainly based on plant-derived resources.

Due to both vegetarian and vegan diets relying on plant-based foods, they are considered high-quality diets favoring a better lifestyle (Lichtenstein et al., 2006). This recognition is because plant-based foods provide fermentable sugars and fibers that promote the growth of beneficial microbes.

Vegan and vegetarian diets are commonly compared with omnivore diets. In this regard, the results are controversial. In some cases, significant differences are found against omnivores, with lower counts of disease-related Bifidobacterium and Bacteroides species found in vegan/vegetarian diets (Wu et al 2014), while other modest differences are found comparing omnivore to vegan and vegetarian diets (Zimmer et al 2012).

Furthermore, the lack of a distinctive microbiome profile in vegan/vegetarian diets is partly due to dietary variation.

However, as long as different plants are consumed, it increases the microbial diversity.

overall diet - vegetarian and meat based.

A plant-based diet benefits your gut health

Although controversial results are found when comparing different dietary patterns at the microbiome level, there is a clear association between a plant-based diet and health benefits. A plant-based diet is characterized by a high intake of plant sources, but meat is not excluded, while a vegan or vegetarian diet usually does not include any animal source on it.

Plant-derived foods promote the development of more diverse and stable microbial systems.

In other words, a proper balance must exist, with the healthy species dominating the harmful microbes. Furthermore, a more diverse gut microbiome is correlated with health status. Each microbial group exerts different functions that together contribute to keeping homeostasis and healthy conditions in the human body.

Microbiome studies aim to decipher these species' potential collective or individual benefits and risks and their differences in human health. Although research does not indicate following a strict and specific diet, moving toward a more plant-based diet is probably the healthiest choice.


Plant-based diet, microbiome, dietary pattern, food groups.


Anderson-Haynes, S. (2021). Diet, disease, and the microbiome. Harvard Health Publishing. https://www.health.harvard.edu/blog/diet-disease-a... processed%2C plant-based diet,the gut microbiome to thrive.

Dahl, W. J., Rivero Mendoza, D., & Lambert, J. M. (2020). Diet, nutrients and the microbiome. In Progress in Molecular Biology and Translational Science (1st ed., Vol. 171). Elsevier Inc. https://doi.org/10.1016/bs.pmbts.2020.04.006

Debret, B. C. (2022). How an Anti-Inflammatory Plant- Based Diet Can Boost Your Gut Microbiome. One Green Planet.

GMFH Editing Team. (2022). Does a plant-based diet improve gut health? - interview with Hana Kahleova. Gut Microbiota for Health. https://www.gutmicrobiotaforhealth.com/does-a-plan...

Gray, D. (2019). 16-Week Vegan Diet Can Do Wonders for Gut Microbiome. Healthline. https://www.healthline.com/health-news/how-a-16-week-vegan-diet-can-improve-your-gut-microbes#Whats-the-gut-microbiome?

Harvard. (2021). The Microbiome. Goodman’s Medical Cell Biology. https://doi.org/10.1016/b978-0-12-817927-7.00015-6

Kubala, J., & Richards, L. (2020). What is the microbiome diet? 1–16.

Lichtenstein, A. H., Appel, L. J., Brands, M., Carnethon, M., Daniels, S., Franch, H. A., Franklin, B., Kris-Etherton, P., Harris, W. S., Howard, B., Karanja, N., Lefevre, M., Rudel, L., Sacks, F., Van Horn, L., Winston, M., & Wylie-Rosett, J. (2006). Diet and lifestyle recommendations revision 2006: A scientific statement from the American heart association nutrition committee. Circulation, 114(1), 82–96. https://doi.org/10.1161/CIRCULATIONAHA.106.176158

Mcclees, H. (2022). How a Plant-Based Diet Naturally Supports Your Microbiome. One Green Planet. https://www.onegreenplanet.org/natural-health/how-...

Park, J. E., Seo, J. E., Lee, J. Y., & Kwon, H. (2015). Distribution of Seven N-Nitrosamines in Food. Toxicological Research, 31(3), 279–288. https://doi.org/10.5487/TR.2015.31.3.279

Sheflin, A. M., Melby, C. L., Carbonero, F., & Weir, T. L. (2017). Linking dietary patterns with gut microbial composition and function. Gut Microbes, 8(2), 113–129. https://doi.org/10.1080/19490976.2016.1270809

Singh, R. K., Chang, H. W., Yan, D., Lee, K. M., Ucmak, D., Wong, K., Abrouk, M., Farahnik, B., Nakamura, M., Zhu, T. H., Bhutani, T., & Liao, W. (2017). Influence of diet on the gut microbiome and implications for human health. Journal of Translational Medicine, 15(1), 1–17. https://doi.org/10.1186/s12967-017-1175-y

Tomova, A., Bukovsky, I., Rembert, E., Yonas, W., Alwarith, J., Barnard, N. D., & Kahleova, H. (2019). The effects of vegetarian and vegan diets on gut microbiota. Frontiers in Nutrition, 6(April). https://doi.org/10.3389/fnut.2019.00047

Wallace, H. (2022). Plant-based diets and gut microbiome diversity. The Food Medic. https://thefoodmedic.co.uk/2022/02/plant-based-die...

Wu, G. D., Compher, C., Chen, E. Z., Smith, S. A., Shah, R. D., Bittinger, K., Chehoud, C., Albenberg, L. G., Nessel, L., Gilroy, E., Star, J., Weljie, A. M., Flint, H. J., Metz, D. C., Bennett, M. J., Li, H., Bushman, F. D., & Lewis, J. D. (2016). Comparative metabolomics in vegans and omnivores reveal constraints on diet-dependent gut microbiota metabolite production. Gut, 65(1), 63–72. https://doi.org/10.1136/gutjnl-2014-308209

Yirka, B. (2021). Increased flatulence from eating plant-based diet found to indicate healthier gut microbiome. Medical Xpress, 1. https://medicalxpress.com/news/2021-09-flatulence-...

Zaharudin, A. (2019). How a Plant - Based Diet Affects Your Gut Microbiome. GUTXY. https://www.gutxy.com/blog/how-a-plant-based-diet-...

Zimmer, J., Lange, B., Frick, J. S., Sauer, H., Zimmermann, K., Schwiertz, A., Rusch, K., Klosterhalfen, S., & Enck, P. (2012). A vegan or vegetarian diet substantially alters the human colonic faecal microbiota. European Journal of Clinical Nutrition, 66(1), 53–60. https://doi.org/10.1038/ejcn.2011.141