Diet & Nutrition

Your Diet Changes Your Microbiome, Fast

Your Diet Changes Your Microbiome, Fast

Whether you’re a lover of dairy and meats or swear by a vegan diet, new research suggests that your gut microbiome changes rapidly in response to your meal choices.

A new study by microbiologist and professor Lawrence David of the Duke Institute for Genome Sciences and Policy sought to discover the answer to the question: what exactly is the relationship between the food that we eat and our gut bacteria?

Although we’ve always known that our health changes based on the food we eat, David’s study proves that when we consume certain foods, our microbiome changes incredibly quickly - beginning just hours after a meal.1

The near immediate effect of diet on the microbes in our body is an important finding in the scientific community. Up until now, many scientists assumed it could take months or even years to shift microbial composition, but now we're learning that significant changes can occur within just a 24-hour period!

This expedient shift in the microbiome is exciting news as we learn about the indispensable role that our microbes play in almost every aspect of our health and wellness.

How exactly does our food interact with our microbes?

David’s study involved observing the apparent changes in microbiota that fluctuated based on the type of diet consumed by the study group.

Study participants were asked to consume either a diet high in plant-based foods or a meat-based diet, and then David and his team scrutinized how their gut bacteria responded. As participants switched between these two opposing regimens, their microbiomes experienced a shift in bacteria mirroring that of common herbivores or carnivores—each harboring a unique set of microbes precise to the nutrients consumed.

Because we harvest meat from previously living animals, it is naturally filled with bacteria. That’s one reason participants who exclusively ate animal products, like meat and cheese, experienced the most dramatic changes in their bacterial community—with 22 animal-specific microbial species found in the participant’s microbiomes, along with a decrease in the beneficial bacteria that are necessary to metabolize complex carbohydrates.

David further found that the alterations in gut bacteria were less extreme (but more valuable) for those who consumed more plant-based foods. While participants were not undergoing extensive changes in their microbiome every time they ate a meal, it appeared that a small number of additional species of beneficial bacteria settled in their gut. These findings opposed those of the meat-eating group, who saw a reduction in certain bacterial species throughout the course of the study.1

While we don’t know if modern agricultural and processing practices (which often subject the meat we buy at the supermarket to hormones, antibiotics, pesticides, and toxins) might have influenced this reduction in helpful bacteria, it is quite interesting that the very same microbes being reduced in the carnivore group were found to be abundant in those who consumed a diet rich in whole fruits and vegetables.

The Benefits of a Plant-Based Diet

David's study affirms that eating a plant-centric diet can provide a gentle, microbial shift; encouraging a high number of prebiotic fibers that nourish your resident flora so that you can better metabolize the foods that you eat and absorb the maximum amount of nutrition possible from all that you consume.

Naturally loaded with fiber, vitamin A, vitamin C, essential B vitamins, and countless other nutrients, a diet high in fruits and vegetables can be powerfully beneficial in supporting our immune and digestive functions. Now we know for sure that eating these foods can positively impact our microbiomes with every meal.

With 80% of the immune system residing within the gut environment, it’s particularly important to maintain an abundance of the beneficial bacteria in your GI tract that keep your core foundation of health working optimally.

Unfortunately, the standard American diet isn’t doing our microbiome any favors. From sugary sustenance loaded with artificial ingredients to deep-fried meats laden with remnants of antibiotics and artificial gunk, the diversity of our gut microbes is being significantly reduced.2 And even some foods that we think are “plant-based” or healthy really aren’t so great—their ingredients are often refined to the point that the nutrition is essentially gone and what remains offers minimal benefit to our bodies.

How Probiotics Can Help Keep You Feeling Great

When faced with a lack of healthy gut flora, we leave room for invaders to proliferate and rule the roost. When it becomes challenging to get a sufficient number or variety of bacteria and prebiotics from our diet, probiotic supplementation is an excellent way to help maintain wellness.

Probiotics are gut-friendly bacteria that can help support and replenish the microbiome. When abundant populations of probiotics are present in the large intestine, unfavorable organisms don’t have the space they need to thrive. A supplement with a variety of diverse probiotic strains, like Hyperbiotics PRO-15, can help support your gut health, regularity, energy levels, and overall health. Probiotics can even support healthy glucose levels already within the normal range and help you with healthy weight management.

Scientific research about how dietary choices fully impact our microbiomes is still developing. As our knowledge of the microbiome increases, it’s important to be mindful of what we eat, since everything we put into our bodies can change our delicate microbiome.

A healthy microbiome helps keep your immune system and digestion efficient and strong, encourages healthy digestion, and helps your body perform at its most vibrant, naturally.


1. David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., . . . Turnbaugh, P. J. (2013). Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505(7484), 559-563.

2. Shehata, A. A., Schrödl, W., Aldin, A. A., Hafez, H. M., & Krüger, M. (2012). The Effect of Glyphosate on Potential Pathogens and Beneficial Members of Poultry Microbiota In Vitro. Current Microbiology, 66(4), 350-358.

Julie Hays is the Communications Director here at Hyperbiotics. Health writer and mama of two little girls, Julie's on a mission to empower others to live lives free of the microbial depletion many of us face today. For more ideas on how you can maximize wellness and benefit from the power of probiotics, be sure to subscribe to our newsletter.