There is a common saying that goes, “You are what you eat.” But by the time you’re finished reading this article, you’ll find that something like, “You are what your microbes eat” may be more accurate. The trillions of microbes that dwell in our large intestines (i.e., the gut microbiome) play a vital role in our health. Disrupting their balance is associated with a host of diseases — including diabetes, obesity and other gastrointestinal (GI) diseases. With our gut microbes exposed to all kinds of food we eat every day, it’s inevitable that our diets impact them — and, in turn, our health. So, how long does it take for the gut microbiome to change after switching diets?

How long does it take for the gut microbiome to change?

What we eat impacts the microbes that call our guts home. But you might be surprised to hear that our microbial communities can respond drastically to dietary changes in as little as three days. This is exactly what a landmark study published in 2013 determined. In the study, 10 people followed a plant-based diet (grains, legumes, fruits and vegetables) for five days and, during a separate five-day time period, an animal-based diet (meats, eggs and cheeses). The researchers made some interesting observations:

• The animal-based diet caused far more substantial gut microbiome changes than did the plant-based diet.
  
  
• Bacteria that digest plant sugars decreased during the animal-based diet time period, while bile acid-resistant microbes increased.
  
  
• The chemical processes that our gut microbes perform also changed: When participants switched to an animal-based diet, two short-chain fatty acids (SCFAs: molecules that help protect the gut and benefit other parts of the body including the brain, liver, spleen and muscles) — acetate and butyrate — decreased. In contrast, bile acids increased in participants eating the animal-based diet.

Interestingly, bacteria found on cheeses, such as Lactococcus spp., were measured in higher proportions in people eating the animal-based diet, showing for the first time that microbes from foods we ingest can actually stick around in our guts — at least for a short period of time.

The study authors also observed an increase in the abundance and activity of a specific species, Bilophia wadsworthia, in people eating the animal-based diet. This observation was particularly interesting given existing work in mice demonstrating that mice eating a diet rich in saturated fats and with inflamed guts had more of this microbe in their large intestines. These results support a potential link between dietary fat, bile acids and increases in microorganisms capable of triggering inflammatory bowel disease (IBD). However, these early studies didn’t determine whether specific foods were “healthy” or “unhealthy” for the gut microbiome or whether specific foods could trigger intestinal inflammation via the microbiome.

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The diet-microbiome-health connection

In the nearly ten years since that landmark study was published, follow-up research has begun to unravel the complex relationship between our gut microbes and our health. It has proven much more difficult to identify microbiome signatures associated with health versus disease, but scientists have made some important observations:

• Similar to the landmark 2013 study, a large study published in 2021 identified different sets of bacteria associated with the plant- or meat-based portions of their controlled diet. Interestingly, some of the correlations identified in the study were associated with bacteria yet to be isolated.
  
  
• Another recent study determined that participants who ate a diverse plant-based and fiber-rich diet harbored more bacteria capable of producing short chain fatty acids (SCFAs).

Dozens of additional studies performed throughout the past decade support these important observations, which has led most top scientists to the following conclusion: “Diets that score higher in healthfulness or diversity, such as plant-based diets, have altered ratios of specific bacteria, including an increase in short-chain fatty acid producers, which in turn have been linked to improved metabolic markers and lowered cancer risk. Contrarily, numerous studies have implicated less healthy, lower-scoring diets — such as the Western diet — with reduced intestinal epithelial defenses and promotion of specific bacteria that affect carcinogenic pathways.”

But while the research strongly points to an important connection between our gut microbes, our diet and our health, no cause-and-effect relationship has been established yet. Additionally, the relationship is complicated even further considering other research showing that a number of factors (medication use, stress, travel, exercise, and more) can also significantly impact our gut microbes.

What can we do to keep our guts healthy?

In addition to the limitations of the studies described above, there are some other important unknowns that can make it difficult to understand the precise relationship between our gut microbes, our diets and our health:

• How much of a food impacts our gut health? In other words, how precise do we have to be with our diets to keep our guts healthy? The 2013 study observed changes to the gut microbiome when people eating recommended levels of fiber switched to a pure animal-based diet. But, what happens when we make more subtle changes?
  
  
• How do changes in our gut chemistry enacted by the gut microbiome affect our body’s immune responses in disease? When bacteria digest different nutrients, they release compounds like SCFAs that can benefit our health. But what about other kinds of compounds, including potentially harmful ones? How might those impact our immune systems?
  
• What role do individual responses to dietary changes play? Research has shown that not everyone, and not everyone’s microbiome, responds the exact same way to dietary changes. Additionally, what might be good for one set of people might not be good for all: for example, certain fiber-rich foods (called FODMAPS), which are generally beneficial, can actually make symptoms worse for people with inflammatory bowel syndrome (IBS).

It’s the difficulties in providing a robust answer to these questions that make it hard to determine whether changes to the gut microbiome cause a disease or are simply just another symptom of disease. Despite this, studies have provided a general set of recommendations for keeping our gut microbes, and our guts, healthy:

• Fiber-rich foods: Dietary fibers are indigestible carbohydrates that our gut bacteria can digest. They are found in whole foods prominent in plant-based diets and whole grains. Fibers serve a wide range of functions including providing a nutrient source for our gut microbes, enhancing nutrient absorption, preventing obesity and maintaining blood sugar control.
  
  
• Foods that boost our immune system: Our immune system plays an important role in fighting infection and repairing tissue damage from injury. A means to shut off inflammation is also essential to prevent our immune system from damaging our guts. A balanced diet comprised of foods rich in vitamins and minerals will help keep this balance. This includes fruits and vegetables, nuts and legumes, and foods of animal origins. Foods rich in antioxidants — such as berries, spinach, and other fruits and vegetables — will also help.
  
• Polyphenols: Polyphenols have antioxidant properties. Eating foods rich in polyphenols is linked with reduced risk of type 2 diabetes and heart disease, reduced UV damage and improved digestion. Foods rich in polyphenols include fruits, vegetables, legumes, and nuts and seeds.

Key takeaways

Our diet plays an important role in our gut health — in part because of the impact our diets have on our gut microbiomes. A diverse diet including plenty of plant-based foods is associated with microbial production of compounds beneficial for our gut health, while the typical high-fat Western diet has been associated with the proliferation of microbes that have been associated with several diseases. How long does it take for the gut microbiome to change? While many questions remain regarding how to tailor our diets, we do know that what we eat can impact our gut health relatively quickly. Pending the time when science reveals more about how specific dietary interventions can impact our gut microbiomes and our health, the best thing we can do is to eat a diet rich in fiber- and polyphenol-rich plants such as legumes, nuts, seeds, fruits and vegetables.