If whatever gut flora enterotype we are could play an important role in our risk of developing chronic diet-associated diseases (see What’s Your Gut Microbiome Enterotype?), can we alter our gut microbiome by altering our diet? Yes. Indeed, diet can rapidly and reproducibly alter the bacteria in our gut, as I discuss in my video How to Change Your Enterotype.

Concern has been growing that recent lifestyle trends––most notably the high-fat and high-sugar “Western diet”––have altered the composition and activity of our resident gut flora. “Such diet-induced changes to gut-associated microbial communities are now suspected of contributing to growing epidemics of chronic illness in the developed world,” yet it has remained unclear how quickly our gut bacteria could respond to dietary change. So, researchers prepared two diets: a “plant-based diet” rich in grains, beans, fruits, and vegetables, and an “animal-based diet” composed of meats, eggs, and cheeses. Neither diet contained refined sugars, as the researchers just wanted to test diets consisting of plant versus animal products. Within just one day of the animal-based diet hitting the gut, there was a significant shift.

What happens when you put a lifelong vegetarian on an animal-based diet? The vegetarian’s baseline microbiota was dominated by Prevotella, unlike everyone else eating a more standard American diet, who had large Bacteroides populations. Remarkably, the animal-based diet inverted the vegetarian’s Prevotella-to-Bacteroides ratio, causing the Bacteroides to outnumber the Prevotella within just four days on the animal-based diet. The entire gut flora got turned on its head and got completely reversed.

The fact that our gut can so rapidly switch between herbivorous and carnivorous functional profiles is probably a good thing in terms of evolution. If you bring down a mammoth and eat meat for a couple of days before switching back to plants, you want your gut to be able to deal with it. This flexibility is manifest in the diversity of human diets to this day, but what is the healthier state to be in most of the time?

Researchers looked at a number of different factors, such as the amount of short-chain fatty acids produced. Short-chain fatty acids, like acetate and butyrate, function to suppress inflammation and cancer, and our gut flora, when on plant-based diets, produce more of these than when on animal-based diets.

Other microbial metabolites, such as secondary bile acids, do the opposite, promoting the development of cancer. With a significant increase in bacterial enzyme activity to create these secondary bile acids on an animal-based diet, it’s no surprise there’s a significant increase in carcinogens like DCA, a secondary bile acid known to promote DNA damage and liver cancer. Microbial enzyme activity producing the rotten egg gas, hydrogen sulfide, also shoots up on an animal-based diet, which stinks because it’s stinky and also because it damages DNA and has been implicated in the development of inflammatory bowel diseases like ulcerative colitis. Hydrogen sulfide is made by pathogens such as Bilophila wadsworthia and is increased on the animal-based diet, again within just days of adopting it, supporting the link between diet and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. Conversely, the only pathogen you see more of on a plant-based diet is just a virus that infects spinach.

Do you know What’s Your Gut Microbiome Enterotype?

See more about gut microbiomes:

I’ve produced a series about the epic fermentation battle in the gut between protein and carbs that offers lots of insight on why it matters who we have living down there:

And check out some other videos on inflammatory bowel disease:

In health,

Michael Greger, M.D.