The Microbiome Diet: What It Is and What It Did for Me


Getty Images / Design by Michela Buttignol

Every year, it's the same: Around March or April, after months of winter hibernation and all the takeout, I get a hankering to give my diet an overhaul. Usually it's a fairly hardcore detox, and usually I'm miserable for a couple of weeks as a result. But in all fairness, it tends to do the trick in displacing a few extra pounds and giving my body a refresh.

This year was different. Perhaps it's the fact that I've spent a good part of the past few months traveling, but I have a feeling that a healthier attitude toward my body is more likely the reason. Either way, when spring rolled around again, I ultimately shrugged my shoulders and said, "meh." Even though my diet could use a reboot, the thought of revisiting the strict plans of years past—raw vegan, ketogenic, even a god-awful stint with the Master Cleanse—just seemed too exhausting to even consider. What was the point?

Then, totally by chance, I was on Amazon searching for a vegan probiotic when a book called The Microbiome Diet ($16) appeared as a recommended purchase. Noting the nearly 200 five-star reviews, I clicked "add to cart." It showed up at my doorstep the next day, along with said vegan probiotics, a hand-held steamer, my favorite Japanese sheet masks, and TLC's Crazysexycool on vinyl. (Love you, Amazon.)

The glowing recommendations from shoppers weren't the only reason why I was inclined to check it out. Written by Dr. Raphael Kellman, The Microbiome Diet is based on the idea that the microorganisms in our gut—the "good" bacteria—play a huge role in the way our body functions. Kellman, who runs a wellness clinic in New York City, posits that by eating a certain way, we can encourage an environment that helps these organisms thrive, in turn allowing for more efficient digestion, absorption of nutrients, overall well-being—and yes, weight loss. 

microbiome diet
Michela Buttignol/Byrdie

Meet the Expert

Dr. Raphael Kellman is known worldwide as the "Microbiome Doctor," and has decades of experience working with patients holistically, treating unexplained and unresolved health concerns including but not limited to brain fog and fatigue.

In the beauty and wellness sphere, microorganisms are an exciting area of research with major potential. Because everyone hosts a different variety of bacteria (by the trillion), many experts believe that studying these ecosystems on an individual level may provide a ton of insight on everything from why different diets work better for some than others to the way our skin reacts to different ingredients. By learning which regimens foster the right combination of bacteria for your body to function optimally, eating plans, skincare routines, and more could be highly personalized in the future. Pretty cool stuff—and it's why probiotics are trending in so many sectors of the beauty industry.

Of course, the real clincher was flipping through the book and realizing that the diet's requirements are actually very doable. While certain foods were definitely off-limits, it wasn't too much of a stretch from my usual plant-based diet, and most importantly, I could drink coffee. (Even wine is allowed on this plan!) It's so low-key, I couldn't help but feel a little skeptical, despite my usual enthusiasm for all things bacteria. Would this actually do anything? I'd have to find out.

How It Works

How It Works
Origin Essentials Probiotic $18.00

As mentioned, The Microbiome Diet centers around the idea that the key to optimal body function—and in turn, high metabolism and weight loss—is a thriving internal ecosystem of bacteria. "Research reveals that when the microbiome goes out of balance, people often gain weight, even when they haven’t changed their diet or exercise," Kellman writes. "An imbalanced microbiome often dooms just about any diet to failure. When the microbiome is balanced, however, people often lose weight, even when they don’t make any other changes."

It makes plenty of sense: we have as many bacterial cells as human cells, and there's strength in numbers. "These intestinal organisms—bacteria—digest your food, govern your appetite, control your metabolism, orchestrate your immune system, influence your mood, and even help determine how your genes are expressed," Kellman says. "They have a major impact on whether your heart is healthy, whether your bones develop properly, and whether your brain feels sharp and clear or fuzzy and unfocused. They sustain the gastrointestinal tract so your food is properly digested and you get all the nourishment you need. They produce crucial vitamins and other nutrients. They even manufacture natural antibiotics."

While current research suggests that there will be a time in the near-ish future when we can discriminate the types and proportions of this bacteria for more personalized diets and medicine, Keller's plan focuses more on fostering a digestive environment—your microbiome—where good bacteria can thrive in general. "An imbalanced microbiome will overpower you with cravings for sugar and unhealthy fats, slowing down your metabolism and increasing your appetite," he says. "Conversely, a balanced microbiome will lead you to crave healthy foods, feel hungry and full at the right times, and, most important, rev up your metabolism and cause you to burn fat instead of storing it." By removing certain foods that cause inflammation in the gut and supplementing a better diet with probiotics, he argues, it's fairly easy to restore health and balance to your digestive system and in turn encourage weight loss.

The Plan

The Plan

A sample homemade meal: kale and cauliflower rice bowl with broccoli, avocado, and chickpeas.

Full disclosure: While Kellman suggests cycling through a few different phases of his diet, I stuck with his first phase for a full three weeks until I was satisfied with the results. The first phase is basically an elimination diet, something that physicians and dietitians may rely on to restore intestinal health in their patients.

A sample homemade meal: cauliflower rice with barbecue jackfruit, avocado, and pickled veggies.


Processed foods of all kinds are out of the question, as are sugar, eggs, soy, gluten, dairy, yeast, dried fruits, and fungus. Even gluten-free grains like quinoa and brown rice and starchy vegetables and legumes like potatoes, peanuts, and kidney beans are off-limits, as the diet suggests the sugars in those foods can feed bad bacteria. 


Most non-starchy veggies and fruits are just fine, with a special emphasis on fermented foods like pickles, sauerkraut, and kombucha (which contain digestion-friendly bacteria). Chickpeas and lentils are the only legumes permitted, and Kellman advises sticking with coconut oil or ghee. For protein, beef, chicken, low-mercury fish, lamb, and shellfish are all fine (though as low-processed as possible).

Kellman also suggests a variety of bacteria-promoting supplements to ingest daily, the most important of which being a probiotic and prebiotic. And here's where things take a turn for the amazing: A couple cups of coffee per day are allowed, as are wine and beer, since they're fermented. (A 2016 study noted that coffee and wine are great for your gut. Cue the happy dance!)

A sample homemade meal: zucchini noodles with avocado-walnut pesto.


It only gets better: Kellman says to avoid calorie-counting and tracking portion size so that you can learn to rely on intuitive eating and your body's natural sense of hunger. Aside from the list of foods to eat and avoid, he also says to avoid stress since that alone has a huge impact on gut health.

The Results

butyric acid
Ecological Formulas Butyric Acid Prebiotic $17.00

Honestly, when I saw that coffee is permitted, I was sold—it's historically the lack of caffeine that almost kills me (or rather, makes me want to kill others) when trying other cleanses. And the rest was totally easy, at least most of the time. Did I have to avoid eating out? Did there ever come a point when all I wanted was to face-plant in a bowl of pasta? Yes and yes. But it was a small price to pay for feeling nourished, caffeinated, and in only a matter of days, de-bloated and energized. I didn't feel hangry once.

I don't weigh myself as a rule, but based on how my clothes fit, I did lose a few pounds. More importantly, I felt great. By the end of the first week, it felt like my body was in balance: My digestion was humming along smoothly, the fatigue that normally plagues my life was ancient history, I was sleeping well, and I had the energy and motivation to work out, which only bolstered this heightened sense of well-being. I even fell in love with a few of the cleanse recipes I threw together. (That jackfruit barbecue bowl = my new favorite thing ever).

All in all, it was just the reboot my body needed, without any of the usual pain and drama. When next spring rolls around, I won't be brainstorming my next cleanse—I've already got this one on the books.

Article Sources
Byrdie takes every opportunity to use high-quality sources, including peer-reviewed studies, to support the facts within our articles. Read our editorial guidelines to learn more about how we keep our content accurate, reliable and trustworthy.
  1. Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the bodyPLoS Biol. 2016;14(8):e1002533. doi:10.1371/journal.pbio.1002533

  2. Nielsen J. Systems Biology of metabolism: a driver for developing personalized and precision medicineCell Metab. 2017;25(3):572-579. doi:10.1016/j.cmet.2017.02.002

  3. Cleveland Clinic. Find the source of your food intolerance (and finally find relief). Updated March 13, 2019.

  4. Zhernakova A, Kurilshikov A, Bonder MJ, et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversityScience. 2016;352(6285):565-569. doi:10.1126/science.aad3369

Related Stories