EXCLUSIVE: Your ultimate guide to a complete microbiome makeover

Take it from someone who wrote the book on the subject (literally): Most of what you’re reading about gut health these days is wrong.

And that’s putting it nicely. I published Boost Your Health with Bacteria years before the concept of gut health was trendy. And even then, I knew that with the fast pace of research—not to mention the amount of hype flying around—it was really only a matter of time before misinformation started to destroy the message at hand.

My aim in this two-part series is to help you cut through all the hype and understand what’s really triggering your imbalanced microbiome. The goal is to help you get back to the basics so that you can heal your gut—and optimize your overall health—from the inside out.

And today, we’re specifically going to focus on the monumental role diet plays in the state of your microbiome.

But first, I want to talk about why the health of your microbiome needs to become a top priority in your life—starting now.

Good health starts in your gut

It may be the trendy topic du jour, but the laser focus on gut health is definitely necessary. Because I’m not exaggerating when I call it one of the main drivers of your health.

For one, it’s obvious that many Americans struggle to balance their microbiomes. The alarming rise in the diagnosis of various digestive disorders perfectly illustrates this point. (I’ll touch on some of these in just a moment.)

Simply put, the state of our insides has turned into a true health crisis. Some of my patients who’ve come to me for help with an off-kilter microbiome have told me how much of an impact this has had on their quality of life.

For many, an unhealthy gut dictated their day-to-day happenings (limiting what and when they could eat, requiring a close proximity to a bathroom at all times, etc.).

But the fact is, your gut  does so much more than digest the food you eat. It helps your body process and absorb critical nutrients. It generates approximately 80 percent of your immune cells. And it also produces brain neurotransmitters—like serotonin—that keep you happy.

In short, your gut helps to keep things running in tip-top shape… It truly is your “second brain.” And when you don’t care for it, the health implications are serious.

That’s because an imbalanced microbiome is a hotbed of inflammation. And if you’ve been a reader of mine for a while now, you know that inflammation leads directly to chronic illness.

So if your gut is compromised, you’ll ultimately have a lot more to contend with than just digestive symptoms like IBS, bloating, constipation, or colitis.

You’ll also be at a dramatically higher risk of conditions like eczema, psoriasis, diabetes, heart disease, osteoporosis, obesity, and even cancer.

And those are just a few of the potential consequences, all of which trace back to microbiome imbalance. From fatigue to brain fog to insomnia… to nagging aches and pains.

The list is literally endless. And if you’ve got a health concern, chances are good that your gut bacteria are both a part of the problem and the solution.

The biggest microbiome mistake you can make

There are plenty of reasons why Americans’ microbiomes are in peril… but hands down, the biggest microbiome mistake you can make is following the Standard American Diet (SAD).1

People are eating too many processed foods, GMO-laced grains, pesticide-covered produce, and way too much sugar. And they’re not getting nearly enough healthy fats, high-quality fiber, or absorbable nutrients. (I’ll talk more specifically about these dietary factors later on.)

Research shows that simple sugars erode bacterial diversity. (And as I’ve said time and again, when it comes to your microbiome, diversity in your gut flora is the key to good health.) High starch and high fructose foods also provide a breeding ground for dysbiosis, an imbalance in gut flora.

Food additives are also linked to inflammation-producing bacterial overgrowth—as are the advanced glycation end-products (AGEs) that result from industrial food processing. And when you pair that with a high intake of antibiotic-loaded, factory farmed animal products, it’s easy to spot the problem.

But what the typical Western diet doesn’t feature is just as important—specifically, an abundance of whole foods, polyphenols, and healthy fats.

Mainstream discussions about feeding the microbiome almost always make two critical mistakes. First, they put high protein and high fat intake on the “black list,” along with excessive sugar consumption. And second, they do this without any regard for the quality of the protein and the fat consumed—when in fact, these are essential to good health. That is,  when they come from the right sources.

As a result, low-carb diets have been dismissed as a disaster for your microbiome. And a handful of dietary myths about how to best feed your body’s bacterial population continue to persist. So let me address a couple of those tall tales now.

A healthy microbiome doesn’t run on yogurt

Those popular “probiotic-packed” yogurts are pretty much the last thing you want to put in your body. That’s because they’re usually packed with processed sugars. Which negates any potential benefit those good bacteria might have had, by instead providing bad bacteria and yeast with their favorite food.

In my opinion, there are much better ways to get active cultures into your diet without having to rely on these types of foods.

I’ll talk more about this in just a moment. But for now, I want to bust one more digestive health myth. And that’s the notion that grains are somehow necessary for a healthy gut.

It’s easy to see where this misconception comes from. Because the truth is, fermentable fiber is important. And here’s what I mean by that.

Fiber is by its very nature undigestible—we don’t have enzymes to break it down, and fiber-rich foods pass through the digestive tract more or less whole. This makes it the perfect food for microbes in your gut.

The natural fermentation process that occurs when fiber moves through your system produces all kinds of beneficial byproducts—like short-chain fatty acids, butyrate, propionate, and acetate—which provide energy and integrity to the cells lining your gut. This not only improves digestion, but it keeps harmful bacteria out and food particles in, where they belong.

But there are a few obvious problems with choosing grains—even “healthy” whole grains—over non-starchy vegetables in the quest to boost your fiber intake.

Why “healthy” whole grains are the worst source of fiber

First and foremost, sugar is sugar as far as your body is concerned. And while some forms, like high-fructose corn syrup, are especially damaging, your body won’t treat a slice of bread any differently than a piece of candy.

Both will raise your blood sugar, spike insulin, trigger inflammation, and make you fat. And both provide a breeding ground for bad bacteria to grow, in excess.

But bread has an additional strike against it in the digestive department: gluten. This wheat protein is easily one of the top causes of digestive problems—indigestion, GERD, bloating, gas, constipation, diarrhea, and of course, IBS.

In fact, all grains—including gluten-free grains like corn and oats—contain potentially aggravating proteins that can pave the way to gut permeability, or leaky gut syndrome.

Needless to say, this is counterproductive to any effort to build a thriving microbiome. Which is why whole grain products really aren’t the gut-nourishing foods that most people think they are.

And yes, I realize this advice may sound counterintuitive. Especially if you’re steeped in the message that so-called “healthy” whole grains are an invaluable source of fiber that your gut needs in order to function…

But let’s face it. That whole “fiber” story is a medical myth in itself. Especially since you can get more than enough fiber to meet your body’s needs from vegetables alone.

Not only that, but whole grains are also chock-full of insoluble fiber (which isn’t easily absorbed by the gut). Plus, too much insoluble fiber can trigger diarrhea and leave you feeling bloated and dehydrated.

So now that we’ve covered what not to feed yoour microbiome, let’s move on to what you should

Feeding your friendly flora

I sing the praises of probiotics all the time. But what a lot of people don’t account for is that this good probiotic bacteria needs nourishment, too. And it comes in the form of prebiotics, which research shows are just as important.

One study, for example, showed that diabetic women who supplemented with a prebiotic called inulin benefited from significant drops in both fasting blood sugar and HbA1c (that all-important measure of long-term glucose control).2

Antioxidant activity spiked, too—and I don’t think I need to explain why that’s a major plus.

Inulin belongs to a class of carbohydrates called fructans. And it’s abundant in onions, garlic, leeks, asparagus, and artichokes—just to name a few prebiotic goldmines. Which is why I recommend eating as many of these foods as your digestive system will comfortably allow.

Of course, prebiotics set the stage for probiotics. And as I mentioned earlier, yogurt isn’t really the best way to get that good bacteria into your diet.

For an added microbiome boost, you can include naturally fermented foods into your diet. Foods like sauerkraut, kimchi, and fermented vegetables contain natural probiotics—and they’re not packed with sugar and other mystery ingredients.

The A-List Diet checks all the boxes

The main takeaway: Optimizing your own personal gut microbiome involves only three simple, but critical steps:

  1. Avoid sugar at all costs.
  2. Fill up on lean protein, healthy fats, a little fruit, and plenty of fiber-rich vegetables.
  3. Eat prebiotic-rich foods to nourish your probiotics.

For now, I want to leave you with this so you can get started on your microbiome makeover right away. And it starts with your eating habits. Fortunately, my A-List Diet is the only diet plan you’ll need to keep your microbiome thriving. (For more information, visit www.AListDietBook.com.)

There’s a whole lot of scientific literature out there touting the probiotic benefits of a Mediterranean-style diet. And my A-List Diet—just like my Hamptons Diet before it—is a variation on that theme.

The bottom line is that what you eat matters to your microbiome—perhaps more than anything else.

But it’s not the only thing that matters. And next month, in part two of my Microbiome Makeover, I’ll outline a few more essential steps in maintaining a rich and diverse bacterial population, including lifestyle factors and supplement superstars.

Before you know it, my plan will get your digestive system running like a well-oiled machine—and keep your whole body leaner and healthier because of it.

FODMAPs are a double-edged sword

There’s a caveat worth mentioning for anyone undertaking a dietary microbiome rehab. And that’s to tread carefully with FODMAPs.

FODMAP stands for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols. And unfortunately, they present something of a catch-22 for IBS sufferers.

On the one hand, as the term “fermentable” suggests, some powerful prebiotics fall into this category. On the other hand, without the right balance of good bacteria, an excess of these foods can trigger a long list of uncomfortable digestive issues—like bloating, gas, and pain—in some people.

My A-List Diet automatically eliminates a lot of the usual suspects, such as: high fructose corn syrup, agave, honey, and artificial sweeteners. (Note that sugar alcohols like sorbitol, mannitol, and xylitol fall into this category, too.)

But there are quite a few FODMAPs that would normally get an enthusiastic “thumbs-up” on my A-List diet that you may want to limit:

If you have IBS, avoiding all of these foods may be necessary to get relief. But if your gut can tolerate them, filling up on these A-List approved foods will actually keep your microbiome thriving.


  1. ncbi.nlm.nih.gov/pmc/articles/PMC5385025/
  2. “Effects of High Performance Inulin Supplementation on Glycemic Control and Antioxidant Status in Women with Type 2 Diabetes.” Diabetes Metab J. 2013 April; 37(2): 140-148.
  3. “Gut Microbiome Composition in Non-human Primates Consuming a Western or Mediterranean Diet.” Front Nutr. 2018 Apr 25;5:28.