How to Fix Your Gut Right Now

A doctor and a nutritionist give you their best advice on maintaining a healthy microbiome, based on the latest research and their expert dietary recommendations.

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fermented foods
Photo by Ronald Tsang

The delicate balance of your microbiome – the bacteria, yeast, viruses and fungi that live in your gut and on your skin – just might be calling the shots when it comes to your digestion, weight and even your mood. But surprisingly, i doesn’t take long to make meaningful changes. Get the need-to-know facts and our doctor-prescribed steps to help cultivate your inner ecosystem for optimal health.

Tell someone you’re going to talk to them about the microbiome – the name given to the collection of trillions of nonhuman cells that live in your gut and on your skin – and you’d probably be met with a big yawn.

Now, tell them that the microbiome might be the underlying reason they haven’t been able to lose weight, the reason they get sick more than their friends and maybe even the reason they get anxious or depressed, and suddenly their ears perk up like a French bulldog’s.

So what is the microbiome, anyway, and why is everyone – at least everyone in the field of nutrition and health – talking about it?

Most people think of microbes, such as bacteria, viruses, yeast and fungi, as something that’s potentially dangerous to them (just look at all the antibacterial handsoaps on the market!). But having the right strains of microorganisms in your body – and just as importantly, the balance among them – is crucial to good health. I often liken the microbiome to a vast and complex garden, albeit one that happens to live in your gut and on your skin. Like an ordinary garden, the microbiome contains species of flora that are mostly good (like roses or daylilies), species that are mostly not good (like dandelion weeds) plus a supporting cast of over 35,000 other species that play intertwining roles. In fact, a consortium of almost 80 universities and scientific organizations are currently contributing research to the Human Microbiome Project in an attempt to decode the normal microbial makeup of our bodies.

A novel way to look at weight

We are only now beginning to appreciate the profoundly important role these tiny microbes have on just about everything that has to do with our health. Take weight, for example. Among the thousands of bacterial species we’re all home to, two in particular have a profound effect on what happens to the food we eat. Firmicutes are the ultimate in fat-loving microbes. They can convert just about anything you eat into a muffin top. Their kissing cousins, the Bacteroidetes, are the exact opposite. When the Bacteroidetes get to work on some food you just chowed down on, it’s like a school of piranhas in a feeding frenzy – they’ll incinerate calories almost as fast as you can ingest them.

As you can imagine, if you have more Firmicutes than Bacteroidetes living in your gut, you’re going to have a particularly hard time losing weight. Transplant the microbes from an obese mouse into the gut of a lean mouse and the lean mouse becomes fat, even if it eats the exact same diet it’s always eaten. Not surprisingly, research confirms that obese people have higher levels of Firmicutes in their gut than lean people, while lean folks have a predominance of Bacteroidetes.

Not only that, but higher levels of Firmicutes “turn on” the genes that increase the risk for diabetes, obesity and heart disease. “The relative proportion of these two groups to each other, the Firmicutes-to-Bacteroidetes (or F/B) ratio, is critical for determining health and risk for illness,” says board-certified neurologist David Perlmutter, MD, in his most recent book, Brain Maker (Little, Brown and Company, 2015) in which he demonstrates the link between the microbiome and many neurological diseases.

The gut-brain connection

The notion of the gut being connected to the brain is not new. Michael Gershon, MD, wrote an iconic book about the subject back in 1999 called The Second Brain (Harper Perennial), in which he pointed out that 90% of your serotonin, the “feel good” neurotransmitter, actually comes from the gut – demonstrating that terms like “gut feeling” and “gut wrenching” have a scientific basis.

Animal research has shown a powerful connection between microbes in the gut and all sorts of symptoms normally thought to be psychological in nature. The probiotic strain Lactobacillus rhamnosus GG helps reduce obsessive-compulsive behavior in mice, while Lactobacillus helveticus can decrease their anxiety. In one experiment, researchers transplanted bacteria from normal-acting mice into the guts of mice that had been bred to be anxious. The formerly anxious mice started acting more bold. Conversely, when they transplanted microbes from the anxious mice into the normal mice, the formerly normal mice started behaving like the Woody Allen character in Annie Hall.

And if weight and anxiety weren’t enough, research has also demonstrated a strong connection between the microbiome and conditions as varied as autism, depression and inflammatory bowel diseases such as Crohn’s and ulcerative colitis.

Which brings us to one of the maddening things about microbiome research: The science of description has far outpaced the science of prescription. To date, we are way better at describing what the microbiome is and what it does than we are at knowing precisely how to keep it healthy.

Everyone now accepts that the microbiome is deeply involved in aspects of human physiology, metabolism and psychology. We even have some very detailed descriptions of the little buggers. We know, for example, that the microbiota on the skin are very different than, say, the microbiota in the gut. And we know that maintaining a healthy microbiome is one of the most important health strategies on the planet, far more important than anyone ever thought just a few short years ago.

But just because we’re not 100% sure of how to create a completely healthy microbiome, it doesn’t mean we’re clueless. In the course of my work, I have had many opportunities to speak with and interview dozens of experts on health and metabolism, and it’s nearly impossible to talk to any of them – no matter what their specialty – without hearing about the microbiome. And though the final word on microbiome health is very, very far from being written, virtually all experts seem to agree on three key actions you could take right now to increase the odds of a healthy gut.

Step One: Eat foods teeming with probiotics.

Probiotics are the class of microbes in your gut that we think of as “good.” They help us digest food, absorb nutrients, keep “bad” microbes (like Candida) from taking over and stimulate the immune system. Well-known examples of these strains are the Lactobacillus species (such as Lactobacillus acidophilus) and the Bifidobacterium species (such as B. bifidum and B. longum). The Lactobacillus family supports microbes mainly in the small intestine while the action of the Bifidobacterium species is concentrated in the large intestine.

Knowing what foods contain probiotics is easy – you just have to remember one word: fermentation. The very process of fermentation produces probiotics galore, which is one reason that virtually everyone in the integrative health and functional medicine world recommends making them a regular part of your diet. Examples are yogurt, kefir, the Korean dish kimchi, sauerkraut, tempeh, kombucha and real (fermented) soy sauce. And even if you do eat these foods on a regular basis (most of us, unfortunately, don’t), a probiotic supplement makes a lot of sense.

Probiotic supplementation is important at all times, especially if you’ve been on antibiotics. Remember that antibiotics are like the nuclear option for your gut – they basically wipe out everything. So yes, you can (and should) take probiotics while you’re on antibiotics (just not at the same time; the National Institutes of Health recommends taking probiotics 2 hours before or after antibiotics).

Get Started now! Make your own fermented veggies at home. Our guide shows you how.

See also 3 Nutritious Meals Featuring Fermented Veggies

Step Two: Go easy on the junk carbs.

Sugar feeds all the bad stuff in your body (from Candida to cancer), disrupts your hormonal balance, is inflammatory and – wait for it – is generally disruptive to the microbiome. Not only that, many of the foods that contain a lot of sugar (or, just as bad, convert to sugar in a heartbeat), are wheat-based, which poses a whole different set of problems. Wheat’s not a problem for everybody, but it’s a definite problem for many, and for those people, high-grain diets are a prescription for gut inflammation, hardly a good strategy for strengthening the integrity of the microbiome.

Not one of the experts I interviewed still recommended a low-fat diet. In fact, most were contemptuous of it, and many took an even stronger position, suggesting that the very opposite of a low-fat diet (i.e., one high in fat and low in carbs) could balance hormones, lower inflammation and increase the health of the microbiome. Perlmutter, for example, lauded the benefits of a high-fat diet. “Fat is the preferred fuel of human metabolism,” he says.

See also The Six Not-So-Superfoods to Nix Now.

Step Three: Eat foods rich in prebiotics.

Prebiotics are simply food for probiotics. Remember, probiotics are living critters – they’re microbes, sure, but even a microbe’s gotta eat! And nothing looks tastier to a microbe living in your gut than prebiotics, nature’s food for the creatures that make up your intestinal flora. What’s really cool is that prebiotics preferentially feed the “good guys” in your intestinal garden. It’s as if they selectively channeled themselves to feed your “roses” rather than your “weeds.”
Prebiotics are usually some type of fiber, the preferred fuel for gut bacteria (and another reason fiber is so important for your health). The little buggers feast on this fiber and ferment it, turning it into compounds like butyric acid, which nourish the intestinal lining and reduce inflammation.

Unfortunately, nobody eats foods that are naturally high in prebiotics. Or almost no one. Foods high on the prebiotic list include raw chicory and raw Jerusalem artichoke, not exactly the most popular foods on everyone’s menu. One of the best (and most accessible) sources is onion – preferably raw, but cooked works too. Onions aside, it’s not all that easy to get a good helping of prebiotics from food, which is why I personally recommend prebiotic supplements or a probiotic supplement with prebiotics in it.

Diet has a powerful shaping effect on the microbiome. And if your microbiome is working against you – say you have an abundance of fat-making bacteria (Firmicutes) and a dearth of fat-burning bacteria (Bacteroidetes) – changing your diet may change the composition of your gut garden and can be a game changer for your health.

“Research shows that significant changes in the array of gut bacteria can take place in as little as six days after instituting a new dietary protocol,” writes Perlmutter.

Considering the possible payoffs, that’s a pretty short investment of time.

See also Gut Feeling: The Latest News Behind Probiotics & Prebiotics

Get Savvy about Probiotics

With so many brands of probiotics out there, how do you weed through the options to find the right one for you?

Look for a dosage of at least 5 billion colony forming units (CFU) daily, though most manufacturers go considerably higher, which is fine.
  • I recommend looking for brands that contain strains of Lactobacillus acidophilus as well as at least one of the Bifidobacterium strains. (There are those who feel that Lactobacillus acidophilus DDS-1 is an even stronger and better strain than “plain” Lactobacillus acidophilus, so if your probiotic supplement contains the DDS-1 strain, so much the better.) Some experts, like Perlmutter, recommend that your probiotic formulation include a superior strain called Lactobacillus plantarum to help balance good and bad bacteria, to restore the health of your gut wall (especially after antibiotic use) and to improve digestion.
  • Your probiotic should also contain prebiotics, food for the probiotics, such as fructooligosaccharides (FOS), or a fiber like inulin or arabinogalactan.
Probiotics should generally be taken with food unless otherwise indicated – that’s the way they come in “nature” (i.e., fermented foods), and the stomach acid environment changes when you eat food, making it a more friendly environment for probiotics to survive.
If you’re using probiotics to manage a specific condition, such as irritable bowel syndrome (IBS) or inflammatory bowel disease (IBD), I recommend working with a health practitioner to find the right formula and dosage for you

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