It happens with some regularity. A young, fit guy will overdo the weekend routine and come to Manhattan alternative doctor Frank Lipman for a course of acupuncture to relieve the ache of a sore back or a strained shoulder. He’ll have his problem muscles addressed, but he won’t leave Lipman’s office without also hearing the doctor’s case for a full dietary plan that emphasizes loads of fresh vegetables and fruits, and eliminates added sugars, gluten, and dairy. “Then they’ll write me an email that says something like, ‘Damn, I didn’t know I could feel like this!’” says Lipman.
These are not unhealthy patients, and they didn’t complain of low energy before their visit. So why should these dietary fixes have such a dramatic effect?
The answer has emerged in a frenzy of scientific activity that, in the past five years, has transformed the way we look at the human body and our health. The object of all this attention is the microbiome, the collective of microbes that live within us, mostly in the gut. These bugs are primarily bacteria, but there are also yeast, fungus and parasites. Ever since the 17th century, when Antonie van Leeuwenhoek scraped a bit of crud from between his teeth and put it under an early microscope, science has known that we are home to single-celled creatures invisible to the naked eye. But not until the recent advent of genomic sequencing that can read the DNA of our cells did biologists appreciate just how many of them there were within us: for every one human cell in our body, there are 10 microbial cells.
“The idea that we’re more microbe than mammal is as or more profound than the theory of evolution,” says anthropologist Jeff Leach, one of the founders of the American Gut Project, which is devoted to genetically mapping the microbiome. Biologists see the human digestive system as a wet home and steady food supply for trillions of bacteria. In return, the bacteria break down and thrive on the plant fiber that we eat but otherwise could not digest, and join forces with our immune system cells to fight pathogenic invaders harmful bacteria like salmonella and E. coli that lurk in spoiled food and in the soil.
The microbiome gives Lipman a new way to express the dietary advice he’s been dispensing to patients for years: eating more vegetables, steering clear of processed foods, and diversifying one’s diet happen to be the best ways to promote healthy bacteria in the body. And a thriving microbiome is essential to overall health. What’s Wrong with Our Gut
When the microbiome is out of balance, it can decrease energy levels, injure metabolism, and give rise to a host of other long-term health problems. It’s like a rain forest that’s been clear-cut: prone to mudslides and unable to shelter the plants, animals, birds and insects that once thrived there. Some of the nation’s top scientists go so far as to say that unhealthy microbiomes lie at the heart of the most prevalent health issues today, like heart disease, obesity, asthma, and even cancer. At last year’s International Human Microbiome Congress, Dr. Martin Blaser, a New York University microbiologist, delivered a shot across the bow. Our modern reliance on antibiotics, he says, has deranged the microbiome, and is likely a major reason for the rise of many contemporary diseases.
Mainstream medicine is finally realizing that antibiotics, which indiscriminately wipe out gut bacteria the good with the bad may alter the balance of the microbiome in the long run and should be used only when strictly necessary. Doctors like Lipman will go a step further to recommend avoiding factory-farmed meat, which contains low doses of antibiotics that can build up in the human system.
But nothing is more important than the decisions we make about what to eat every meal of the day. For this, there’s a simple rule: “Eat as many high-fiber fruits and vegetables and legumes as you can,” says Stanford University’s Justin Sonnenburg, a microbiologist who studies how diet impacts bacteria in the gut. “Our hypothesis is that a variety of plant fibers supports a diversity of gut microbes.” If you don’t get enough variety, it weakens your gut bacteria. The Real Reason to Eat Fiber
The so-called standard Western diet, full of processed foods and carbs and lacking in vegetables, does little to nourish our microbiome. Our body’s good bacteria feed primarily on dietary fiber. In a process similar to the way bacteria turn milk into yogurt or cabbage into sauerkraut, the bugs in our bodies break down the fiber by fermenting it, satisfying their needs and leaving behind organic acids that nourish and repair the cells of the colon.
“The old view was that you needed the fiber to keep your bowels regular,” says University of Pittsburgh gastroenterologist Dr. Stephen O’Keefe, “but now we know there are much more important reasons.” This goes so far as to include cancer prevention: O’Keefe recently published a study linking increased diversity of the gut microbiome with lower colon cancer rates.
Dietary fiber also feeds our best friends in the bug world, like the bifidobacteria and lactobacilli, which help maintain an acidic environment in the gut and are inhospitable to potentially nasty strains of bacteria, yeast and parasites. When a colon turns more alkaline, these nasty microbes multiply, which can cause chronic symptoms like fatigue and brain fog. The colon walls can also become more permeable when the good bugs aren’t well fed, allowing bits and pieces of bacteria to enter the bloodstream. This is commonly called leaky gut syndrome, and it triggers low-grade inflammation, which is increasingly thought to cause massive problems throughout the body, from heart disease to obesity.
Other disturbing scenarios are possible. “One of the things that happen when we eliminate dietary fiber is the bacteria shift over and start eating us,” or, more specifically, the lining of our colon, says Sonnenburg, who discovered this phenomenon in lab mice. This may be another way that a bad microbe-human marriage contributes to the inflammation that undermines human health.
It all adds up to more reasons to double down on those vegetables and fruits. The government recommends 38 grams of fiber a day the equivalent of about seven servings of broccoli. Nutritionist Kathie Madonna Swift, co-author of The Inside Tract: Your Good Gut Guide to Great Digestive Health, suggests starting with a base of eight to 10 servings of veggies and fruits a day, and building on that foundation with servings of legumes, whole grains and nuts.
Sonnenburg also says to load up on vegetables like onions, garlic and celery, which contain the compound inulin, a preferred food for the bifidobacteria, which in turn feed our colons. The Promise of Probiotics
Prebiotics are the dietary fiber—fruits, vegetables and whole grains—that feed the bacteria we’ve already got in our guts. Probiotics, on the other hand, are infusions of new bacteria that enter our systems on board the food we eat. They may come from the soil the plants are grown in, or from fermented foods, which contain bugs that are actively feeding on them, breaking them down into acidic compounds like lactic acid and vinegar. This is what gives yogurt and sauerkraut their tang.
Fermented foods are everywhere, even if you don’t realize it. Go to the refrigerated section in a supermarket and the sauerkraut, kimchi (a fermented Korean cabbage) and pickled beets likely sit next to kombucha (an effervescent fermented tea) and kefir (fermented milk made with grain). Even some soy sauce is fermented and full of good bacteria. The best products are unpasteurized, since pasteurization kills most of the valuable bacteria. Everyday sandwich pickles, though, aren’t fermented, just steeped in vinegar, which gives the taste but not the live bacterial cultures to do God’s work in your colon.
Yogurt, of course, is the most advertised probiotic in the supermarket. While brands like Dannon’s Activia promise a boost of good bacteria, all yogurts contain a fair number of microbes. But that doesn’t mean that a yogurt a day will satisfy all your probiotic needs. The gut is host to thousands of different strains of bacteria (yogurt typically contains three), and while quantity is important, diversity is also key. This is why the jury is still out on supplements like Culturelle and Align, which pack billions of bacteria but represent just a handful of strains. Lipman recommends them to his patients, but admits that figuring out the right dosage and bacterial strains is a “crapshoot.”
O’Keefe is even more skeptical that we have the know-how to deliver what an individual gut wants or needs. “There are thousands of species of bacteria in the colon, and they’re more like an orchestra,” he says. “They play together to come up with a final sound.” Still, when a patient is in gastrointestinal distress—typically after a course of antibiotics—he will prescribe probiotics.
Some experts predict that probiotics will evolve from an all-purpose supplement to a pharmaceutical therapy targeted to specific diseases and conditions. For now, this is a new science that has doctors, researchers and proactive patients redrafting the terms of engagement with microbes in and around us. The scorched-earth policy is out, replaced by the idea that our gut flora is a garden that must be carefully tended. Whether or not it turns out, as Michael Pollan speculates in his recent book, Cooked: A Natural History of Transformation, that these bacteria are the key to a “grand unified theory of diet and chronic disease,” we know enough now to say, when you’re good to the microbiome, the microbiome is good to you.•