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What Your Microbiome Wants for Dinner

You may think twice about your diet when you follow the metabolic fate of your food.

Let’s admit it. Few of us like to think, much less talk about our colons. But you might be surprised at the importance of what gets…By David R. Montgomery & Anne Biklé

Let’s admit it. Few of us like to think, much less talk about our colons. But you might be surprised at the importance of what gets into your colon and what goes on inside it. This little-loved part of our bodies is actually less an onboard garbage can and more like the unlikeliest medicine chest.

There is abundant medical evidence that diet greatly influences health, and new science is showing us why this is so. It is also showing us that advocates of trendy paleo and vegan diets are missing the big picture of how our omnivorous digestive system works.

Your colon is the home for much of your microbiome—the community of microbial life that lives on and in you. In a nutshell, for better and worse, what you eat feeds your microbiome. And what they make from what you eat can help keep you healthy or foster chronic disease.

To gain an appreciation of the human colon and the role of microbes in the digestive tract as a whole, it helps to follow the metabolic fate of a meal. But, first, a word about terms. We’ll refer to the digestive tract as the stomach, small intestine, and colon. While the colon is indeed called the “large intestine,” this is a misnomer of sorts. It is no more a large version of the small intestine than a snake is a large earthworm.

The stomach might better be called a dissolver, the small intestine an absorber, and the colon a transformer. These distinct functions help explain why microbial communities of the stomach, small intestine, and colon are as different from one another as a river and a forest. Just as physical conditions like temperature, moisture, and sun strongly influence the plant and animal communities that one sees on a hike from a mountain peak to the valley below, the same holds true along the length of the digestive tract.

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How is it that the bulk of what humanity now eats could undermine our health?

Imagine you are at a Fourth of July barbecue. You saunter over to the grill to take a look at the fare. The pork ribs look great so you spear a few and add a heap of homemade sauerkraut on the side. You grab a handful of corn chips and a few pieces of celery. The vegetable skewers look good too, so you add one to the pile on your plate. And what would the Fourth of July be without macaroni salad and pie?

You lift a rib to your mouth and start gnawing. A forkful of sauerkraut mingles well with the meat and you crunch your way through another mouthful. The macaroni squishes between your teeth, but the celery takes some chewing. It all slips down the hatch and lands in the acid vat of your stomach where gastric acids start dissolving the bits of food. On the pH scale, where 7 is neutral and lower values are more acidic, the stomach is impressive. Its acidity ranges from 1 to 3. Lemon juice and white vinegar are about a 2.

After the stomach acids work over your meal, the resultant slurry drops into the top of the small intestine. Right away bile from the liver shoots in and starts working over the fats, breaking them down. Pancreatic juices also squirt into the small intestine to join the digestive party. Your Fourth of July feast is now on its way to full deconstruction into the basic types of molecules—simple and complex carbohydrates (sugars), fats, and proteins. In general, there is an inverse relationship between the size and complexity of these molecules and their fate in the digestive tract. Smaller molecules, primarily the simple sugars that compose the refined carbohydrates in the macaroni, pie crust, and chips are absorbed relatively quickly. Larger or more complex molecules take longer to break down and are absorbed in the lower reaches of the small intestine.

DOWN THE HATCH: Once broken down in the stomach, simple carbohydrates, most fats, and proteins are absorbed in the small intestine. Fiber-rich complex carbohydrates, however, drop into the colon where microbial alchemists transform them into beneficial compounds our bodies need. But it takes the right microbes.Courtesy of the authors

The sausage-like loops of the small intestine provide an entirely different type of habitat for your microbiota than the stomach. Acidity drops off rapidly and, in combination with all the nutrients, the abundance of bacteria shoots up to 10,000 times more than that in the stomach. But conditions still aren’t ideal for bacteria in the small intestine. It’s too much like a flooding river. And understandably so, considering that about seven quarts of bodily fluids, consisting of saliva, gastric and pancreatic juices, bile, and intestinal mucus flow through it every day. And that’s not including the two additional quarts of whatever other liquids you consume. The rushing swirl of fluids entrains food molecules and bacteria and carries them rapidly downstream. The constant motion means that nothing stays put for long, so bacteria can’t really settle in and contribute much to digestion.

By the middle to lower reaches of your small intestine, the fats, proteins, and some of the carbohydrates in the Fourth of July slurry are sufficiently broken down for absorption and pass into the bloodstream through the intestinal wall. Notice we said some of the carbohydrates. A good amount of them aren’t broken down at all. These complex carbohydrates, what your doctor calls fiber, have a completely different fate than simple carbohydrates.

They drop, undigested, into the slough-like environment of the colon. With a neutral pH of about 7, the colon is a paradise for bacteria compared to the acid vat of the stomach or the churning rapids of the small intestine, where the pH is slightly lower.

Deep within the safety of our inner sanctum, communities of microbial alchemists use our colon as a transformative cauldron in which to ferment the fiber-rich complex carbohydrates we can’t digest. But it takes the right microbes. For example, Bacteroides thetaiotaomicron makes over 260 enzymes that break apart complex carbohydrates. In contrast, the human genome codes for a paltry number. We can only make about 20 enzymes to break down complex carbohydrates.

Grain Wreck

Our built-in cauldron and the fiber fermenters that run it are akin to personal pharmacists. They can churn out a great many medicinal compounds, and all of them are vital to the health and normal functioning of our colon cells. But we will only reap the benefits of butyrate and other alchemical products from our microbiome if we send lots of fiber down the hatch.

In thinking about such connections, the seeds of the world’s major cereal crops (grains) are a good place to start, as they account for the lion’s share of what the world eats. Lucky for us, grains offer a nearly perfect nutritional package. Whether wheat, barley, or rice, all have the basics—proteins, fats, and carbohydrates, along with health-boosting vitamins, minerals, and phytochemicals. But how is it that the bulk of what humanity now eats could undermine our health?

It has to do with the structure of a plant seed and what we do to them after they are harvested. Consider a grain of wheat. The outer seed coat (the “bran”) and the inner embryo (the “germ”) are small in terms of the overall seed weight. The bran composes about 14 percent of the total weight, while the germ adds another 3 percent. Despite their low weight, these two parts of a seed are packed full of nutrients. And the bran in particular is rich in complex carbohydrates, although a chemist calls them polysaccharides—very long chains of sugar molecules.

Many diet gurus shun our inner omnivore. We are constantly urged to eat a narrow (and ever-changing!) slice of omnivory.

The remaining 83 percent of a seed by weight is the endosperm. It contains most of the simple carbohydrates and nearly all the proteins found in a seed. In effect, the endosperm is like the placenta of a plant. Had the seed fallen to the ground and germinated, the simple carbohydrate-rich endosperm would have provided for the seed until it grew roots and leaves and could feed itself. While a sprouting plant clearly needs this type of supercharged energy supply, it’s not so good for us in large amounts.

When someone says a grain is “refined,” it means that the bran and the germ are stripped out when the seed is milled. Only the endosperm remains. Grind up the endosperm of wheat grains and you have white flour, which to your small intestine is an easily absorbable sugar.

THE BAD SEED: The seed coat (“bran”) and inner embryo (“germ”) are packed full of nutrients. When a grain is refined, the bran and germ are stripped out, leaving the endosperm, a simple sugar. When we eat a lot of refined grains it can lead to excess glucose in our bloodstream, which leads to a host of other problems.

All cereal grains are amenable to refining. It’s the basis for all those eye-popping choices of boxed and bagged items in grocery stores around the globe, especially in the Western world. Refine corn, add some fats back, toss with salt, and you get the perfect tortilla chip. Do the same with wheat and you can make a fine cracker or bread.

Part of the reason grains are refined is because the fats go rancid—things made from refined flours last longer. Also, bakers don’t like bran in flour because it interferes with the elasticity of dough and inhibits rising. Removing these pesky parts of a grain solves those problems. But it causes a whole host of new ones for our bodies. When a seed goes through milling and processing, its perfect nutritional package falls apart.

Looking back at carbohydrate consumption over the last century reveals some interesting trends. Americans ate about the same amount of total carbohydrates in 1997 as we did in 1909—just not the same kinds. Over this time period, the proportion of carbohydrates from whole grains dropped from more than half of what we consumed to about a third. What replaced whole grains was food products made from different kinds of refined grains. In other words, for the first time in human history we now eat mostly the simple sugar part of a grain (the endosperm) and far less of the complex carbohydrate part of a grain (the bran and the germ).

The small intestine and colon handle a whole grain very differently than they do a refined grain. When complex carbohydrates remain bound together with other molecules in whole grains, it takes longer for enzymes to find the carbohydrates and start breaking them down. It’s like trying to open a cardboard box triple-wrapped in duct tape versus a box with an easy-open pull tab. Also, the sugar molecules from whole grains have to jockey for space with the protein and fat molecules to make contact with the absorptive cells in the small intestine, further slowing the sugar-absorption process. Plain and simple, when whole grains remain intact, your body absorbs the sugar component at a markedly slower rate. And the indigestible part of whole grains (and many other plant foods) pass into the colon where the fiber fermenters feast on it, producing copious amounts of butyrate.

In contrast, refined grains release a veritable fire hose of glucose, which our small intestine dutifully absorbs and passes on to the bloodstream. This sends insulin charging out of the pancreas to shuttle glucose from the blood into cells. But using cells as a place to endlessly stockpile sugar can eventually lead to other problems. And so, our wonderfully efficient bodies attempt to solve this problem—by converting excess sugar into fat and moving the overage into depot-like fat cells. When we need this energy, like in the middle of the night long before breakfast, it’s there for our use. But an abundance of refined carbohydrates converted into fats overshoots the needs of the average American. It’s a recipe that fuels inflammation and the onset of Type 2 diabetes, obesity, and other maladies.

The amount of meat in the Western diet can also pose problems. When consumed in relatively large quantities, animal protein is not completely broken down by the time it reaches the lower end of the small intestine. Eat too much meat and your overwhelmed small intestine delivers partially digested animal protein to the colon. When bacteria in the colon encounter intact or partially digested protein, a different kind of alchemy gets underway—protein putrefaction.

The problem with putrefaction stems from some of the elements of which animal proteins are made—a fair bit of nitrogen and small amounts of sulfur. Ammonia, nitrosamines, and hydrogen sulfide probably don’t mean much to the average person. But they are among the nitrogen and sulfur-containing compounds that bacterial putrefiers create. These compounds pack a toxic punch to cells lining the colon. They interfere with the uptake of butyrate, which deprives colonic cells of the energy they need to keep the colon functioning in top shape. The spaces between cells begin widening and the contents of the colon itself begin seeping out into surrounding tissue and leaky gut syndrome sets in. Undernourished cells start falling down on the job and cellular waste products begin to accumulate inside cells, which gums up other cellular operations. In addition, goblet cells, whose main purpose is to make and secrete the mucus that coats and protects the colon lining, slow down on mucus production. This makes the colon lining more vulnerable to pathogens and physical damage. This is not a trivial point. The colon is a busy place and the cells lining it constantly regenerate throughout a person’s life. If cells aren’t regularly replaced, the effects are somewhat like a house that goes unmaintained. Lots of little problems add up to bigger problems, and eventually the house starts to fall apart.

Other problematic byproducts are made in the colon. Eating lots of fat stimulates the liver to produce bile and deliver it to the small intestine. We need bile. It acts like a detergent and breaks fats into smaller molecules so they can be absorbed. Almost all of the bile used in the small intestine gets transported back to the liver after fats are sufficiently broken down. The key word here is almost. About 5 percent of bile secretions keep moving down the digestive tract and land in the colon. So, people who eat lots of fat secrete more bile to break down the fats, which means more bile ends up in the colon.

But guess who gets ahold of this bile and transforms it? Our colonic microbiota. They convert bile into decidedly vile compounds called secondary bile acids. And like putrefaction byproducts, secondary bile acids are toxic to cells lining the colon.

The Omnivore Within

As adherents of the paleo diet like to remind us, humans have long eaten meat. They stress that meat is a fabulous source of many nutrients, especially if the animals being eaten were raised without antibiotics and allowed to follow their normal way of eating. Vegetarians and vegans also admonish us, pointing out that people who eat a plant-based diet generally have lower rates of cardiovascular disease and Type 2 diabetes. They also point out that plants possess what animals don’t—an astounding arsenal of cancer-fighting phytochemicals.

In other words, both of these countervailing dietary perspectives—paleo and plant-based—contain more than a germ of truth. So consider another perspective. Combining elements of each diet makes a lot of sense given what our colonic microbiota do with the meat, fats, and plants we eat.

Here’s how it might play out. Imagine the putrefaction byproducts from undigested meat and secondary bile acids soaking the cells lining the colon. DNA mutations occur and a few abnormal colon cells start regenerating and gain the upper hand, ignoring instructions from immune cells to self-destruct. But follow this scene with a tsunami of butyrate, and the colonic cells perk up. Renegade cells succumb to immune cells. Prodigious amounts of undigested complex carbohydrates from plant foods enter the colon, dislodge and mop up secondary bile acids, thereby reducing contact between these carcinogens and the colon lining. Normal cell growth and functions resume, maintaining the health of the cauldron and thereby the body at large.

This scenario is ingenious from both a health and an ecological perspective. The fiber fermenters have solutions for problems the protein putrefiers create. Plus, everyone in the cauldron gets fed—with either complex carbohydrates, or the castoffs of undigested proteins and leftover bile acids. So long as the byproducts of the fiber fermenters prevail, the colon serves as a medicine chest rather than a toxic dump.

Here’s another way to think of your colon: The gut of each and every one of us is akin to a garden.

We are the most omnivorous creatures on the planet, with a vast array of domesticated crops and animals and wild foods at our fingertips. There is hardly anything people don’t eat—from the blubber of whales, the intestinal lining of pigs, caterpillars, rotten fish, raw fish, and seaweed, to the more mundane items like meat, dairy, bread, fruits, nuts, and vegetables. Yet many diets and diet gurus shun our inner omnivore. Instead, we are constantly urged to eat a narrow (and ever-changing!) slice of omnivory. Ideas for what we should eat have swung like a pendulum—more toward meat, or more toward vegetables, away from fats, then toward certain kinds of fats, toward whole grains, now away from all grains.

No wonder so many of us are either sick or tired, or both. Perhaps it’s worth focusing on what to feed our personal alchemists so that we realize the benefits. The mechanics are pretty simple. Pick a modest-sized plate and make meals using vegetables, legumes, leafy greens, beans, fruits, and unmilled whole grains as the main ingredients. Add some meat if you want and dollops of healthy fats on the side or sprinkled through the plant foods. Desserts and sweets are special, so save them for the special times.

We realize a diet like this doesn’t lend itself to being packaged and sold. It emphasizes how to think about food in the context of one’s microbiome, rather than prescribing a narrow choice of foods, counting calories, or advocating “dieting” as a daily activity. This advice is far from sexy and certainly not earth-shattering.

Understandably, special dietary considerations apply to people with gut dysfunctions or who are diabetic or allergic to specific foods. But for most of us the key to healthy eating may be as simple as balance and diversity—and sidelining refined carbohydrates. In other words, provide plenty of mulch for your fiber fermenters so that they can churn out far more of their nutritional gold than what your protein putrefiers and bile acid modifiers conjure up. Keeping the fiber-lovers on top means filling the cauldron every day with fermentative fodder so that it bubbles with things that are good for you.

If you haven’t grown any fonder of your colon and its capabilities by this point, try another way to think about it. The gut of each and every one of us is akin to a garden. And as many gardeners know, the plants that make a garden are only as vibrant and resilient to pests and pathogens as the soil in which they are rooted. The real key to a vibrant and healthy garden—both inside and outside our bodies—comes from cultivating legions of beneficial bacteria. The not-so-secret ingredient for doing so? Mulch. That’s right, plant matter for the tiny alchemists in our colonic cauldron to feast upon just as they do in garden soil. When they fill up on such fodder, we harvest a well-stocked medicine chest.


David R. Montgomery is Dean’s professor of geomorphology at the University of Washington and a MacArthur Fellow. Anne Biklé is a biologist and gardener.

Excerpted from The Hidden Half of Nature: The Microbial Roots of Life and Health by David R. Montgomery and Anne Biklé. Copyright © 2016 by David R. Montgomery and Anne Biklé. With permission of the publisher, W.W. Norton & Company, Inc. All rights reserved. This selection may not be reproduced, stored in a retrieval system, or transmitted in any form by any means without the prior written permission of the publisher.

Lead photo by H. Armstrong Roberts/ClassicStock/Getty Images

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