In recent years, we've started to learn that almost everything we eat, from probiotic yogurt to a serving of asparagus to a fatty pork chop, has an effect on the microbes that live in our bodies, which, in turn, it has an effect on us. It is becoming clear that these microbes, in turn, play a key role in translating our diet into health outcomes, good and bad. But in many cases, our focus on what foods to eat to benefit the microbiome has been misplaced. For example, fiber turns out to be better than probiotics. You want to know why? Keep reading.

Why fiber in the gut is more important than probiotic

When it comes to our biomes, we can divide microbes into two key categories: those that live permanently in the human gut, and those that are passing through. It's simplistic and not exactly how microbes would see it, but it's a key distinction that is often left out of conversations about our gut microbiota, especially when it comes to food. And it is one that leads us to great confusion about what to do with all the new information that we are obtaining about our important inhabitants.

This difference is often overlooked or overlooked entirely amid the growing enthusiasm for live fermented probiotic foods, which are those that contain strains of bacteria or fungi that have been shown to have a beneficial effect on health. We get distracted by the most inventive new kombucha flavor, the best kale kimchi, or the most local goat milk kefir.

And who can blame us? They are interesting, alive, fizzy grown foods. But the microbes in our probiotic foods don't actually reside in our guts. They may be of value to your health, but generally speaking, they are not replenishing an anemic microbiome.

By focusing solely on these modern products, we are neglecting to maintain our microbe’s full time. And what our native microbes need is fibre. Complex fiber, rustic, now elusive.

The microbes that reside most permanently in our guts, day after day, do not come from yogurt or kimchi. They are our native microbes. These microbes are acquired at birth, during infancy, and early childhood, and some are found here and there later in life.

These gut microbes are essential to our health and survival. They help train our immune system. They are in constant conversation with our nervous system. And they help maintain the delicate balance of our entrails. "These microbes evolve in their environment," says Justin Sonnenburg, a microbiologist and immunologist at Stanford University. And we may have evolved to them. "We don't just have a random collection of microbes that we collect," Sonnenburg says. "We are passing microbes between us and through generations." Through millennia of adaptive evolution, these humble gut microbes have become some of our best allies.

Bacteroidetes and firmicutes make up 80% of our microbiome

Who are these invisible friends? Our gut is usually dominated by bacteria from the Bacteroidetes and Firmicutes filaments, which together make up about 80 percent of our microbes (although there are at least 10 other phyla that appear). These groups of microbes are not unique to the human gut, but some species can only live there. Our entrails are your planet earth.

Within the gut, these populations are dynamic. Most individual microbes have very short lives. So, you'll wake up to totally new generations of them every morning. Some, like members of the genus Lactobacilli, travel their entire lives in as little as 25 minutes. Others even faster. So, while you were dreaming about that horned dog talking last night, your gut populations of Lactobacilli could already be 20 generations beyond those you fell asleep with. That is the relative timescale between you and your ancestors who lived in the 17th century.

It's tremendous having to burst your highly cultured bubble, but with a dollop of yogurt, you haven't reset your native gut bacteria.

Many changes can occur in those generations of microbes, especially if something in the environment changes, such as an increase in pH (a drop in acidity), the introduction of a new food, a lack of the microbes' preferred fiber, or an atomic bomb of antibiotics.

Generally speaking, the gut is not a naturally microbe friendly place. Our digestive tract is a harsh environment by design. An acidic stomach helps break down food to facilitate digestion, but it also disarms many of the foreign organisms, from viruses to bacteria, that we encounter every day.

Plus, the gut is ideally a crowded microbial metropolis, and most outsiders just can't cut it. As fermentation guru Sandor Katz puts it, the gut “is a competitive environment. The bacteria that are there don't just move around and say, “Oh yeah! Come on! Welcome, neighbor! “It is a world of microbes that eat microbes. All of this is good for us. Only rarely does a microbe, harmful or otherwise, actually manage to support digestion and multiply in our system.

There are, however, some microbes that can survive the rough ride. A handful of these cause disease, such as certain strains of Escherichia coli. Most are probably nominally neutral, and a small fraction is actually beneficial. Good, bad or harmless, yet none of these microbes are really in our guts to stay.

Yogurt does not save you from a bad intestinal flora, fiber does

You should know that with a tablespoon (or a full box) of yogurt, you have not really reset your native gut bacteria, regardless of what the market would have you believe, and no matter how many live and active bacteria or strains are included. These microbes are perfectly happy to spend their time in a watery world of lactose-filled yogurt. And they can, surprisingly, persevere through the acid-filled digestion process. But they just aren't that suitable for long-term life in your human gut.

Fiber in the gut

What is the best way to feed our microbes? In a word: fiber. We have known for a long time that fiber is good for us. Helps reduce caloric intake and maintain regularity. But it is also perhaps the most powerful tool we have to help our native microbes. It's your bread and butter, so to speak.

Fiber is made up of long chains of carbohydrates. Because these carbohydrates are connected by complicated bonds, these molecules are difficult, and sometimes impossible, to digest. Humans simply do not have the enzymes necessary to break down many types of fiber. And that means these compounds end up, intact, in the lower part of the gut, where helpful microbes can feast on these wastes. When these compounds stimulate the growth and health of beneficial microbes, they are known as prebiotics.

More fiber is missing in our diet

In recent years and decades, we have not been very good at providing this long-awaited forage to our native microbes. And without fiber to feed them, their populations plunge, leaving us without their many benefits.

The average person now consumes less fiber than recommended, which is 30 or more grams and which is probably about a third (or less) of what a more traditional diet could offer. Even the upper end of this range is a fraction of what our ancestors probably ate every day. All of that means that we are eating only 10 to 15 percent of what our microbes would have expected. And it seems that they are feeling the deficiency, like us.

For example, an archaeological study of cave sites in the Chihuahuan Desert inhabited by humans for about 10,000 years found evidence of "intensive utilization" of local plants high in prebiotic fibers. Clues collected from cooking materials, human skeletons, and coprolites (fossilized excrement) suggest that the inhabitants ate approximately 135 grams of a specific type of microbial fiber (inulin) each day

The ancient inhabitants of the desert might have been an exceptional case, but we know that throughout history, as a general rule, humans had much more fibrous foods. Study after study points to the diversity of Paleolithic diets. An investigation of a 23,000-year-old site in Israel found that local cuisine included more than 142 different species of plants (including seeds, nuts, fruits, and grains).

Although the work did not specifically investigate the fiber content of the residents' diets, the impressive diversity of plants at the site suggests fiber-rich foods, and many different forms of that.

Prebiotic fiber the best for our intestinal microbiome

When we eat foods that contain prebiotic fibers, the gut microbes in turn reward us by making compounds that can help calm inflammation or defend against infection. These compounds, known as metabolites, are microbial by-products, expelled during the metabolic process by microbes to digest the food that comes their way. Fortunately, these by-products turn out to be beneficial to us.

Leaky intestine due to lack of prebiotic fiber

Beyond these health links, early animal studies show another reason for feeding microbes the food they need: protection against food allergies. Our large intestine has a thin barrier that separates its contents from the rest of our bodies. When our resident microbes starve for too long, they begin to eat through most of that barrier, opening holes for all kinds of material to escape into the bloodstream - a condition known, unappealingly, as leaky gut.

The body will detect this material as foreign and will send the immune system into attack mode. This is certainly good if the leaked material is a harmful microbe, but if it is, for example, a food particle it could trigger or exacerbate food allergies.

More prebiotic fiber equals more useful microbiome

Adding more prebiotic foods also simply means more helpful microbes. Some research has suggested that for every 10 grams of prebiotic carbohydrates that reach the gut microbiota, approximately three grams of additional bacteria flourish in life.

That's roughly 3 trillion new organisms for just adding those 10 grams of microbial fodder each day. It's not a bad trade-off for eating some extra whole grains, and a cold potato salad.

So, when it comes to prebiotics, instead of "build 'em and they'll come," think "eat' em and they'll multiply," and possibly even help protect you from a host of increasingly common health problems. All you need to do is pay a little more attention to what you are feeding your microbes.

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