The Good Gut: Taking Control of Your Weight, Your Mood, and Your Long-term Health

by Justin Sonnenburg

The species of bacteria and fungi that colonize the gut may determine our interactions with the environment, protecting us from or predisposing us to the development of allergy and autoimmunity. They may protect us from or predispose us to becoming obese or diabetic. They may inhibit or intensify inflammation in the body. They may interact with artificial sweeteners to cause insulin resistance and weight gain in some individuals. They may even influence mental function and emotional wellness.

Nurturing our gut bacteria so that they produce the compounds that our bodies need is one of the most important choices we can make for our health.

the next time your infant sticks a new object into his or her mouth, if it is not a choke hazard, instead of rushing to pull it out or clean it with a sanitizer, consider how the bacterial patina is providing valuable microbes to help form the new microbiota.

We have already begun to see the effects of the Western lifestyle on our health in terms of obesity, diabetes, and autoimmune diseases. These diseases are not typically found in societies with a more diverse microbiota.

Each species of microbe within your microbiota has its own genetic code, or genome. The collection of genes encoded within all microbes is called your microbiome, a second genome.

Nature long ago figured out what so many of us still struggle with today: the key to success in a competitive environment is to delegate and work together!

There have been a slew of recent studies looking at C-section babies and their propensity for everything from obesity to allergy and asthma, celiac disease, and even cavities; and it is all bad news for those babies that miss out on the bacteria associated with a vaginal delivery.

Human milk also contains a less-well-known special ingredient called human milk oligosaccharides, or HMOs. HMOs are a collection of complex carbohydrates that are the third most abundant class of molecules in breast milk after fat and lactose. Their chemical structure is incredibly complex, so complex in fact that humans do not have the capacity to digest it. That’s right, one of the main ingredients in breast milk is not digestible by the infant who’s drinking it. Why would a mother put precious energy into making something her baby can’t use? The answer is that HMOs aren’t for feeding the baby, they’re to provide sustenance for his microbiota.

It’s clear that one of the mistakes our society has made is not doing enough to promote breast-feeding. Remember that any amount of breast milk you can provide your child can only help get his or her microbiota started out on the right trajectory.

feeding your children what you eat only makes sense if you eat a healthy diet yourself. Eating for health and a robust microbiota needs to be a family endeavor.

Laboratory mice given low doses of antibiotics early in life, like farm animals, increased their percentage of body fat. Along with this ability to gain weight more easily, these mice have a microbiota that resembles that of an obese human and is different from that of a lean human. The antibiotic-treated mice ate the same number of calories as the nontreated mice but were better able to extract and store those calories in the form of added weight.

Our systemic immune system—the immune system that circulates throughout our entire body—is also being instructed through its communication with the microbiota.

The lesson here is that it is possible that raising children in an overly hygienic environment could have a long-lasting detrimental impact on the development of their immune systems.

One of the most abundant microbiota waste products is short-chain fatty acids, or SCFAs (more on these special molecules in coming chapters). These molecules help the intestine accumulate T-reg cells.

First, even a single type of bacterium can be instructive to the immune system. Before targeting bacteria for elimination, especially those that have been associated with humans for thousands of years, the potential damage to our immune system needs to be considered. Second, some of our associated bacteria exhibit Jekyll and Hyde personalities. We don’t yet completely understand the factors that can turn a seemingly friendly bacterium into a pathogen.

Probiotic bacteria, through their ability to reinforce the intestinal border and prime the immune system, should be effective allies in the fight against gastrointestinal infections.

we feel that fermented foods, which contain a diverse collection of microorganisms, offer the best chance of encountering a microbe that will have a positive effect.

Because companies can benefit from selling a probiotic without demonstrating its effectiveness, there is little incentive to explore new potential probiotics.

Increasing dietary fiber is essential to cultivating diversity in the microbiota. Microbes in the gut thrive on the complex carbohydrates that dietary fiber is primarily composed of.

Providing more dietary fiber for microbiota fermentation would likely result in weight loss, lower inflammation, and decreased risk of Western diseases, not to mention a more stable, diverse microbiota.

It is the simple sugars used for sweetening and the easily digested starches that have given carbohydrates a bad name. These “bad” simple carbohydrates cause blood sugar to spike soon after consumption. The body responds to high blood sugar by releasing insulin, allowing cells in the liver, muscles, and fat to absorb the circulating sugar. Insulin also prevents the body from using fat as energy until all the sugar has been either used up or stored away in the form of glycogen. If blood sugar levels are constantly elevated, say from a diet high in simple carbohydrates, insulin-responsive cells become resistant to insulin. These cells become desensitized to the constant high levels of insulin and begin to ignore it—a common step in the progression of type 2 diabetes. The outcome of this desensitization is dangerously high blood glucose levels that can result in heart disease, stroke, and kidney failure.

Steamed or boiled (or even microwaved, in a pinch) edamame, fresh fruit and nuts on yogurt, and whole grain bread with hummus are some of our favorite low-glycemic-load, high-MAC snacks.

the richness (or lack of richness) of your microbiome is a better predictor of Western disease risk than your weight.

To increase the richness of bacteria that reside in the microbiota, just consuming more microbes won’t work. We all eat microbes, and some inevitably come from other people’s microbiota. But the health-promoting ones will not stick around unless we are eating a diet that helps them persist within the gut.

Technology has provided us “rich man’s flour” inexpensively, but our microbiota’s diet has become poorer. As milling technology improved, wheat could be ground into ever finer particles until it came to resemble the ultrafine talc that fills the bags on grocery store shelves today.

Sourdough bread is also available commercially. Look for those that are made with whole grain flour for a higher MAC content.

It may be that modern humans are the result of generations of microbiotas helping our ancestors make wise, life-extending decisions. While the role they play in our personality and intelligence is still unclear, gut bacteria are certainly doing more than just helping us digest food.

There are a number of fledgling companies that are taking the bet by designing custom mixtures of microbes to be used for microbiota transplants. Some of these mixtures are even being packaged in pill form, which would also drastically reduce the cost and risks associated with delivery by enema or nasogastric tube. These “crapsules,” as they are sometimes called, could become part of a routine postantibiotic regimen to mitigate microbiota damage.

When people make the transition from independent living to a long-term-care facility, their diet also undergoes a transition. The higher-fiber diet that typified the community dwellers and those in the day hospital gives way to a diet that is markedly lower in fiber in the long-term-care facility. While the reason for the fiber-poor diets in these facilities is not clear, decreased fiber is common in food prepared in cafeteria-like settings, and the problem may be compounded by a desire to make food easy to chew for the elderly. This difference in fiber consumption mirrored the differences seen in microbiota composition. People on a low-fiber diet had a lower-diversity microbiota, whereas a high-fiber diet made for higher microbiota diversity. The higher-fiber-eating community elders also had more health-promoting SCFAs, lower markers of inflammation, and in general were in better health.

In this case, diet change happened first and the microbiota change followed. Most important, measures of frailty corresponded to the biggest differences in the microbiota shift. The data from the ELDERMET study points to a chain of events in the elderly that starts with diet deterioration followed by microbiota change and then health decline.

We know there is a link between the state of the microbiota and frailty during aging. Specifically, a more diverse microbiota is associated with better health parameters like lower inflammation, greater muscle mass, and less cognitive decline.

when thinking about ways to prevent or rid our body of diseases like cancer, we need to take an approach that minimizes damage to the beneficial aspects of our biology, like our microbiota.

for diseases like cancer, coupling treatments such as chemotherapy and radiation with measures to improve the ability of the microbiota to boost the immune system may provide a more durable response.

taking advantage of the malleability of the microbiota to minimize the damage and deterioration it incurs as we age could improve the quality of our later years.

Homes on farms contain a much higher diversity of microbes than urban dwellings. Children raised on farms are much less likely to suffer from asthma and allergies, presumably because of increased encounters with environmental microbes.

Children who grow up with family pets are, like children raised on farms, protected from respiratory infections and allergies and are less likely to require antibiotics compared to children in pet-free homes.

Petting the family dog is not an automatic hand-washing trigger in our home. Our dog is free from topical flea medication, is routinely checked for transmissible intestinal parasites, and spends most of his time in our pesticide- and herbicide-free yard. In this situation, we feel the potential benefit of being exposed to more microbes outweighs the risk of harm from not thoroughly washing hands.

children whose parents cleaned their pacifier by sucking on it as opposed to rinsing or boiling it in water were much less likely to have eczema,

The main goal of the dietary interventions we recommend is to improve the diversity of bacteria within your microbiota and increase the amount of SCFAs produced through bacterial fermentation. Multiple scientific studies show that people with a diverse microbiota producing lots of SCFAs are healthier and less prone to Western diseases than people with fewer bacterial types in their gut.

There are four main tenets of a microbiota-friendly diet. The first is to consume foods that are rich in dietary MACs.

A second important facet of a microbiota-friendly diet is to consume meat in limited quantities.

The third pillar of a microbiota-friendly diet is limiting saturated fat intake.

The final component of a microbiota-friendly diet is consuming beneficial microbes, or probiotics.

this microbiota-focused diet shares many features with the Mediterranean and the traditional Japanese diets. These diets support exceptional health and longevity. Likely not by coincidence, these diets have in common high fiber content, low saturated fat, low red-meat consumption, and the regular incorporation of fermented food.