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33. Take Control of Your Diet (and Your Microbiome)

The food and flavor industries have taken over the job of adding taste to our food[i]. And we are being encouraged to accept that decision and that process. With every petition to the Food and Drug Administration to market genetically modified, genetically uniform, highly inbred crops that produce food items that are easy to harvest, pick, pack, ship, store, cook, eat, and are pretty to look at, we are losing quality in our foods.

And while the food industry has convinced the FDA that there are no “significant” differences between the old crops and the new crops, we are ceding control of our diet to grossly uninformed and commercial-based decision making. Our diet is the basis of our health and our food is being produced with commercial profit in mind, not consumer health. We not only have simplified the environment, but we have allowed the crops we want to grow in the environment to be simplified. The result is food that does not support the things that require complexity. Those things, of course, would be us as individuals and, more importantly, our internal ecosystem.


In this regard, Aldo Leopold (from Round River, 1972) should be a source of guidance.


“The last word in ignorance is the man who says of an animal or plant, "What good is it?"

If the.... whole is good, then every part is good, whether we understand it or not. If the

biota, in the course of aeons, has built something we like but do not understand, then who

but a fool would discard seemingly useless parts?” (emphasis added)


If the food we make does not support our microbiome, which is the source of our physiological flexibility, our defense system, and our capacity to respond to changes in our environment, then this action is equivalent to us discarding 99% of our available genes. On top of that, our environment is definitely changing. At no point in our history has this been more evident.

We have become so disconnected from the source of our health (especially from the production of food), that we are actually confused about what we should be eating to be healthy, which is both amazing and tremendously alarming. We cannot depend on the food industry to educate us on that point because it is the food industry, from farming to processing, that has been leading the charge to keep food prices low at the expense of food quality. This process has been continuous and accelerating since the 1950s and is now the norm rather than a recent aberrancy. While we may appreciate the continued low cost of food, we are assuming the quality has not changed over time, and we are ignoring the basic rules of ecology, physics, chemistry, and even economics.

Today, our food, which is our source of nutrition and the slow medicine we take every day to stay healthy, is less and less a source of nutrition or slow medicine. As we assault our bodies with the constant barrage of chemicals that characterize human civilization in the 21st Century, we are being stripped of our natural protections. Our relationship with our environment is broken and our bodies are not capable of defending us against an ever-changing world. There is little evidence that anything significant is being done to address this situation at a governmental level. Our legal protections related to food are focused on safety issues related to toxins (such as food dyes and pesticides), carcinogens (mostly additives), and allergens (certain food components).

In the US, there are no particular rules about food quality per se and very few laws protecting consumers against what might be dangerous. By that, I mean we are not protected against changes to foods that might affect food quality in ways that we can’t yet predict or understand. Typically, discoveries about negative effects are made well after the fact and institutional changes are only grudgingly and usually in response to litigation only after a great deal of data has been collected for many years.

And so, we must take control of our own health and we do that by intentionally strengthening our relationship with our microbiome through a high-quality diet.


Basic rules of eating (and shopping)

We need some guidelines for evaluating our food and those guidelines must be based on the principles of evolutionary biology and should include what we suspect might be true. By that, I mean we must err on the side of caution. We don’t have conclusive data about the nuances of the microbiome and food quality in relation to our day-to-day health, but we can’t wait for that eventuality. In fact, the health food and fad diet industries have always taken this approach, but not for the same reasons that we should. Unfortunately, capitalism has a way of blinding good intentions such that the terms “good” and “bad” become watchwords for consumers, but with a lot of variation in the intended meaning.

The primary word of guidance for us should be “quality.” And we should be wary of anything that reduces what we understand to be quality. We may not always know what “quality” specifically, but we know enough to err on the side of caution.

I’m going to suggest some guidelines for selecting foods that will more or less imply quality, support the microbiome, and direct the chooser toward better foods. This is by no means an exhaustive list and readers should feel free to add their personal touches to their buying choices.


*Fresh is best. Food should be as fresh as possible with little to no prior processing. Such food can be eaten in its original state. Ideally, the food has been rinsed only with water and not with chemicals. The rinsing process should be needed only to remove dirt and unnecessary debris, but not as a necessary precaution against potential toxins, such as pesticides. Foods, such as fruits, that are stored for months in refrigerators (during and after shipping) are less desirable than those arriving directly from the field. Fresh foods may be our best source of appropriate probiotics (new bacteria). The processing and sterilizing procedures of the commercial food industry will diminish this source.


*Slow to digest. Perhaps this should be the first guideline, but the goal in selecting quality food is to remember the difference between PFC foods and microbiome foods. PFC foods will tend to be more processed and will not resemble the original organism. That includes meats which are increasingly treated before, during, and after processing with chemicals. Plants are prebiotics; the original compounds found in plants are the substances that feed the microbiome. Slow-to-digest foods also give a greater sense of satiety which assists in curbing the desire to eat again. Use this criterion of satiety as a measure of your food quality.


*Feed your microbiome first. This is a corollary to the previous statement, but it’s so important it should be said twice. As an individual, you need 1500-2000 calories a day to meet your metabolic needs. You’ll get them, don’t worry, but a focus on the microbiome implies a focus on food quality. Eating more plant material will reduce your PFC calorie intake because you will not feel as hungry after feeding the microbiome. I predict that as you focus on meeting the needs of the microbiome, you will have less desire to eat lower quality foods anyway. A healthy microbiome requires the highest quality plants you can consume and remember that high quality, in this sense, means cellulose and secondary compounds. That is, high quality plants are chewy and naturally flavorful.


*Organic implies probiotic. Field-gown produce is more likely to possess probiotic bacteria if it is grown without pesticides. The bacteria associated with commercially grown produce will also be bacteria that can survive the chemical environment of the commercial farm. While this does not necessarily imply unhealthy, these are not the bacterial strains of the natural ecosystem and are likely to be bacteria that are resistant to chemical treatments. While we know little about the recruitment of new bacteria into our microbiomes, we know that there is flux and the new arrivals must be coming from our environment. And it makes sense that a healthy food production environment will be less likely to harbor harmful bacteria.


*Consider your probiotic environment. As a follow up to the previous guideline, research on the development of the microbiome in toddlers indicates a strong influence of family members, and from the people we live with later in life. That means we are sharing our microbiomes with our housemates. This should have a protective aspect because new bacteria increase our personal diversity. When a shared community (such as a household) experiences similar health problems, it does not necessarily mean a genetic predisposition because it can also mean an unhealthy probiotic environment. In other words, we are what we eat, but it also may be true that we are what those around us eat.


*Challenge the microbiome. Expand your variety of plant foods. The greater the variety of foods, the greater the diversity of bacteria you are supporting in your colon. Diversity is the cure for many things. It prevents an unhealthy dominance by a small number of bacterial species. It can prevent gastric upset and flatulence after eating new and different foods. Ecological studies have shown that more diverse systems can extract a greater quantity and variety of resources from the environment. We can assume that a diverse microbiome is better able to better able to provide a greater variety of nutrients than a depleted microbiome. Exercise your digestive system with a diverse diet.


*Quality comes with age. Most of us want to hear that, but what I mean is this: Eat plants that are grown slower, take longer, have stronger taste, and are chewier. (Unfortunately, they may also be more expensive.) These plants are not always the prettiest. Food producers are acutely aware of food appearance and young foods are prettier because haven’t had the exposure to pests or the time to age. Yes, age can take its toll on appearance, but age implies maturity and for plants that maturity is the foundation of quality. Skip the baby foods; go for foods with life experience.


*Superfoods are real. They’re called plants. However, eating plant extracts is not the same as eating the actual plant. When medicines are developed from plants, the active chemical is isolated, purified, concentrated, and then packaged in a delivery system. Whatever context that chemical was in while part of the plant is lost. The slow medicines that are in plants are in their original context which typically means in the presence of many other slow medicines. We do not understand the importance of the natural cocktail of these chemicals with regard to their actions as slow medicine. We may never untangle that knot, but we can trust that the context is important. Eat the plant, not the extracts.


*Eat whole foods. Don’t peel fruits or roots; always eat the skin. The skin (or peel or rind) usually has many nutrients not found in the sweet or starchy areas. And the skin is mostly cellulose. The skin (cellulose) is complex and provides information to your digestive system that helps reduce the sensation of hunger and thereby reduces overeating. While the juicing fad is a healthy fad, I would advocate for smoothies that incorporate whole foods rather than juicing, which saves the liquid but discards most of the cellulose. Eat like an adult.


*Shop with an attitude. Try to be an environmentally, ecologically, scientifically responsible consumer. It is hard to know how much genetic alteration and breeding our produce has been subjected to in order to get the marketable characteristics we see at the store. Assume it’s a lot. We should understand that any plant that requires only a short time to grow is being manipulated and probably has been for decades. In part, this is because breeding efforts for short-lived plants can be conducted in months rather than years. On the other hands, tree fruits and nuts are less modified than the plants that can be grown indoors. That isn’t to say they haven’t been as subjected to breeding for improvements, but a tree typically requires several years of growing before it produces fruit or nuts and that is a major investment for farmers. And as the perennial plant ages, it produces food with greater chemical complexity (to which anyone in the wine industry will attest.)


*Learn your food sources. In addition to the above, find out where your fresh food was grown. Food produced in the US can travel 3000 miles to the market, will take days to get there, and is often picked at an unripe stage. Some fruits are treated with ethylene gas (a natural ripening hormone) to generate a “ripe” look by the time they get to their destination. On the other hand, grapes in winter and early spring come from Chile and Mexico, bananas are from Central America. Ask other questions about your fresh food. Are there more local sources? Does the farmer have a human name and face? How was the food grown? For foods labeled “organic”, meeting the letter of the law is not the same as meeting the intent of the law and knowing something about the grower can be important. Some “all natural” foods come from more responsible growers than do some “organic” foods. Educate yourself about the source of your food and how it was produced.


*Question food longevity. Long shelf life implies missing ingredients, added ingredients, and always means preservatives. Products with a long shelf life are only distantly related to fresh foods. Long shelf life means the more volatile chemical components have been removed and that often means vitamins and beneficial oils are missing. The extracted chemicals are then added back in a more stable form or left out. Personally, I have a concern about preservatives, even natural preservatives. If bacteria and fungi can’t eat it, then should I? At issue is whether foods containing antimicrobial chemicals (i.e., preservatives) that can make it to the colon will have adverse effects on my beneficial bacteria. It is true that the secondary compounds produced by plants are often antimicrobial. But if we eat plants and we don’t experience digestive distress, we are either breaking those compounds down ourselves or our microbiome is coping with them. On the other hand, chemicals we add to food that suppress microbial growth are chemically stable (hence, long shelf life), are not natural to our food environment, and I advise consumers to find out more about them or to avoid them.


I’m sure there are a number of other criteria we can use to assess the quality of our food. Indeed, you should probably make up a Quality Control Handbook for easy reference until you have your dietary guidelines firmly in your mind as you shop. However, the very act of asking questions about quality is the important starting point. It means you are taking control of your nutrition and, most importantly for this discussion, taking control of the health of your microbiome (and you as an ecosystem.)


If you would like a take-home message, it is this: We need high quality food to maintain a high-quality microbiome. Those foods are not PFC foods. However, our modern problems with diet are rooted not only in the production of low quality, mostly PFC foods, but also in the continued reduction in quality in our traditional non-PFC foods. We have to be smarter eaters. A healthy and diverse microbiome is likely to the be the greatest tool we have for maintaining personal health, but only when the microbiome is supported by thoughtful and responsible eating behavior.

[i] Mark Schatzker. 2015. The Dorito Effect. Simon and Schuster.

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