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30. The Care and Feeding of Your Microbiome

A number of fad diets have emerged in recent years that support microbiome health to some degree. These diets insist on whole, fresh, and unprocessed foods. They are usually centered on plants but, if not, they still focus on food quality. In general, the fad diets are well-intentioned and are often philosophically focused on the health of the human as well as health of the environment. None of them are specifically focused on the microbiome in the sense that we have discussed it here, but that understanding is creeping in. I’ll go over some of the more popular diet options, but this is meant to be comparison of diet approaches rather than a comprehensive discussion of the merits of the fad diets.

Obviously, any vegan, vegetarian, and macrobiotic diet will support the microbiome most directly. These mostly or wholly plant-based diets are challenging for many people because of the perception that they lack sufficient PFC components (protein, fat, carb) to meet our metabolic needs. That perception is rooted in the belief that the plant-based diet is made up primarily the leafy parts of plants, which are low in oils, starch, and protein, but high in fiber and micronutrients.

While this viewpoint is true of the “vegetable” parts of the plant, the fruits, seeds and roots tend to contain high levels of one or more of the high calorie components and also have many important micronutrients. The perception that a plant-based diet lacks sufficient protein for maintaining muscle mass ignores the many high-energy and high-protein food options that are part of the plant-based diet. So, let’s consider the basics of a few of the (currently) popular diet plans and how well they support both microbiome and caloric needs.


Diets emphasizing unprocessed foods, such as the Raw or Paleo diets, are supportive of the microbiome. These diets are plant-based and the focus is to eliminate processed foods and other modern manipulations that reduce the natural nutrients of the food. Following a raw food diet is tricky because of the orientation of modern culture to highly cooked and processed foods. One of the important considerations is including enough PFC calories, but this is not a significant problem because fruits, seeds and roots complement green vegetables, and meat can be included in the diet.

The Paleo diet has perhaps a stronger focus on seeds and fruits that can have a high protein content and often a high fat content, and meat is popular component. From the microbiome perspective, it is important to remember that plants should be a primary focus and, from an historical perspective, hunter and gatherer cultures were highly dependent on plant materials. For most hunter and gatherer societies, hunting for meat was a constant activity, but plants formed the base of the diet.

These “pre-historical” diets are a conscious move away from modern processed foods and toward a diet that strongly supports the microbiome. Any of these diets that maintain a high level of fresh or unprocessed plant materials on a daily basis should promote microbiome health, diversity, and stability.

Diets emphasizing seasonal foods are also supportive of the microbiome. The Macrobiotic, Ayurvedic, and Seasonal diets recommend eating foods, mostly plants, grown in the current season and usually from local sources. On these diets, summer foods should be eaten in the summer and winter foods in winter. Of course, this greatly restricts the diversity of plant types in the diet to particular times of year and one’s recipe box has to be adjusted accordingly.

One assumption of these diets is that the summer or winter metabolism of the human body may be better supported by food produced during that time of year. For example, humans may experience seasonal changes in our physiology that affect body fat deposition, hormonal patterns, and energy expenditure. We certainly see such changes in behavior and metabolism in many species of animals (and all plants). However, we know nothing at all about whether the composition of the microbiome is sensitive to changes in the external environment or whether the microbiome reflects changes in the human body as it adjusts to the external environment.

What we do know is that our modern life no longer requires us to shift our eating patterns because of food availability and we can suspect this may influence the benefits we derive from the microbiome. For many people, an important consideration for an invariable diet that disregards seasons is that eating summer foods in winter requires those foods to be grown in distant places. Those foods are grown in other parts of the world, transported across thousands of miles, and require enormous amounts of energy by the time they get to market. This is not an environmentally sustainable practice, or course, but it also means the foods have been in storage for weeks to months and will not be as fresh.

Similar to seasonal diets, another approach is what we could term a terroir diet; that is, a diet based on the location where the foods are grown, which is also influenced by the season. Such diets would include Mediterranean, Indian, Nordic, and Locavore diets that emphasize the influence of location on the quality of the foods.

This emphasis implies that the plants we eat are conditioned by the local environment, especially the soil, and the qualities imbued in locally-grown plants are important for supporting the health of the people living in those localities. This philosophy extends to the animals that feed on those plants that are then eaten by humans.

The climate shapes the soils or every region. The rain and temperatures determine the kinds of plants that will grow there and the ranges of adaptations plants will have. The plants determine the diversity and abundance of all local animal species including microbes. The chemical compounds plants produce to protect themselves from insects and microbes are all adaptations to the specific location. We can assume that humans living and eating in every environment are awash in the chemicals contained in the local plants and these plants have a conditioning effect on the microbiome.


From a microbiome perspective, all of these dietary approaches toward plant-based nutrition will provide support for the diversity and health of the bacterial community in the gut. These plant-based diets have one important commonality: a focus on fresh and non-processed plant materials. We don’t know much about the movement of bacteria from the environment into the gut, but we know it is taking place. Eating raw, fresh, or unprocessed plants will increase the likelihood of consuming bacteria that are best at breaking down those particular plants. This movement of bacteria into the gut with the plant materials is the movement of environmental and genetic information into our body.

The flow of information into the gut will keep the microbiome flexible and up to date with regard to the world around us. Eating plants that have been highly processed, over cooked, or grown under unnatural conditions will be lacking many of those benefits. This should be particularly concerning to everyone because the vast majority of whole plant foods we buy at the market are produced under conditions that are designed to reduce and even eliminate the natural ecosystem.


Other popular diets tend to focus on “good and bad” in terms of PFC food types. While programs like Weight Watchers have no penalty for plants, the emphasis of the diet is to get participants to recognize “problem” foods and, not surprisingly, those are exclusively PFC foods. Many fad diets tend to support the microbiome (well, more so than in the past), but all have restrictions based on perceived negative aspects of certain foods, including some plants. In other words, a great many fad diets are exclusively concerned with metabolic foods – those that provide calories for the body – and less on foods that feed the microbiome.

The majority fit into the “low-carb” fad diets for which certain types of plants are restricted, such as sweet fruits and roots. (e.g., Atkins, South Beach, Keto, Paleo). These diets are avoiding high glycemic index sugars (Atkins and South Beach) and “modern” carb-rich plants (Paleo) or just carbs altogether (Keto). However, the “high protein” fad diets typically focus on meat, dairy, and plant-extract-based protein such as tofu. Plants are “allowed”, but the emphasis is often a one-size-fits-all approach when it comes to carbs (which is more or less true of all recent fad diets). That is, these diets tend to consider carb calories as “bad calories” regardless of their origin.

As most dieters are focused first on weight loss and second on overall health, it might be worth noting that plant-based diet plans, especially those focused on unprocessed foods, are almost impossible to gain weight on. Indeed, it would be a challenge to eat a diet based exclusively on oil-rich plant foods such as seeds, nuts, and legumes and manage to gain weight. And the more of each plant (i.e., leaves and stems) that is included in the diet, the harder that would be. Regardless of the caloric content, the more one focuses on following a diet with the health of the microbiome in mind, the easier it is to forget about calories.

A plant-based diet is self-limiting in the sense that it’s hard to overeat. Consider this: If I make mashed potatoes with four large potatoes, I could probably eat most of it (Seriously, I could.). However, I can eat only one whole baked potato and, even then, I might not be able to eat the rest of my dinner. I can eat a large jar of apple sauce, but I can only eat one whole apple. Why? Because when I’m eating only a part of a food, my stomach does not receive or send the same signals about being full as when I’m eating the whole food. Foods that are derived from parts of plants (for example, processed foods) do not generate the same sensations of “satiety”, and overeating is easy. In addition, processed foods are quick to digest and the feeling of satiety is short-lived.

And so, whether we follow a personal diet plan, a commercial diet program, or just follow our nutritional wisdom (i.e., our gut), the focus should be on a diet that emphasizes plants that are as fresh and whole as possible. Eat as much of green vegetables and whole fruits as you want. Eat the whole fruit and vegetable whenever possible. Eat them raw or lightly cooked. Eat as great a diversity of plants as you can and that includes seeds and nuts. Don’t worry about plant fats. Eat strongly flavored plants and use plant-based seasonings. Bottom line: assume that expressing your full potential will require all 400 secondary compounds found in the garden tomato and not just the 30 associated with “tomato” flavor.


Listen to your body. As you get more and more in tune with your diet, you will find yourself craving or desiring certain flavors and foods. By this, I don’t mean craving PFC-based foods and an urge to binge on ice cream. I’m referring to a desire for certain herbs or flavors or fruits. When eating a food makes you feel better, it may well be a food you need. When eating a food results in a good feeling, we tend to gravitate to that food again. This “good feeling” may be related to the nutrients contained in that food and that craving may be a hint that your body needs more of those nutrients. This is what is meant by “nutritional wisdom”. However! Be aware of the desire for foods (such as highly engineered fast foods and junk foods) that prey on our deep-seated attraction to sugar or salt. You can’t hear the quiet inner voice of food wisdom over the clamor created by highly addictive components in junk foods.

Remember who you are eating for. The microbiome gets only leftovers. If food can be easily digested and absorbed in the 90-minute race through the convolutions of the small intestine, it will not reach the colon. Tougher materials that can’t be broken down in that amount of time will make it to the slow, warm, anaerobic confines of the large intestine. The slow march through the much-shorter and wider colon is ten times longer than the small intestine. This is the time needed for bacteria to attack and decompose the tough cellulose molecules that make up plant fiber.

What about meat? Eating meat is an ethical and moral decision that everyone has to make. I have some additional comments about meat production in the next chapter. However, meats are PFC and are for you as an individual, not for you as an ecosystem. All processed grains are for you as an individual. All fried food. All baked goods. And it’s probably not surprising that just about anything you are tempted to binge on is a processed PFC food. If it comes in a box at the store, that food is for you, not for your microbiome. Consider it carefully because it has been designed by the food industry to generate a craving that is based on largely empty, but abundant, calories.

Occasional processed foods will not kill you. Like plant toxins, they are not inherently bad in small amounts. If your diet is plant-centered, eating a donut once in a while may be a pleasure. The PFC foods are not poison if the diet is oriented around maintaining a healthy microbiome. It’s not cheating to eat pizza, but whole vegetables come first and more frequently. Having said that, the world of modern, highly processed, engineered-for-taste, fast food and junk food is not a healthy place for an ecosystem like your microbiome. These foods are designed to be attractive to your head, not to your gut, and they are insidiously addictive. We grew up with these foods and they are hard to resist.


Something to keep in mind, however, is this: most foods, whether whole or processed, have probably decreased in quality over the past couple of decades. You may try to start dinner with a familiar healthy salad, but that salad has changed its character over the past few decades because of the methods and technology we now use to grow crop plants.

In fact, the loss of food quality is a slow process that has been happening in every facet of food production, whether processed or unprocessed. This is a serious problem if we are trying to increase the percentage of healthy foods in our diet yet relying on a commercial food production system that does not inherently value the qualities we are looking for in that food. This is now where we find ourselves and this is the topic of the last chapter.


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