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2. Let's have a caveat for breakfast

Updated: Jun 3, 2021

First, there is no such thing as good or bad bacteria. The entirety of the advertising world will disagree with that statement as well as a good portion of the medical world, but it’s true. If you watch TV, you know that a number of food products, like prebiotic products will “feed the good bacteria” or probiotic yogurts that supply “good bacteria” which somehow then suppress the "bad bacteria". Honestly, that isn’t how bacteria work.

Bacteria are tiny organisms that feed on large molecules (especially complex carbohydrates), break them down, and obtain energy from them. We do the same thing with our digestive enzymes in the small intestine. When bacteria are in a good environment, they reproduce in the most basic way - by splitting in two. The more food molecules there are for bacteria, the faster they can split in two and the more the bacteria there are. One happy bacterium can produce prodigious numbers of descendants in a very short time (for example, ~60 billion in 12 hours). If there is a very particular food supply, the bacteria that are best at eating it will grow faster than other bacteria and will eventually take over.

Bacteria and fungi are old. They have been trying to eat the dead material in the world for a very long time and they are serious competitors with each other. In fact, to influence the outcome of competition with each other, they often produce toxins to discourage other species of bacteria and fungi from trying to eat their food. Many of these toxins that can kill other microbes have been given a name by humans: antibiotics (that is, they are ‘anti-life’). It’s very likely that most, if not all, bacteria have some form of chemical defense for dissuading competitors.

When we encounter bacteria that cause disease, we consider them “bad” because they attack us and we take that personally. Some bacteria get a reputation for being bad, but that can be problematic because that label is pretty general and may not always be true. For example, we get very concerned when we detect “coliform bacteria” in drinking water and swimming pools. Coliform bacteria are primarily forms of Escherichia coli (E. coli) which is a bacterium found in literally every human and mammalian gut. Yours and mine, right now.

E. coli is not usually harmful; it can break down lactose sugar from the dairy products we eat and may even be a necessary inhabitant of our large intestine for our health. However, being a bacterium, E. coli can reproduce fantastically fast and, being a bacterium, it generates a lot of mutations. So, while the E. coli I have in my colon are absolutely harmless to me, they may be very different from yours and if you were to get mine, or vice versa, there could be trouble.

My point is that bacteria have a context. In the right context, such as the human intestine, E. coli has a job and does it well. However, when a pathogenic mutant comes into the same setting, it can create a variety of digestive problems. When we detect E. coli in the environment, it indicates the presence of mammalian feces and, perhaps more importantly, it’s an indicator that there may be hundreds of other fecal bacterial species present as well.

So, if that’s the case, then managing bacteria is a problem of managing context. When bacteria interact in one way, they can be beneficial or just neutral; if they interact in a different way, they can be dangerous pathogens. Many digestive disorders have a bacterial underpinning, but the problem is typically not the bacteria so much as the conditions that the bacteria are in. And those conditions are almost always conditions that are unusual, out of balance, or the result of disturbance.


Second, for bacteria to be useful to us, context is everything. If the environment that supports bacteria is basically the food they eat, then managing the bacterial environment is really a food problem. I mentioned that happy bacteria can produce prodigious numbers of descendants quickly, but “happy” is the contextual part. Happy for a bacterium means having a lot of food in the appropriate environment, but happy bacteria for humans also means the bacteria are behaving themselves and not making us sick.

One important way to keep bacteria in line is to create conditions that make a LOT of different kinds of bacteria happy, but not necessarily plentiful. That is, a situation where there is a lot of food of many different types, but no one bacterium species can become super-abundant.

The microbiome bacteria in our colon are mostly vegetarians. They derive their energy from undigested plant material, which is to say the portions of our diet that we are unable to digest quickly. We lack the enzymes to digest plant fiber and cellulose, but the bacteria produce enzymes that attack specific kinds of molecules making up the plant material. We can house and feed hundreds of species of bacteria if we eat a diversity of plant types which then provides a high diversity of food molecules for the bacteria.

The higher the diversity of plants in our diet, the more species of bacteria we can support and the lower the likelihood that any one species becomes super-abundant. So, for a healthy microbiome, we must create a context that promotes as many opportunities for bacteria as possible, and that means eating a wide variety of plant materials.


Third, food for humans should be food for bacteria. If we understand that we are not eating for ourselves alone, but for the trillions of bacteria in our colon that are helping to manage our health in very important ways, then it changes our relationship with food. I need carbs, fats, and proteins every day for energy and to maintain the systems in my body. But that’s just for me.

I can eat my human food and think I’m eating very well without providing anything useful to my microbiome. On the other hand, when I eat for the microbiome, I am not really eating for me because most plant material does not provide much (relatively speaking) of the three food sources we tend to focus on. Leafy veggies just don’t provide carbs, fats, and protein in huge amounts. On the other hand, seeds can provide those molecules, but seeds may provide little indigestible fiber for the microbiome.

So, making good food choices is important and it should be a daily process. In older times, just eating the food we grew on the farm meant some meat and lots of garden produce. Typically, the food we grew consisted of roots in the winter, greens in the spring, and fruits and seeds in the summer. The food we ate had an annual cycle.

Today, in most affluent countries, food that is normally from a certain time of the year is available at any time. And that out-of-season food is coming from faraway places such as Mexico, Chile and New Zealand. There isn’t anything particularly wrong with that, but it should be part of our decision-making process. Yes, I can eat apples every day, but I should also remember that fruits and seeds are not the same as leafy greens. And “vegetable” refers to vegetation, not to fruits and roots. Fruits are sugary and roots are starchy and both are good food sources, but that kind of food is more for you and less for your microbiome unless the food includes significant indigestible fiber.

In addition, for the past 60 years as the world population has skyrocketed, we have been actively breeding crop plants to grow faster, faster, faster in shorter and shorter amounts of time. And now, much of the (non-tree) produce we find in the store is grown in greenhouses under non-natural, highly-fertilized conditions that often include a great many chemicals to reduce bacteria, fungi, and insect pests. Because they are grown in such a short amount of time, these foods have fewer nutrients, lower levels of fiber, and lower intensity of flavors than they used to.

The fiber and the flavors are molecules that are important to the microbiome, but many of these plant chemicals take time to be produced. Our commercially and industrially produced foods usually look quite normal, but they are of lower nutritional quality than in the past.

It is important to keep in mind, the nutritional quality for you might be exactly the same as always because you need mostly carbs, fats, and proteins, but the nutritional quality for your microbiome is suffering. And this means that we not only have to eat with a careful eye toward our microbiome, but the food that we think is good for our little friends may be dramatically lower in quality than it was in the past.


Fourth, you are not alone. The battle to be healthy is one that everyone shares. Our society and potentially the human species may be in considerable trouble because of the way we have been treating our microbiomes for the past 70 years. We have been dramatically and rapidly changing the quality of our environment since the end of WWII. In 1945, we introduced antibiotics and began a social program to kill all bacteria. We did not know about the importance of the microbiome to our health. In 1947, synthetic pesticides became widely available and killed vast numbers of pest species, but a great many very useful and beneficial species were also killed as collateral damage. Simultaneously, synthetic fertilizers began to replace manure and other natural fertilizing techniques and caused great damage to the health of agricultural soils.

The numbers of these new chemical compounds exploded rapidly and are now ubiquitous in the human environment. Food quality is affected by the use of pesticides and fertilizers and our personal ability to handle food is affected by our microbiome. Plastics, pharmaceuticals, and a diversity of household chemicals were introduced by the thousands from the 1950s onward and were quickly incorporated into every aspect of our lives. Today, through our rapidly escalating technological expertise, we are literally surrounded by an invisible chemical chaos at every moment of the day.

Today, we are all facing health problems and concerns that have never been part of the human experience before this. Our approach has always been to focus on each individual disease and find the single environmental factor that causes it because this is how humans tend to deal with problems. Find the root cause and change it. However, this time, the root cause is our lifestyle. We have changed so many variables in our environment that we cannot find the root cause of individual problems. Instead of looking for the culprit, we need to step back and consider what it is that makes humans healthy, focus on that instead, and eliminate those things that prevent us from experiencing normal robust health.

These issues are not yours alone; they are ours as a society and as a species. We have to come to grips with the fact that our medical world is lost in a foreign land and standing on thin ice (to mix a few metaphors). Our external world is damaged and that has caused damage to another world that is within us. The two are inextricably connected. However, if we accept that the foundation of our personal heath is the health of the internal ecosystem we call the microbiome, then we can focus on changing our behavior in ways that promote the health of that foundation.


Wait, what do I eat?

Most of us eat the Western Diet, which is comprised of highly processed foods rich in carbs and fats. In broad terms, let me redefine the Western Diet somewhat differently than you may have seen in the past: The Western Diet is focused on feeding the human body and not on feeding the microbiome within the human body.

As a consequence, at every turn in the grocery store and restaurant, we are sold carb-fat-protein-rich and plant-fiber-poor foods that prevent the microbiome from managing our internal physiology and biochemistry. And that means our immune system and nervous system and metabolic functions are impaired. It’s not that fast-food is poison per se and that you can’t have a guilty pleasure on your cheat day, but this is not a daily diet that is good for us. It’s a diet that (purposefully) appeals to our weaknesses, it preys on our cravings, rather than representing a small treat or dessert.[i]

For our health, our daily diet must be a diet that is focused on feeding our microbiome. Our microbiome needs plants and it needs plants that provide a lot of diversity in terms of materials. We do not need to prepare the plants for the bacteria either. Overcooked plants may be easy to chew, but that means they are already broken down chemically. We need to give our bacteria jobs, difficult jobs that require special skills, not minimum wage jobs that any common bacteria can do. To do this, we have to consider the quality of the plant foods we are eating.

For example, we need fresh (or flash-frozen) green leafy vegetables such as kale, spinach, cabbage, collards, and other greens, that are cooked as lightly as possible. We need fresh fruits, not juices. We should eat the entire fruit, skin and all, of apples, tomatoes, and grapes. The skin is important! We should eat nuts and seeds and not be afraid of the oils. (However, it’s useful to know your ethnicity and other important genetic factors that may make some foods dangerous for you.)

Lastly, we should eat plants with strong flavors. We are breeding flavor out of our food. The food industry is now in the business of adding flavor to maintain uniformity[ii] and that means the food industry prefers plants and animals to be produced in such a way that flavor is de-emphasized and our desire for certain food can be manipulated.

Throughout our history, we have eaten plants because of the flavors, not in spite of them. The flavors are indicators to the human palate of the qualities of the plant. All plant-eating animals choose their plants very carefully and primarily by taste. We do the same. Why? I propose we do it because the plant flavors are an indicator of food quality and very important to our microbiome. It is one of our ways of feeding our microbiome and the reward for eating plants with strong flavors is HEALTH.

Keep in mind that plant flavors are toxins for insects and other would-be predators. Many of those toxins are likely to be anti-bacterial and anti-fungal as well. If we find certain plant flavors pleasurable, there is almost certainly a very good historical (and evolutionary) reason: consuming such flavors improves our health because they influence our microbiome which influences our immune system which influences our survival. It is no accident that humans have a very good sense of taste and smell.

Our food is truly our medicine. At least, it should be. We must insist on good and strong medicine. And the best way to gauge that is by the flavor of the plants we eat. Our modern world is awash in synthetic medicines designed to solve our health problems when all the while we are surrounded by answers to our health questions in the form of good old traditional food. The difference now is we are beginning to appreciate that we are not alone in another way- we have to feed 30 trillion bacterial partners when we eat. This was the missing piece. Knowing this, we can re-evaluate food and our eating habits and what we will find is that we have more control over our health than we imagined.


[i] Read The Dorito Effect by Mark Schatzker (2015) for an entertaining and frightening look at how the flavor of our foods are being manipulated to induce eating rather than improving health. [ii] The goal of all large food-producing corporations, especially fast-food chains, is to serve a dependable, consistent, uniform product. The MacDonald’s Corporation created the business model. No matter where you go in the world, the Macdonald’s burger and fries will taste exactly as you remember them from your home town. This is literally a promise that MacDonald’s makes to you as a customer. This is accomplished by adding very specific flavors to otherwise flavorless foods.


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