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28. The Owner's Manual: Getting Our Diet in Order

We have been obsessed with diets for decades, but especially since the 1950s. Year by year, our fad diets have been getting more sophisticated and more “science-based” in terms of the specificity of the recommendations and the reasons behind them. Some diet plans focus on specially prepared (often highly processed) foods and others have shifted towards more natural foods. Some diets provide guidelines for eating and leave the specific decisions to the dieter and other plans are very prescriptive.

None of the fad diets are effective for the majority of the participants and this is most often blamed on difficulties sticking to the diet. This seems strange because it really shouldn’t be hard to eat right, to feel full, and to stick to a meal plan, and it shouldn’t be hard to maintain a healthy weight that doesn’t fluctuate wildly. Yes, our body shape does change as we age, especially as we become less active, but disease should not be a normal expectation.

At this point, we’ve covered a lot of ground about the microbiome, evolutionary biology, ecology, and ecosystems, but what does a few trillion bacteria in our colon have to do with our diet plan? We are learning that our microbiome doesn’t just live in the colon and its influence extends throughout the body. It communicates with the immune system and the brain, and it supports itself by supporting us.

We will never know all there is to know, but we know enough to be good stewards of the microbiome, which in turn is adapted to support the ecosystem in which it resides. We know enough to make smart dietary decisions, which means we can make smart health decisions.

Our diet should focus first on microbiome support and second on metabolic support.


Microbiome support: As we consider what to eat on a daily basis, we should first consider what the microbiome needs to be balanced, diverse, informed, and that means the majority of our diet should be plants. Not plant-based, mind you, but actual plants. What we want to get from plants can be quite diverse, but our number one criterion is fiber, which is to say cellulose. Cellulose is the structural component of plants that we, as humans, cannot digest and it will move quickly through our upper digestive tract to the colon. Cellulose is the foundation on which the microbiome is built because it is the material that provides the microbiome with an energy source.

Cellulose is by far the most abundant of the huge variety of molecules in plants that supports the microbiome. The qualities of cellulose differ from plant to plant. Pure cellulose is a polysaccharide made by linking together glucose (sugar) molecules, but cellulose can contain other related substances like pectin, hemicellulose, and lignin. These components vary in abundance in the cellulose molecule and that variation is key to the qualities of fiber from different plants. Bacteria tend to be specialists at breaking down particular molecular components of cellulose and therefore a diverse plant diet can support a greater diversity of bacterial types.


Metabolic support: In addition to cellulose for support of the microbiome, our diet should provide calories to support our metabolic needs. Those calories come as proteins, fats, and carbohydrates – let’s call them the PFC portion of our diet – and we all need about 1500-2000 calories per day for our resting metabolism. The more physically active we are, the higher our metabolic rate and the more calories we need to consume.

However, these calories are not useful to the bacteria in the microbiome. Under normal circumstances, the PFC food materials are broken down rapidly, absorbed in the small intestine, and never make it to the colon. So, our obsession with counting calories and PFC grams in our diet should always take a back seat to our primary goal of providing cellulose materials to the microbiome.

What this means is that fad diets that claim certain types of food are “bad” are making the wrong point that our primary concern relating to the diet is calories. The “good” and “bad” foods that are the focus of all fad diets are always PFC foods and never plants. The “bad” foods are highly unlikely to be overtly bad for you (excluding allergens, perhaps), but the emphasis on PFC is itself indicative of a poorly balanced diet with respect to the source of yourhealth, which is the microbiome.

Nonetheless, we have to eat PFC foods to support our metabolic energy demands (and because they’re delicious), so condemning some of them makes no sense, nor does trying to replace them with nutritional supplements. Supplements are not food and the supposed need for supplements again masks an imbalance in the makeup of the diet. With few exceptions, every nutritional supplement we take is derived from a plant and the need for plant-based supplements implies a lack of appropriate plant material in the diet. And so, let’s take the villains out of this story and focus instead on the heroes.


To sum up, the obsession with calories in the diet is based on an inaccurate view of what in our diet makes us healthy.

*The indigestible portion of our food is always plant materials and it’s the only part that feeds

the microbiome. A healthy rule is to feed the microbiome first and feed yourself second.

*The focus on proteins, fats, and carbs is a focus on the calories that provide energy and

building blocks for the physical body. These materials provide nothing for the microbiome, but a lot of money for diet companies.

*The need for vitamins and minerals is an indicator of an imbalanced diet that is lacking fresh

plant materials. Supplements do not replace fresh plants in the diet.


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