by Inge Lindseth

Human vs. Microbiome - our nutrition from the perspective of microbes

Storm microbiome
Humans see many things differently and thus create a perfect storm for our microbes.

First: Think food quality. Second: Think meal based - not total amount of nutrients during a day.

It may be uncertain what the main drivers of the current obesity epidemic are, but claiming that “fat is bad” or “carbohydrates are bad” appears to be far too simplistic, given the accumulated knowledge. The way the microbiome influences us makes it easier to see how it is not necessarily the amount of fat or carbohydrates per se that leads to differences in health outcomes.

There is a difference between how the microbes in our guts and we as humans view one and the same meal. Putting your microbial glasses on – not just your own glasses – when you choose what to eat could make a difference as to how a meal will affect your body. But what does a bacterium and other microbes see through their glasses that is different from what is seen through our own glasses? Food-processing and meal frequency are two bullet points that are of importance in this regard.

… a series of bad meals may be easy for the human cells to bounce back from, if that were the only insult. But if these meals have changed the microbiota in the gut to become a constant disruptor of our metabolism, then our own human cells may not so easily bounce back. It has then become the new modus operandi of the body.

Nestling birds
Nestling birds © Виктор Иден -

A bacterium faces the same challenges as nestling and fledgling birds. If the daily fights for the food with the bird’s siblings is often lost, the young bird may die. Many bacteria and other microbes residing within us, face this imminent “death or prosper challenge” at distinct times during the day: after meals. While human cells receive what they need in spite of lack of food for many days, every meal becomes a fight for survival for a microbe. The microbes best fitted for the use of the food we happen to eat will get an advantage. What happens then, when the food the microbes are exposed to is either too abundant or too scarce, or the type of food the microbes are fed is not in sync with what is best for us as humans?

The microbiome changes the nutrition research landscape

For the purposes of this article, food can be divided into two categories based on how foods affect our biology. One category is how much nutrients we get from the food over the long term, be it too much or too little. If a nutrient is lacking, or for instance gluten is eaten when a person has celiac disease, symptoms and disease may ensue.

The other category is how meals affect us acutely, and, not to forget, how lack of meals affects us acutely. The sum of the quality of meals over time may lead to disease. As an illustration of this, let’s say you get a little paper cut in your finger. A healthy body will fix this with ease within a short amount of time. Get a little wound in and around the same cut in your finger every day for many weeks and infection may develop. The same goes for meals. Repeated insults can in the end cause disease.

One difference between how meals can affect our own cells on the one side and our microbial cells on the other is the fact that the microbiome has the potential to be changed permanently, while our own cells will stay roughly the same.

Therefore, a series of bad meals may be easy for the human cells to bounce back from, if that were the only insult. But if these meals have changed the microbiota in the gut to become a constant disruptor of our metabolism, then our own human cells may not so easily bounce back. It has then become the new modus operandi of the body.


Potato cells
Potato cells under the microscope (Picture: © Karoline Lyngstad Skjerve)

The perfect storm for your microbiota

It is known that nutrient density is related to how bacteria behave. In general, the higher the nutrient density the more virulent (= to exhibit “bad behavior”) a bacterium will become (1). Picture the latter as a kid with few limits imposed on him or her. Such kids indeed tend to become limitless and behave badly.

So, what constitutes a high nutrient density to a bacterium? This is different from how our human eyes “see” nutrient density. A bacterium can only see directly what is in its immediate vicinity. Thus, to a bacterium, chunks of a potato, as opposed to pure potato starch, is not necessarily perceived as a delivery of starch, but rather as a delivery of fiber. Although fiber is food for bacteria, starch means more bang for the buck. The starch in a potato, or most other unprocessed foods, are encapsulated within fiber walls, and are gradually broken down along the digestive tract. Interestingly, how, and the rate at which these walls are broken down in different foods, is not well characterized. However, precisely the possible gradual release of nutrients from whole foods’ cells along the small intestine may hold one of the clues as to why a diet consisting of minimally processed foods is consistently associated with good health, and why a diet heavy in ultra-processed foods is not. Apple juice, pure starch or milled grains (flour) – are examples of foods that have nutrients that are not encapsulated - and could signal a high nutrient density and thus be conducive to bad behavior by the microbiota. In other words, it may not matter much that a chunk of pure potato starch reaching the small intestine contains the exact same amount of energy as a chunk of boiled potato. The microbiota may perceive the energy content as different based on the food’s structure.

If nutrient density and a steady delivery of nutrients (snacking) is a bad thing for the homeostasis of a sound ecosystem in the gut, then a perfect storm diet could have these hallmarks:

  • A high intake of acellular/non-encapsulated nutrients (such as refined sugar and bread)
  • Frequent meals during the day and a relatively short time between the last and the first meal of the day (leading to shorter periods of food absence for bacteria in the small intestine)
  • A low content of phytochemicals (Meaning: Less inhibition of the growth of microbes)

Such a diet is actually to some extent what is part of official dietary guidelines as of today: Eat a fair amount of grains, such as bread, and eat small and frequent meals.  

Several aspects could be added to the meal above to make the storm intensify. If fat is added to a meal in which the microbiota is fed in a wrong way, perhaps as outlined above, things could be made worse. One reason being that inflammation provoking substances such as LPS (Lipopolysaccharides, derived from the bacterial cell envelope, trigger immune responses), that are produced by the microbiota, are fat soluble, and thus more easily enter the bloodstream when fat is available (2-5). Phytochemicals have been found to abolish this effect (5).

Putting it all together, this could explain how both low-fat diets (6-7) and low carbohydrate (high fat) diets (8) can be somewhat effective in reducing fat mass: The relatively large amount of flour based foods often used in low-fat diets may not have a negative effect when there is little fat to transport the LPS into the bloodstream. And in a low carbohydrate diet the carbohydrates that could have provoked increased LPS production is not there, and thus the fat in the diet is not harmful. However anecdotal, some claim that the avoidance of the fat-carbohydrate-combination in meals indeed gives good results on health.

The healthy French diet?

If the above-mentioned factors are to be considered an important way that food contributes to bad health, there can’t be significant exceptions to the above. In other words, a nutrient dense diet that consists of a large share of highly refined foods should lead to some signs of bad health in all populations.

So, how about how people ate in France in 1980 for example? The French diet at the time contained a whopping 720 kcal of wheat flour per person per day, based on wholesale figures. Overweight was far less prevalent in France than today. Wouldn’t this be an inexplicable anomaly to the above hypothesis? Well, overweight was far from nonexistent in France at the time, at 27 percent of the population (9). Furthermore, the French meal pattern at the time was very low in in-between-meals (10). It could also be that other aspects of the French diet such as eating rate, amount of fruits and vegetables and the level of ultra-processing played a role. Furthermore, a non-optimal diet can also require time in order to lead to negative effects. This can even span across generations, such as when diet induced changes in an individual’s microbiome are passed on to the offspring, perhaps only exerting the full negative effects when the offspring is exposed to an altered microbiome from infancy.


Certification consultant for probiotics
Inge Lindseth
registered dietitian

Inge Lindseth is a registered dietitian from the University of Oslo with over 20 years experience in nutrition. His special areas are fasting, the microbiome, obesity, obesity, diabetes and autoimmune diseases. He has written two books on nutrition and published several peer-reviewed articles.

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