What the Microbiome Actually Is
The term "microbiome" refers to the totality of microorganisms in a specific habitat—particularly the gut—as well as their genes, metabolic activities, and the products resulting from them. It is therefore not just about who lives there, but what happens there.
You can think of it as a lively interior: it is not the mere presence of individual inhabitants that determines the character of the place, but rather their interaction, their density, their roles, the conditions under which they live, and how they behave toward one another.
Diversity as a characteristic—not as a goal
Diversity plays an important role in microbiome research. This refers to how diverse and balanced a microbial ecosystem is. A diverse system is often considered more adaptable than a one-sided environment.
This does not mean that diversity is automatically always beneficial or that simple rules can be derived from it. However, it does show why the issue cannot be meaningfully reduced to individual “good” or “bad” microorganisms. The structure of the overall system is often the decisive factor.
What Microorganisms Do: Metabolic Products
What is particularly fascinating is that microorganisms are not merely present but are actively engaged in metabolic processes. They break down food components—especially those that the human body cannot fully digest on its own. This process produces metabolic byproducts that, in turn, interact with the intestinal mucosa, the local environment, and higher-level regulatory processes.
Food is therefore not merely sustenance for humans themselves. It also serves as a substrate for microbial processes. The microbiome does not merely react to the body—it reacts to what is offered to it. It therefore depends largely on our diet. When we change our diet, we also change our microbiome.
What the research shows
Modern research approaches the microbiome from several angles: the composition of microbial communities, the formation of bacterial metabolites, the influence of diet and plant compounds, and the question of how stable or dynamic microbial environments are.
This reveals an important pattern: the focus is not on individual microorganisms alone, but on their functions and interactions. At the same time, the research remains challenging. Microbiomes vary significantly from person to person. It is rarely possible to make simple, general statements.
A Perspective from Traditional Chinese Medicine and Empirical Medicine
TCM does not speak of the microbiome—rather, it has long described functional systems in which transformation, environment, moisture, and the quality of the center play a role. The idea of an internal ecological balance is not a new concept in TCM.
Traditional medicine has long viewed the digestive tract as a vital environment—not merely a mechanical passageway. Diet, rhythm, bitter substances, and aspects related to fermentation were considered in connection with internal balance.
The crucial question
Not: 'Which bacteria are good or bad?' But rather: 'What kind of internal environment is being promoted?' This is less simplistic, but biologically speaking, it is usually closer to reality.
In this context, research is focusing on diet, dietary fiber, polyphenols, fats, bitter compounds, and certain fungal compounds—not as isolated solutions, but as part of a microbial ecosystem.
In the next post, we’ll turn our attention to the liver—the quiet hub of metabolism.