The balance of two concepts related to the bacteria in the gut microbiota is very important; 1. Species diversity 2. Numerical balance
The preservation of species diversity and the existence and maintenance of numerical balance among species are related to health. The imbalances in both parameters, however, are related to diseases.
As long as the numerical balance and species diversity are maintained, all bacteria continue to perform beneficial tasks for us. However, in the case of a disruption in species diversity and/or numerical balance, the same bacteria that are beneficial to us can facilitate the development of various diseases and health-related issues.

In summary: It is not scientific to categorize the bacteria in the gut microbiome as 1. Beneficial bacteria 2. Harmful bacteria.

When species diversity and numerical balance are disrupted, the same beneficial bacteria behave like harmful ones. Because the numerical balance of the relevant bacteria is also being disrupted, leading to undesirable results.