Sometimes looking at where a supplement comes from can help us to better understand it clinically. Berberine is probably the best example.
People use berberine for infections, dysbiosis, inflammation, intestinal barrier function, and glucose/lipid metabolism. It is concentrated (and supported by alkaloids with a similar property), within an herb called Coptis/Huang-lian.
If you compare the side effects lists of berberine and coptis the overlap between these substances is strong, even if it is not perfect —diarrhea, constipation, abdominal pain, bloating, gas, nausea… all of these effects are in common.
Why bother? Because coptis has been used, explored, and documented for two millennia. By extension, many of the problems people have with berberine today are long known, and there are distinct groups of people who predictably should or should not take it. In other words, that tradition can help us anticipate berberine’s limitations.
You should carefully consider whether coptis is necessary if your digestive system is too weak or if your body leans towards dryness and malnourishment. In the wrong context, or when used as a narrow approach, coptis/berberine can harm you.
We call these situations “Spleen qi deficiency” and “Stomach yin deficiency” and they are vulnerable states of the body and digestion that a strong substance like berberine can worsen.
From this point of view, not everyone needs a strong antimicrobial, even in a state of infection. Some need a mild one or a low dose, with the remainder of their clinical approach pointed towards strengthening and regulating a system in decline. After all, there’s limited strategy in attacking an invader, if the castle walls are already down, and the attack would hurt you as much as the enemy.
Lastly, consider that berberine is in 70 Chinese herbs (see symmap.org for details). All of those herbs are potential choices, even if berberine is a starting point. Each of them has a different character and effect and may better suit a particular case.