Antimicrobial compounds in medicinal herbs/fungi vs. Personal Microbiome

I'm well aware of the damage that antibiotic medication can cause to the microbiome, but what of the antimicrobial compounds that many plants and fungi have in the context of a healthy microbiome? What kind of biochemical black magic goes on in the gut when we eat those compounds or take them medicinally? And specifically, why the difference in healthfulness between broad-spectrum, concentrated antibiotics (often derived from natural sources) and eating a broad spectrum of antibiotic compounds in plant medicine-foods? If we see the gut as an ecosystem is it the difference between frequent, small-scale disturbances vs. catastrophic disturbances? When are biocides not all that bad?

Thanks!

Excellent question.  It's a similar argument I heard non-organic farmers argue about with the organic certification process.  

My thoughts are that they should be treated with the same care, but herbal sources are typically more readily available and don't damage the environment to make.  Herbal sources tend to be less concentrated and often are not sterile, but push the system towards a different composition of microbiome. For instance, apple cider vinegar, cranberry juice, or kimchi are all things that can help adjust biomes without destroying them.  

It's an unfortunate miss conception that herbs are harmless or organic is necessarily wildlife friendly. With organic vs nonorganic, I tell people it's a better option, but not ideal.

I hope that helps.

As for the difference between catastrophic and small disturbance, an ecosystem adapts to small disturbances because there's still life to breed and repopulate.

Excellent question.

I am working on the other side of the story (Heretic!) as i work with Antibiotics and how to use them more carefully etc.

I would say the biological antibiotics can be harmful too of course. I would like to take the problems of antibiotics to three sub-problems, and one is the microbiom (other to is simply pharmacological interactions and side effects and the resistences).
If you treat something that is mostly a bacteria alien for your body or a local citizen going rogue due change in the body, of course the first one is easier because it doesnt belong to you but still i can hardly imagine any compound which kills only on type of bacteria so there is always a change in the microbiom. Always. We are getting to understand the importance of the microbiom and that almost everything is connected to it, so change it and the consequences will be there, we just cannot tell the dimensions yet.

And just regarding to the other to risks: biological, herbal antibiotic compounds have those risks too! Therefore i would suggest absolutely the same caution using them! They can induct harmful interactions and presumably also resistences (however the influence to the antibiotics is unclear.

Ceterum censeo use every kind of antibiotics regerdless of source!