I agree. But the key is going to be that you can't easily classify most microbes as "good" or "bad" without talking about the host factors (genetic, diet, etc).

Uropathogenic E. coli are a good example of this:

Bacterial virulence phenotypes of Escherichia coli and host susceptibility determines risk for urinary tract infections https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5653229/

One size doesn't fit all: unraveling the diversity of factors and interactions that drive E. coli urovirulence https://pubmed.ncbi.nlm.nih.gov/28217693/