I would like to use a surfactant to dissolve some water insoluble compounds to test them against some microorganisms, what is the best surfactant that does not interfere with the antimicrobial activity?
depends on surfactant, its concentration and microorganisms ;) In general, I would say Tweens (20 & 80) could be utilized since several microbes are using them as substrates. Of course, you need a control of surfactant without your substrate..
This is an interesting question. We have worked on solute-water and macromolecular-water interactions (as well as interactions between water, hydrophobic substances and cellular macromolecules) in the context of microbial stress mechanisms and stress responses. Whereas our approach relates to cellular biology (we are not thoroughbred chemists), my sense is that the physical chemistry that determines water-solute interactions (sufficiently to dissolve insoluble compounds) is the same - and of the same energetic order - as that which impacts water-biomacromolecule interactions. In other words, whereas some surfactants are more inhibitory to cells than others, any surfactant sufficiently active to solubilise the substances you mention will also adversely affect the outer membrane and any other cellular macromolecules with which it comes into contact.
In this context, hydrophobins (small amphipathic proteins) might be a suitable alternative. Some of them are already comercially available, and to my knowledge no detrimental effects on cells have been reported. However, they can be utilized to dissolve numerous hydrophobic compounds!
Beside looking onto the effect on cell membranes one has to also consider the interaction with the antimicrobials. If the would have no effect on them then why not testing without. Generally nonionic surfactants as mentioned will have the smallest effect on the microbes. One then should chose those with overall high polarity. Option beside surfactants would be use of cyclodextrins.
Nevertheless, I rather would search for antimicrobial formulations with synergistic effects then for noninterference.
Please let me know if Tween 20 worked well for you, I'm looking for a surfactant that doesn't interfere with testing the antimicrobial effect of some antibacterial treated hydrophobic fabrics.