Bacterial two hybrid methods (B2H or BTH) are usually carried out in E. coli and have some advantages over yeast-based systems. For instance, the higher transformation efficiency and faster rate of growth lends E. coli to the use of larger libraries (in excess of 10). The absence of requirements for a nuclear localisation signal to be included in the protein sequence and the ability to study proteins that would be toxic to yeast may also be major factors to consider when choosing an experimental background organism.
The methylation activity of certain E. coli DNA methyltransferase proteins may interfere with some DNA-binding protein selections. If this is anticipated, the use of an E. coli strain that is defective for a particular methyltransferase may be an obvious solution. The B2H may not be ideal when studying eukaryotic protein-protein interactions (e.g. human proteins) as proteins may not fold as in eukaryotic cells or may lack other processing.