Horizontal gene transfer is certainly a component of the microbiome, but without the appropriate organism as a chassis and the right genetic regulatory elements to express a gene it won't operate as expected. Indeed, the bacteriocins that are endogenous to S. salivarius are harbored on a transmissible megaplasmid of about ~190kbp that ensure it can spread to others of its own kind. However, those genes being transferred to other streptococci or oral bacteria may be much more difficult, as the recipient organism must be naturally competent, and the exogenous DNA must be intact.

The ecological niches that are occupied by bacteria are certainly still a major component, it is just now evident that there is more horizontal gene transfer than we had previously assumed; one does not negate the other, just expands the repertoire of usable (or unusable) genetic components.

I chose this as the chassis organism because of the high population numbers that already inhabit the average human mouth, and that it has existing probiotic functions in the oral microbiome. Perhaps other organisms could fill this role, but S. salivarius seemed like the most viable option if we were to achieve success as it already has existing activity which appears to be under constitutive expression; we just wanted to arm it further, but not so much that it burdens the cells or impairs replication/growth/function/life itself.

If you have any other questions I would be pleased to answer them! Hope this clarifies my line of reasoning and answers your inquiry :)