I googled. It appears bad breath is (mainly?) due to the presence of hydrogen sulfide and methyl mercaptan [1]. These are mostly not produced by s.mutans but instead by gram-negative bacteria. otoh, S. salivarius K12 appears (and it being studied) to produce substances which inhibit s. mutans and the gram-negative bacteria [same article].

[1] http://www.scientificamerican.com/article.cfm?id=beat-bad-br...