bad breath was caused by the types of bacteria found in people's mouths as opposed to the overall amount of bacteria. In their research which was published in the May 2010 journal of Applied and Environmental Microbiology they found that there exists four types of bacterial community compositions. The two parameters for bad breath (the concentration of volatile sulfur compounds in mouth air and the organoleptic score) was noticeably lower in one of the groups. In this group that had very low bad breath, there were significantly higher concentrations of Streptococcus, Granulicatella, Rothia, and Treponema than in the other groups.
These results clearly correlated the global composition of indigenous bacterial populations with the severity of oral malodor. Call this the "good" bacteria.
There results also suggest alternative strategies to improve bad breath by trying to modify the bacterial composition rather than pursuing treatments geared towards elimination (or decreasing overall amount) of bacteria which do not work.
Of note, there was another (earlier) study that found that eating yogurt improved bad breath which goes along with this idea of altering bacterial composition instead of eliminating it to improve bad breath.
Of course, all this assumes a person does not have cryptic fetid tonsillitis for which tonsillectomy or cryptolysis would be of greater benefit.
Read the research here.