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The microbes used in Bokashi are grown together and create an acidic anaerobic environment that are not conducive to pathogens like e-coli and salmonella.
You are right, there are anaerobic microbes that are pathogenic, however these little guys are not.
The microbes typically are lacto-bacillus bacteria, beneficial yeast (fungi) and sometimes Phototrophic bacteria (PNSB)
To answer your question...yes bokashi is great for plants. Just mix some as a top dressing and watch how well your plants react.
Some great info on Bokashi on www.mygoodgreen.com