Account for the fact that E. coli is methyl red-positive and E. aerogenes is methyl red-negative.

The methyl red test, in conjunction with the Vogues-Proskauer, detect the end products of sugar fermentation.  Methyl Red is used to detect a large amount of acid production [with a pH around 4.5'ish] and VP is used to detect end products with a result ~6.5.  The major difference, honestly, is the fact that E. coli can break glucose down to many in organic acids where as E. aerogenes only breaks glucose down to acetoin.

Hope this helps!

[However, these two tests are relatively finicky and when they work, great!  But normally, the best bet it to look at the other rxns in your phase 1 biochemicals...  Ahh, the joys of learning micro! :-)]