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LB, TB media, and yeast extract are also yellow but at the heart of the question. What chemical(s) make E. coli yellow?

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If I had to guess, I would say FMN/FAD. – bobthejoe May 14 '12 at 20:58
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It's likely the proteins (general, nebulous answer). Yeast extract of course tints the LB and TB media. There is obviously a range of compounds involved because we are seeing the result of non-yellow wavelengths being absorbed. – leonardo May 18 '12 at 21:33

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You will be surprised that when describing the colonial morphology of E. coli on a Blood agar plate, the word choice for colour is "grey". I believe that user leonardo up there had a very good explanation about this "yellowish colour" question.

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I think of E. coli being more white than yellow. When you compare E. coli and S. aureus on an agar plate, the Staph colonies have a much more distinctive yellow tint. The yellow tint in Staph colonies is due to staphyloxanthin, a carotenoid pigment.

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