I am using gfp tagged chloramphenicol marked staph aureus and normal gfp tagged pseudomonas for my antibiotic studies. I find that there are few rod shaped bacterias in the staph aureus cultures while doing confocal imaging. Can the appearance of rod shape give rise to changes in shape of staph aureus? Or could there be a contamination of pseudomonas? Or what are the chances of e.coli engulfing staph aureus and glows green?

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