Confocal micrograph of Bacillus subtilis. Bacillus subtilis is a Gram-positive, rod-shaped bacterium, commonly found in soil. Fluorescent proteins (TagRFP-T, sfGFP, TagBFP, mKate2 and mOrange2), time-lapse confocal microscopy and biophysical models are being used to understand the organization of bacterial biofilms.