Inclusion body formation occurs naturally in prokaryotic cells, but is particularly common when heterologous foreign proteins are overexpressed in bacterial systems. The plant disease virus protein CMV 3a (cucumber mosaic virus movement protein) and the 56kDa Orientia tsutsugamushi (OT56) protein (an outer membrane protein), which causes tsutsugamushi disease, were expressed in Escherichia coli, and found to form inclusion bodies. Confocal laser scanning microscopy revealed that these inclusion bodies are localized at the cellular poles within E. coli. Cells expressing inclusion bodies appeared to be interconnected, and divided abnormally. The clustered cells exhibited biofilm-like characteristics in that the interior cells of the community were protected by the antibiotic resistance of the outer cells. We compared the number of colony-forming units in inclusion body-forming versus non-forming E. coli to demonstrate the effects of lysozyme, sonication or antibiotic treatment. E. coli clustering provided significantly improved protection against cell disruption/lysis by physical and biochemical stress. This is the first report that shows that abnormal cell division caused by inclusion body formation can cause cellular clustering, resulting in improved resistance to stress in vitro.