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The survival of pathogens in the human body has been rigorously studied for well over a century. Bacteria are able to colonize, persist and thrive in vivo due to an array of capabilities, including the ability to attach to host tissues, produce extracellular virulence factors, and evade the immune system. Most bacterial pathogenesis studies have focused on mono-culture infections; however, it is clear that many bacterial infections are not simply the result of colonization with a single species, but rather ensue from the actions of polymicrobial communities. Microbes within polymicrobial infections often display synergistic interactions that result in enhanced colonization and persistence in the infection site, although the molecular processes controlling these synergistic interactions are generally not known. Here, I will discuss how interactions between biofilm bacteria impact community development, resistance to host innate immunity, and in vivo persistence. I will also discuss the use of novel technologies for probing bacterial interactions in small biofilm populations.