Differential coping strategies exerted by biofilm and planktonic cells of Bacillus subtilis in response to a protozoan predator

The human protozoan parasite Entamoeba histolytica causes amebiasis and interacts with both beneficial and harmful members of the microbiome. In previous studies, it was shown that E. histolytica can break down pre-established biofilms of Bacillus subtilis in a time- and dose-dependent manner. Inhibiting parasitic cysteine proteases impairs biofilm degradation. However, it is still unknown whether bacteria can sense this process and respond to the degradation of the biofilms. Here, our research demonstrates a multilayered response of probiotic bacteria to the parasite, which differs between planktonic bacteria and pre-established biofilms. Sensing the activity of cysteine proteases from E. histolytica , the bacteria activate the general stress response and, to a lesser extent, the cell wall stress response. This activation helps the surviving members of the biofilm become more resistant to mild stressors such as ethanol, hydrogen peroxide, and sub-mic concentrations of ampicillin. On the other hand, planktonic cells exposed to the predators’ lysate deactivate the expression of genes associated with biofilm formation while inducing their motility to avoid predation. Overall, our results indicate that bacteria have evolved to recognize amoeba predators capable of degrading biofilms. Furthermore, the partially digested biofilm cells may have unexpected disadvantages over bacteria that did not encounter a predator. These findings may be useful in developing more efficient probiotic strains that are resilient to amebiasis. IMPORTANCE The human protozoan parasite Entamoeba histolytica feeds on intestinal microbiota to survive. To enhance the effectiveness of probiotics, we characterized how they respond to amoeba predators. We found that probiotics decrease the expression of biofilm-related genes to avoid predation while simultaneously inducing their stress response and increasing their motility. Our results can provide novel directions for engineering probiotic bacteria to overcome gastrointestinal-associated parasitic diseases. Additionally, it highlights a fundamental mechanism through which bacterial prey can evade predation in the gastrointestinal tract.