Proteus mirabilis Utilizes a Contact Dependent Growth Inhibition System to Kill Competitor Species

The microbial organisms that colonize the human body are more abundant than somatic cells and contain more genes than the human genome. An estimated 500–1000 species of bacteria exist in and on the human body. The composition of polymicrobial communities in locations such as the gut and the urinary tract is shaped by the host but also by cooperative and competitive interactions between species. The study of bacterial competition systems has received significant attention in recent years, as they represent promising narrow-spectrum tools to eliminate pathogenic species. However, only few interbacterial competition systems have been identified and many more remain to be discovered. We observed competition between two common gut commensal bacteria that could be due to the action of a new competition system. In the gut of neonatal mice, commensal Proteus mirabilis eliminated Escherichia coli. We replicated this phenotype in vitro and demonstrated that mouse P. mirabilis killed Gram negative bacteria. However, P. mirabilis could not kill Gram positive or eukaryotic target cells. Killing required direct contact between P. mirabilis and its target cells, but killing was independent of the Type 6 Secretion System (T6SS), which is the only contact-dependent killing system described for P. mirabilis. The killing system was regulated by components secreted into the supernatant. Target cells lost nucleoid integrity and reduced transcription and metabolic activity. Through genomic comparison, we discovered that P. mirabilis encodes for a Contact Dependent growth Inhibition (CDI) system. The CDI system is a two-partner secretion system wherein the CdiB protein exports and displays its partner CdiA, the effector toxic protein. CDI producer cells are protected by an immunity protein, CdiI. A P. mirabilis mutant in the cdiA toxin did not kill target cells. Additionally, heterologous expression of the immunity gene rescued viability of E. coli in co-culture with P. mirabilis. Based on sequence homology, we grouped Proteus CDI systems into three classes. To our knowledge, this is the first report of CDI-mediated interbacterial competition for P. mirabilis. This system could be used by P. mirabilis to eliminate competitor species during a polymicrobial infection.