41% of Gram-negative bacteria encode a Type Six Secretion System

The type six secretion system (T6SS) is a highly studied, versatile bacterial nanoweapon that is important in bacterial pathogenesis and evolution. Despite extensive study, its prevalence remains poorly quantified. Analyzing 35,467 representative genomes, we find that approximately 41% of genomes in the average well-sampled Gram-negative genus (more than 30 sampled genomes) encode a T6SS. Further, we show that the distribution of the T6SS is patchy at all taxonomic levels. The uneven distribution we found is consistent with context-dependent selection, repeated evolutionary loss, or greater evolutionary lability. Our dataset provides a foundation for studying the drivers of T6SS distribution, and our pipeline enables similar surveys of other secretion systems, gene clusters, and multi-protein complexes across bacteria.