investigation of the genus type VI secretion system reveals genetic diversity in organization and putative effectors.

Bacterial type VI secretion systems (T6SSs) are contractile nanomachines that deliver proteinic substrates into target prokaryotic or eukaryotic cells and the surrounding milieu. The genus encompasses 39 recognized species and 13 subspecies, with many belonging to a group known as ‘emerging pathogens’. Within , seven species have been identified to harbour a complete T6SS cluster but have yet to be comparatively assessed. In this study, using systematic bioinformatics approaches and the T6SS-positive 488 strain as a reference, we explored the genus-wide prevalence, similarity and make-up of the T6SS amongst 372 publicly available ‘complete’ genomes. Our analyses predict that approximately one-third of species possess a T6SS. We also putatively report the first identification of a T6SS in four species: and . The T6SSs cluster into three distinct organizations (I–III), of which two break down into further variants. Thirty T6SS-containing genomes were found to harbour more than one gene, with strain NCTC 11845 possessing five. Analysis of the Pathogenicity Island-1 confirmed its conservation amongst T6SS-positive strains, as well as highlighting its diverse genetic composition, including additional putative effector–immunity pairs (e.g. PoNe and DUF1911 domains). Effector–immunity pairs were also observed neighbouring s in several other species, in addition to putative genes encoding nucleases, lysozymes, ATPases and a ferric ATP-binding cassette uptake system. These observations highlight the diverse genetic make-up of the T6SS within and provide further evidence of its role in pathogenesis.