The landscape of bacterial contractile injection systems across large-scale metagenomes.

Bacterial contractile injection systems (CISs) have evolved as sophisticated mechanisms that enable bacteria to interact with and manipulate their hosts. Resembling bacteriophage tails, these systems inject effector proteins directly into target cells, facilitating complex bacterial-host interactions. Despite significant advances in understanding CISs, exploration has largely been constrained by the availability of completely sequenced microbial genomes, potentially underrepresenting their diversity in natural environments. In this study, we identified 1,129 CISs from metagenome-assembled genomes spanning 14 bacterial phyla and 1 archaeal phylum. Notably, CISs were identified in many uncultured microorganisms and were highly enriched in the phylum IMPORTANCE: Overall, this study expands our understanding of the ecological diversity, evolutionary adaptations, and functional roles of contractile injection systems (CISs) in microbial communities. The findings particularly highlight their adaptations to human-associated microbiomes. In addition, we conducted preliminary functional studies targeting the cargo protein BDI_2459 in