Expansion, restructuring and characterization of the Legionellaceae family

Legionellaceae are a large and widespread family of facultative intracellular bacteria with high clinical relevance. While Legionella pneumophila, the most clinically relevant species, is relatively well studied, very limited information is available regarding the other species belonging to this family. Here, we analyzed all publicly-available Legionellaceae genomes and metagenome-assembled genomes, nearly doubling the number of recognized species and highlighting the need to restructure the familys taxonomy to include multiple genera that present distinct clinical relevance. We found that secretion systems and traits linked to host invasion vary significant across genus clusters and species, likely influencing their survival in their environment. While genus clusters presented different metabolic capabilities, species closely related to L. pneumophila were characterized by a more complete metabolism with fewer auxotrophies. Finally, we showed that while species have distinct environmental distributions, niche overlap increases at higher metabolic similarity. Together, our results shed light on the ecology of these microorganisms, highlight the diversity of traits that can occur in closely related facultative intracellular bacteria, and call for the restructuring of this clade to align with genomic information and clinical relevance to aid the management of Legionellaceae bacteria. Significance StatementLegionellaceae bacteria are responsible for Legionnaires disease, the leading waterborne disease in many industrialized countries. Historically, attention was focused on Legionella pneumophila and the ecology of other species remained largely unknown and unexplored. However, several water safety regulations cover the entire Legionella genus, currently the only recognized within this large family, including microorganisms with unknown health relevance. Using a comparative genomics approach and leveraging public genomes and amplicon data, we shed light on the scale, diversity and ecology of this family, finding a surprisingly diversity of the traits linked to host invasion and metabolism, likely driving the species environmental distributions. This study proposes to restructure the family Legionellaceae in multiple genera to align with known clinical associations and predicted phenotypes.