The genus Serratia revisited by genomics

Area of Science:

• Microbiology
• Genomics
• Phylogenetics

Background:

• The genus Serratia comprises clinically significant and environmentally diverse bacteria, studied for over a century.
• A lack of comprehensive genomic data and a robust phylogenetic framework hinders a deep understanding of Serratia evolution and diversity.

Purpose of the Study:

• To establish a robust whole-genome-based phylogenetic framework for the genus Serratia.
• To investigate the genomic, phenotypic, and plasmid diversity within Serratia.
• To elucidate patterns of gene flow and population structure across the genus.

Main Methods:

• Assembly and analysis of 664 representative Serratia genomes, including historical isolates.
• Phylogenomic analysis to determine population structure and evolutionary relationships.
• Comparison of genomic data with historical phenotypic data.

Main Results:

• A well-defined population structure within Serratia was revealed, with deep divisions correlating with ecological niches.
• Strong congruence was observed between historical biochemical data and contemporary genomic findings.
• Significant genomic, phenotypic, and plasmid diversity was highlighted, alongside varied gene flow patterns.

Conclusions:

• The study establishes a comprehensive genomic framework for the genus Serratia.
• Phylogenomic analysis clarifies the evolutionary relationships and ecological associations within Serratia.
• This work facilitates understanding the emergence and diversification of clinical and environmental Serratia lineages.