Taxonomic classification of genus Aeromonas using open reading frame-based binarized structure network analysis

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Accurate bacterial species demarcation is crucial for understanding microbial diversity and function.
• The genus Aeromonas presents a taxonomic challenge due to its complexity and numerous species.
• Whole-genome sequencing offers a powerful resource for microbial taxonomy.

Purpose of the Study:

• To evaluate the utility of open reading frame (ORF)-based binarized structure network analysis (OSNA) for taxonomic inference in the genus Aeromonas.
• To compare OSNA-based phylogenetic analysis with traditional core-genome single-nucleotide polymorphism (SNP) methods.
• To assess the reliability of OSNA for delineating species within a complex bacterial genus.

Main Methods:

• Phylogenetic trees were constructed using OSNA on 335 Aeromonas genomes, representing 30 species.
• OSNA utilizes binary sequences derived from the presence or absence of ORFs.
• Comparative analyses included core-genome SNP-based phylogeny and orthologous average nucleotide identity (OrthoANI) calculations.

Main Results:

• The OSNA-based phylogenetic tree successfully delineated most Aeromonas species into distinct conspecific clades.
• Results were corroborated by high OrthoANI values within identified clades.
• OSNA demonstrated high compositional similarity to core-genome SNP-based analysis, as indicated by the Fowlkes-Mallows index.

Conclusions:

• OSNA is a valuable and effective tool for the taxonomic classification of complex bacterial genera.
• This method aids in clear species demarcation within challenging bacterial groups like Aeromonas.
• OSNA provides a reliable alternative for bacterial phylogenetic and taxonomic studies.