Using Core Genome Alignments To Assign Bacterial Species.

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Increasing bacterial genome data necessitates standardized species designation methods.
• Classical methods like DNA-DNA hybridization are unsuitable for unculturable bacteria, e.g., Rickettsiales.
• Current bacterial taxonomy faces challenges with high-throughput sequencing data.

Purpose of the Study:

• To develop and validate a standardized, high-resolution method for bacterial genus and species designation using core genome alignments.
• To create a workflow that recapitulates classically obtained taxonomic results.
• To reevaluate existing taxonomic designations, particularly within the Rickettsiales order.

Main Methods:

• Generated nucleotide-based core genome alignments for diverse bacterial genera.
• Developed a workflow incorporating alignment length, sequence identity, and phylogenetic relationships.
• Applied criteria including core genome alignment length (≥10% of genome) and sequence identity (≥96.8%) for taxonomic assignments.

Main Results:

• The core genome alignment method successfully recapitulated classical taxonomic results for most genera.
• Anaplasma and Neorickettsia genera require taxonomic reevaluation as they did not meet established criteria.
• Rickettsia genus has an overabundance of species designations (9 proposed vs. 27 current), and Wolbachia species are delineated differently from current supergroups.

Conclusions:

• Core genome alignments provide a robust, portable, and high-resolution method for bacterial nomenclature.
• The proposed method aids in resolving inconsistencies in bacterial taxonomy, especially for challenging taxa.
• This approach supports accurate and standardized bacterial classification in the genomic era.