Reorganising the order Bacillales through phylogenomics

Area of Science:

• Bacterial taxonomy and phylogenomics
• Microbial evolution and classification

Background:

• Current bacterial classification relies on 16S rRNA phylogeny and phenotypic traits, which may not accurately reflect genotypic relationships.
• The order Bacillales exhibits phenotypic diversity (aerobic/anaerobic, spore-forming/asporogenic, rod/coccoid) challenging traditional classification.
• 16S rRNA gene phylogeny struggles to resolve the taxonomic positions of several families within Bacillales.

Purpose of the Study:

• To re-evaluate the taxonomy of the order Bacillales using whole genome-based phylogenetic approaches.
• To identify and resolve taxonomic anomalies at family and order levels within Bacillales.
• To propose a consensus phylogenomic approach for improved bacterial classification.

Main Methods:

• Phylogenomic analysis of 80 representative taxa from eight families and six families incertae sedis within the order Bacillales.
• Application of a suite of phylogenomic approaches to assess phylogenetic relationships.
• Comparison of whole genome-based phylogenies with existing classifications.

Main Results:

• Identified significant anomalies in current family and order classifications of Bacillales.
• Revealed the existence of four distinct Bacillaceae clades and two Paenibacillaceae clades.
• Demonstrated that Staphylococcaceae and Listeriaceae families belong to the Lactobacillales order, not Bacillales.

Conclusions:

• Whole genome-based phylogenomic approaches provide a more accurate resolution of bacterial higher taxonomic levels than traditional methods.
• The current classification of Bacillales requires revision based on phylogenomic evidence.
• A consensus phylogenomic approach can mitigate algorithmic biases and enhance the accuracy of bacterial classification.