Comparative Analysis of Evolutionary Distances Using the Genus Mycobacterium

Area of Science:

• Genomics and Bioinformatics
• Microbiology and Infectious Diseases
• Evolutionary Biology

Background:

• Nontuberculous mycobacteria infections are a growing global health concern, particularly in vulnerable populations.
• Accurate identification and understanding of evolutionary relationships within the Mycobacterium genus are crucial for effective disease management.
• Existing methods for species identification and genus delineation require refinement to address the increasing complexity of mycobacterial infections.

Purpose of the Study:

• To evaluate various genomic metrics for their efficacy in distinguishing the Mycobacterium genus from related taxa within Mycobacteriales.
• To establish reliable thresholds for genus delineation using ribosomal RNA (rRNA) genes.
• To assess the validity of proposed genus splits and estimate the total number of species within the Mycobacterium genus.

Main Methods:

• Comparative genomic analyses including average nucleotide identity (ANI), genome-genome distance calculations, Mash, multilocus sequence analysis (MLSA), and average amino acid identity (AAI).
• Evaluation of 16S rRNA (rrs) and 23S rRNA (rrl) gene sequences for genus delineation.
• Phylogenetic analysis using whole-genome sequences to construct a genus tree and estimate species diversity.

Main Results:

• Average amino acid identity (AAI) demonstrated the highest discriminatory power for genus-level identification within Mycobacteriales.
• Confirmed 94.5-95.0% identity threshold for the 16S rRNA gene (rrs) and established an 88.5-89.0% threshold for the 23S rRNA gene (rrl) for genus delineation.
• The proposed splitting of the Mycobacterium genus into five distinct genera was not supported by the genus-delineating thresholds; at least 402 species are estimated, with 246 found in human clinical samples.

Conclusions:

• AAI is the most effective metric for distinguishing the Mycobacterium genus.
• Established rRNA gene thresholds provide a robust framework for genus delineation.
• The current study provides a reliable phylogenetic framework and species list for the Mycobacterium genus, crucial for accurate taxonomic positioning and identification of novel species.