Classification of Bacteria and Archaea: past, present and future

Area of Science:

• Microbiology and Taxonomy
• Evolutionary Biology
• Genomics

Background:

• Bacterial classification began in the late 19th century using phenotypic markers.
• The distinction between prokaryotes and eukaryotes emerged in the 1960s.
• Chemotaxonomic and genotypic methods advanced prokaryotic classification beyond numerical taxonomy.

Purpose of the Study:

• To review the historical evolution of bacterial and archaeal classification systems.
• To discuss the current polyphasic approach integrating phenotypic, chemotaxonomic, and genotypic data.
• To explore future directions and challenges in prokaryotic taxonomy, including the impact of gene flow.

Main Methods:

• Historical review of taxonomic methodologies.
• Analysis of current polyphasic approaches in bacterial and archaeal classification.
• Discussion of phylogenetic and genomic data integration.

Main Results:

• Classification has progressed from phenotypic to integrated polyphasic and phylogenetic methods.
• The 'Candidatus' status accommodates uncultured prokaryotes with determined phylogenetic relationships.
• Genomic fluidity due to lateral gene transfer presents challenges but core characteristics remain for classification.

Conclusions:

• The polyphasic approach, integrating diverse data, is crucial for current bacterial and archaeal classification.
• Phylogenetic analysis using core and character genes aids in higher and lower taxon delineation.
• Achieving a definitive, theory-based classification system remains an ongoing challenge in prokaryotic taxonomy.