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The binomial system, developed by Carl Linnaeus, assigns each organism a genus name and species epithet written in italics. This two-part naming convention provides a standardized way to identify microorganisms. For example, Allochromatium warmingii uses Allochromatium as the genus and warmingii as the species epithet, enabling precise scientific communication across the microbiology field.

Microorganisms are classified into progressively more inclusive groups based on phenotypic similarity or evolutionary relationships. The hierarchy progresses from Domain at the broadest level, through Phylum, Class, Order, Family, Genus, and finally Species at the most specific level. For instance, the Domain Bacteria includes Phylum Proteobacteria, which contains Order Chromatiales, demonstrating how taxa nest hierarchically.

The International Committee on Systematics of Prokaryotes (ICSP) governs the nomenclature and taxonomy of bacteria and archaea, ensuring accuracy and standardization in microbial classification. This committee oversees the International Code of Nomenclature of Bacteria, which outlines formal procedures for validating new species names and maintaining consistency across the scientific community.

The Candidatus prefix is assigned to provisional names for organisms that cannot yet be cultured or obtained in pure form. Examples include Candidatus Pelagibacter ubique, a widespread bacterial species difficult to grow in laboratories, and Candidatus Heliomonas lunata, which cannot be maintained as a pure culture. This designation acknowledges valid species while indicating cultivation limitations.

Validated bacterial and archaeal names are maintained in the List of Prokaryotic Names with Standing in Nomenclature (LPSN) database and Prokaryotic Nomenclature Up-to-Date. Bergey's Manual of Systematic Bacteriology, published since 1923, remains the most widely recognized classification system, offering detailed information, systematic tables, and identification tools for bacteria and archaea.

National microbial culture collections, such as the American Type Culture Collection, preserve viable cultures in conditions that maintain genetic integrity. These repositories store type strains that serve as reference points for future taxonomic comparisons, enabling continued study and characterization. Unlike museum specimens, living cultures support ongoing research and safeguard microbial biodiversity.

A new bacterial species name must be accompanied by a detailed description of distinguishing characteristics and viable culture deposits in at least two international repositories. These requirements ensure that new taxa are properly documented and accessible for verification by other researchers. The validation process is governed by the International Code of Nomenclature of Bacteria to maintain taxonomic accuracy.