7.2: Microbial Classification System

Classification is the process of organizing organisms into hierarchically inclusive groups based on their phenotypic similarities or evolutionary relationships. A species comprises one or more strains, and closely related species are grouped into genera. Genera are further classified into families, families into orders, orders into classes, and so forth, up to the domain level, which is the broadest taxonomic rank derived from a combination of phenotypic and genotypic data.

The nomenclature of organisms follows the binomial system developed by Carl Linnaeus, where each organism is given a genus name and a species epithet, written in italics. The naming of new microbial taxa is governed by International Committee on the Systematics of Prokaryotes

(ICSP) that oversees the International Code of Nomenclature of Bacteria (Also known as the Bacteriological code). It outlines the formal procedures required for validation. A new species name must be accompanied by a detailed description of its distinguishing characteristics and the deposition of viable cultures in at least two international repositories. When organisms cannot yet be cultured or obtained in pure form, a provisional name is given with the prefix "Candidatus." For example: Candidatus Pelagibacter ubique (it is a widespread bacterial species that’s very difficult to grow in a laboratory), Candidatus Heliomonas lunata (a bacterial species that cannot be grown as a pure culture in a laboratory). Updated and validated lists of bacteria and archaea can be found at List of Prokaryotic Names with Standing in Nomenclature

(http://www.bacterio.net ), and Prokaryotic Nomenclature Up-to-Date (http://www.dsmz.de).

Bergey’s Manual of Systematic Bacteriology is the most widely recognized classification system for bacteria and archaea. Since its inception in 1923, it has been an essential resource for microbiologists, offering detailed information, including systematic tables, figures, and identification tools. Another important resource is The Prokaryotes, which provides extensive insights into the physiology, ecology, phylogeny, and cultivation of prokaryotic organisms.

National microbial culture collections such as American Type Culture Collection, Belgian Coordinated Collection of Microorganisms, Collection of the Institut Pasteur, and many more play a vital role in microbial systematics. These repositories store viable cultures in conditions that preserve their genetic integrity, ensuring accessibility for research and biodiversity conservation. Unlike traditional museum specimens, these cultures are maintained in living states, enabling continued study and characterization. Such collections also safeguard type strains, which serve as reference points for future taxonomic comparisons.