Principles of Microbial Classification

Modern nomenclature and classification schemes for bacteria are elaborated under the guidance of International Committee on Systematics of Prokaryotes (ICSP). The ICSP summarizes all the data of current bacterial classification within International Code of Nomenclature of Bacteria and publishes International Journal of Systematic and Evolutionary Microbiology, where the last changes of bacterial taxonomy are indicated.

The existing principles of bacterial classification as well as the detailed descriptions of all bacterial taxa are also given in second edition of Bergey’s Manual of Systematic Bacteriology (published in 2001-2012). It is worthy to note that first publication of the manual of determinative bacteriology was prepared by the US bacteriologist D.H. Bergey as far as 1923. The current version of Bergey’s Manual comprises an immense scope of data of all known bacterial representatives.

Modern classification of viruses is performed by International Committee on Taxonomy of Viruses (ICTV). In contrast to any other biological objects, the ICTV states that “nomenclature of viruses is independent of other biological nomenclature”.

Several basic principles are employed for microbial taxonomy.

Numerical taxonomy (also known as computer taxonomy, or phenetics) was introduced into microbiological practice from the late 1950s. Numerical classification schemes use a large number of taxonomically useful phenotypic characteristics (usually 100-200 or even more). Among them are morphological, cultural, biochemical, antigenic, and many other microbial features.

The process of identification discriminates bacterial strains at defined levels of their overall similarity that results from the frequency of their common traits (for instance, more than 80% of similarity at the species level). Following the advances of molecular genetics, molecular-based methods, especially genotyping, created new opportunities for bacterial taxonomy.

Genetic-based taxonomy plays now a pivotal role in the process of identification of unknown microbial representative.

According to genetic-based scheme, bacterial identification at species level is made by molecular hybridization analysis. Genomic DNA of tested bacterial strain undergoes hybridization with DNA of bacteria that are typical for certain species (species-specific strains). If the level of DNA similarity between the bacterial strains (DNA relatedness) exceeds >70%, the tested bacteria can be accounted as members of the same species.

The ranks of bacterial classification from genus and above (family, order, etc.) are established on the base of sequence of 16S ribosomal RNA genes.

It has been found that genes encoding ribosomal RNAs and ribosomal proteins are highly conserved throughout evolution and they diverged more slowly than other chromosomal genes. Comparison of the nucleotide sequence of 16S ribosomal RNA from various microbial groups demonstrates evolutionary relationships among broadly divergent microorganisms (phylogenetic taxonomy). As an example, it has led to separation of two distinct domains Bacteria and Archaea from primary domain Prokaryota.

Nevertheless, despite outstanding achievements of genetic-based taxonomy, a lot of questionable situations in microbial classification cannot be resolved solely on the ground of genetic methods. By fact, this is clearly evident for closely related bacterial species. Many of them are of great medical relevance. For instance, Bordetella pertussis and Bordetella parapertussis; E. coli and shigellae; Yersinia pestis and other yersiniae; bacterial species from genus Brucella share DNA similarity >80-90%. However, these bacteria are distinct by many phenotypic traits especially in their virulence for humans. Thus, they remain placed into separate bacterial species.

In order to make numerical and genetic-based taxonomy consistent with existing laboratory and clinical data the concept of polyphasic taxonomy is generally adopted for current microbial classification. Here the identification of bacterial species is performed on the base of genetic analysis but in combination with the most important phenotypic characteristics.

The value of this universal approach becomes evident in the light of recent inventions of high-throughput one-step tests for bacterial species identification. Among them are the methods based on mass spectrometry of bacterial chemical components (eg, matrix-assisted laser desorption ionization–time-of-flight detection or MALDI-TOF analysis), whole cell fatty acid analysis and others. Such tests generate the huge array of data about chemical composition of investigated bacterial culture. These individual chemical patterns are the unique characteristics of any microbial representative. Being compared with the known data from microbiological computer databases the results of these tests provide rapid and precise identification of bacterial isolates, strains and species.