Microbial taxonomy is a complex and frustrating study that will continue to evolve as techniques to classify microorganisms become more sophisticated and available.
For those who work or study in the field of microbiology, microbial taxonomy can be confusing and frustrating. One of the reasons for this is a change or evolution in the manner in which microorganisms have been assigned to “genus” and “species” designations. With the advent of molecular technologies, many organisms previously named according to phenotypic characteristics are now being reclassified based on genetic similarities.
Phenotypic classification involved designation of “genus” and “species” based solely on the physical characteristics of an organism:
- appearance of an organism (morphology),
- diet (substrate utilization),
- and waste production (metabolic by-products).
Genetic analysis and gene sequencing have improved, and in many cases, changed our understanding of microorganism classification and the relationship between different microorganisms.
The American Academy of Microbiology recently released a report to address the complex issues that surround microorganism taxonomy (Reconciling Microbial Systematics and Genomics). The report describes the complex issues that surround microbial classification, but offers little consolation to those struggling with the naming and renaming headaches currently experienced. It would appear that microbial taxonomy will remain murky for some time to come.
Currently, species designation is assigned according to rules that require a species’ genome to have more than 70% DNA-DNA relatedness or 97% 16S rRNA identity to the nearest relative of another species. The current naming convention is considered inadequate because it is linear in its approach and is based on investigation of relatively few of the millions of microorganisms that exist in our environment. It is expected that studies of community genomics (metagenomics) will assist in delineating boundaries between species.
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