What are the different types of prokaryotic subspecies?

Microbial subspecies, often referred to as strains or ecotypes, can be determined based on genetic data by examining various types of genetic variations and characteristics. These genetic differences can lead to the classification of microorganisms into distinct subgroups within a species. Here are some of the different kinds of microbial subspecies that can be determined by genetic data:



Strains are populations of microorganisms within a species that have distinct genetic differences, which may lead to variations in traits, such as antibiotic resistance, metabolic capabilities, or virulence.

Genetic Basis

These differences can include variations in DNA sequences, such as single nucleotide polymorphisms (SNPs), insertions/deletions (indels), or genomic rearrangements.


Different strains of Escherichia coli (E. coli) may have unique genetic variations that lead to differences in their behavior, such as the ability to cause different types of infections.

Genomic Clades or Lineages

Microbial populations within a species can be categorized into genomic clades or lineages based on the overall genetic makeup of their genomes. These clades often represent different evolutionary branches or distinct phylogenetic groups within the species.

Phylogenetic Variants

Genetic data can reveal phylogenetic variants or subgroups of a species with unique evolutionary histories or genetic relationships. These variants may have diverged from a common ancestor and have distinctive genetic characteristics.

Single Nucleotide Polymorphism (SNP) Clusters

Strains or subspecies can be defined based on clusters of SNPs, where groups of closely related isolates share a set of characteristic SNPs. This approach is commonly used for high-resolution typing and tracking of microbial populations.

Antigenic Variants

Microbes may exhibit antigenic variations, which can lead to the classification of serotypes or serovars. These variations are often associated with differences in surface antigens or immunologically relevant molecules.

Functional Strains

Strains within a species may differ in their functional capabilities, such as metabolic pathways, ability to utilize specific substrates, or tolerance to environmental conditions. These functional differences are reflected in their genetic makeup.

Pathogenicity Types (Pathotypes)

Pathogenic microorganisms can be categorized into different pathotypes based on their genetic traits related to pathogenicity. This classification helps differentiate strains with distinct disease-causing abilities.


Ecotypes represent microbial populations adapted to specific ecological niches or environments. These adaptations are often encoded in their genomes and can include genes for specialized metabolic pathways or environmental tolerance.

Host-Specific Strains

Some microbial subspecies may exhibit host specificity, where they are adapted to colonize or infect specific host organisms. Genetic differences related to host interactions can be used to define these strains.

Genetic Variants Associated with Antibiotic Resistance

Strains with unique genetic variations, such as the presence of antibiotic resistance genes or mutations in drug targets, can be classified as antibiotic-resistant variants or strains.

Geographic Variants

Microbial populations may show genetic differences based on geographic locations. Strains adapted to different geographic regions can exhibit distinct genetic markers.

Specialized Clusters

Some microbial strains form specialized clusters with unique genetic features. These clusters may be associated with specific functions or adaptations, such as nitrogen fixation in certain rhizobia strains.


In RNA viruses like HIV or hepatitis C virus, quasispecies represent a population of closely related but genetically diverse variants within a single host. These variants can have important implications for drug resistance and viral evolution.

These are just some of the various ways in which microbial subspecies or strains can be defined based on genetic data. The classification depends on the specific characteristics being studied and the genetic markers or traits that are most relevant for the particular microbial group under investigation.

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