Mikrostrains

Mikrostrains is a term used in microbiology and evolutionary genetics to describe small, genetically distinct sublineages within a larger clonal population of microorganisms. The concept emphasizes microdiversity within a population, where minor variants differ by limited sets of mutations that do not disrupt the core genome. Mikrostrains may arise by mutation, recombination, or horizontal gene transfer and can persist in defined niches or spread locally.

Terminology and scope: The term is not universally standardized, and its usage varies by group. In some studies, mikrostrains are considered equivalent to subclones or microlineages that can be distinguished by high-resolution sequencing and SNV patterns.

Detection: Advances in metagenomics, genome-resolved metagenomics, and single-cell sequencing enable detection of mikrostrains by identifying consistent SNV patterns and haplotype structure. Abundance estimates rely on read mapping and variant frequency.

Ecological and pathogenic relevance: Mikrostrains can differ in metabolic capabilities, stress responses, or host adaptation. In environmental contexts, they contribute to niche partitioning; in clinical settings, minor strains may preexist at low abundance and expand under selective pressure, influencing outbreak dynamics and treatment outcomes.

Challenges: The lack of standardized thresholds for defining a mikrostrain complicates comparisons across studies. Distinguishing true microdiversity from sequencing errors, incomplete assemblies, or sampling bias remains difficult.

See also: Microdiversity, clonal lineage, haplotype, ecotype.