In the field of microbiology and related life sciences, 'microbial strains' are a crucial and frequently emerging core concept. It is like the "atom" in the biological classification system, a fundamental unit for precise research, technological development, and industrial applications. A deep understanding of the meaning of microbial strains is not only the foundation for mastering microbiology knowledge, but also the key to gaining insight into the cutting-edge development of modern biotechnology.


1. From species to strains: Precision of microbial classification
To understand microbial strains, it is first necessary to place them within the hierarchical framework of microbial taxonomy. The classic hierarchy of biological classification from high to low is: domain, realm, phylum, class, order, family, genus, and species. 'Seed' is the basic classification unit, representing a group of individuals who are highly similar in morphological and physiological characteristics and can mate with each other to produce fertile offspring. However, for the vast majority of microorganisms that reproduce through asexual binary division, such as bacteria and archaea, the definition of "species" relies more on the similarity of gene sequences (usually using 16S rRNA gene sequence homology greater than 97% as a reference standard).
However, there are still significant genetic and functional differences among individuals within a species. This leads to the concept of 'microbial strains'. Microbial strains can be understood as a genetically highly pure microbial population originating from the same single-cell ancestor, purified, cultured, and isolated. It is a different subpopulation within the same species that can stably inherit subtle differences in genetic background, physiological and biochemical characteristics, or ecological functions due to events such as gene mutations, gene horizontal transfers (such as obtaining plasmids, bacteriophages, etc.).
A vivid metaphor is that the "species" of microorganisms are like the "dog" species, while different "microbial strains" are like different breeds such as Chihuahuas, Labrador Retrievers, and Shepherds. They all belong to the category of 'dogs', but there are significant differences in body size, fur color, and habits. Similarly, within the same type of Escherichia coli, there are both harmless symbiotic strains present in the human gut and pathogenic strains carrying toxin genes that can cause severe food poisoning (such as O157: H7). Therefore, microbial strains are more precise identification and operational units than "species".


2. Core characteristics and identification criteria of microbial strains
The basis for distinguishing different microbial strains is multifaceted, mainly including the following aspects:

2-1. Genetic differences: This is the most fundamental and accurate basis for differentiation.
Whole genome sequencing: Whole genome sequencing can reveal the slightest DNA sequence differences between strains, including single nucleotide polymorphisms, gene insertions/deletions, genome rearrangements, etc. This is the 'gold standard' for identifying microbial strains.
The presence or absence of specific genes or plasmids: for example, pathogenic strains may carry "virulence island" genes encoding toxins or invasion factors; Industrial fermentation strains may contain plasmids encoding specific metabolic pathways. The presence of these genetic elements is key to defining specific functional strains.
Molecular typing techniques: such as pulsed field gel electrophoresis, multi site sequence typing, repetitive sequence PCR, etc. Like fingerprint identification, these techniques can quickly distinguish and trace different strains by analyzing the restriction digestion map of genomic DNA or sequence variation of specific sites.

2-2. Phenotypic differences: Differences in genotype will ultimately be reflected in observable or measurable phenotypic features.
Metabolic characteristics: Different strains may have varying abilities to utilize carbon and nitrogen sources. For example, certain strains of lactobacilli can ferment specific sugars to produce lactic acid, while other strains of the same species cannot. This is often detected in microbial identification through API reagent strips or BIOLOG systems.
Resistance characteristics: There are strain differences in tolerance to antibiotics, heavy metals, or bacteriophages, which is crucial for clinical treatment and pollution control in industrial production.
Morphological features: Although relatively minor, small differences in colony morphology (size, color, edges, bulge) and cell morphology can sometimes serve as preliminary distinguishing clues.
Product characteristics: For the production strain, its ability and yield of metabolic products such as enzymes, antibiotics, and organic acids are the core phenotypes, which directly determine its application value.

2-3. Ecological niche and source: 
Strains of the same species isolated from different geographical environments, hosts, or habitats often become different strains due to their adaptive evolution. The source of isolation is important information for strain naming and characterization.


3. Naming and Preservation of Microbial Strains
Microbial strains usually have a scientific naming convention that follows the format of "genus name+species name+strain identifier". The strain identifier can be a combination of numbers and letters, or a laboratory number or the access number of the strain collection center. For example, Bacillus subtilis 168， Among them, "168" is the identifier of the specific Bacillus subtilis strain.
Microbial strains with important scientific research or application value will be submitted to international strain collection centers for preservation, such as the American Type Culture Collection Center or the Chinese General Microbial Strain Collection Management Center. These institutions assign a unique preservation number to each strain of bacteria to ensure its genetic purity and accessibility, making it easier for scientists worldwide to replicate experiments and conduct comparative studies. This standardized preservation and management is the foundation for the sustainable utilization of microbial resources.




4. The Importance of Microbial Strain Diversity
The diversity of microbial strains is one of the most fascinating characteristics of the microbial world, and its importance is reflected in multiple aspects:

4-1. The foundation of basic scientific research: Many major discoveries in life sciences rely on in-depth studies of specific model microbial strains. For example, the study of Escherichia coli K-12 strain revealed the operon model of gene regulation and the basic mechanism of DNA replication; The study of specific strains of Streptococcus pyogenes led to the discovery of restriction endonucleases, which gave rise to molecular cloning technology. Selecting standard strains with clear genetic backgrounds and stable characteristics is a prerequisite for ensuring the reproducibility and accuracy of scientific research.

4-2. The key to clinical application and public health: In medical microbiology, the identification of microbial strains at the bacterial strain level is crucial. The pathogenicity, drug resistance, and epidemic potential of pathogenic bacteria are closely related to specific strains. For example, distinguishing between sensitive and multidrug-resistant strains of Mycobacterium tuberculosis directly determines the selection of treatment plans and the development of infection control strategies. In epidemiological investigations, tracking specific strains of pathogenic bacteria through molecular typing techniques can accurately pinpoint the source of the epidemic and cut off the transmission chain.

4-3. The engine of industry and biotechnology: The core of most industrial microbial fermentation processes is a carefully selected and optimized microbial strain. Whether it is the production of antibiotics (such as high-yielding strains of Aspergillus flavus), enzyme preparations (such as protease producing strains of Bacillus licheniformis), amino acids (such as Corynebacterium glutamicum), or functional strains used for wastewater treatment and environmental remediation, their performance depends on the genetic potential of the strains themselves. Modern metabolic engineering and synthetic biology techniques design "cell factories" that can efficiently synthesize target products by selectively modifying the genomes of microbial strains.

4-4. Applications in agriculture and food fields: In agriculture, microbial strains with specific functions are used as biofertilizers (such as rhizobia) or biopesticides (such as Bacillus thuringiensis). In the food industry, the starting fermentation agent for producing fermented foods such as yogurt, cheese, and kimchi is also a specific strain of lactic acid bacteria or yeast, which determines the flavor, texture, and safety of the product.


5. Summary and Prospect
In summary, microbial strains are a concrete manifestation of the genetic and functional diversity within microbial species, serving as a bridge between macroscopic species classification and microscopic gene function. It is not a vague concept, but an entity with a clear genetic identity and unique functional characteristics. The precise identification, characteristic analysis, and resource preservation of microbial strains constitute the cornerstone of modern microbiology and its application technologies.

With the development of cutting-edge technologies such as high-throughput sequencing, metagenomics, and culture omics, we have gained an unprecedented level of understanding of the diversity of microbial strains. In the future, research on microbial strains will focus more on understanding the interactions between strains, the interactions between strains and the environment, and how to extract and design excellent strains with specific functions from complex natural microbial communities, in order to play a greater role in human health, industrial production, environmental protection, and sustainable agricultural development. Recognizing the basic unit of "microbial strains" is the first step in harnessing the enormous potential of the microbial world.