For a long time, it was believed that identifying and quantifying biological units within any ecosystem was sufficient for its full understanding. Medicine approached the vaginal microbiome with this same principle: researchers grouped bacteria according to dominant species and divided health status into five main Community State Types (CSTs). This was an era where the presence of Lactobacillus was considered a “guarantor of health,” while its deficiency was viewed as a prognostic indicator of pathological processes.
However, the development of molecular genetics revealed that this classification reflected only a superficial picture of reality. In clinical practice, scientists often encountered a paradox where patients with identical microbiomes at the species level exhibited completely different immune responses and treatment outcomes. This led to the clear conclusion that the main challenge lies not in specific bacteria, but in the hidden genetic differences tucked away within the same species.
In response to this methodological flaw, researchers utilized an expanded catalog of genes (VIRGO2) and created an innovative algorithm called VISTA. This system is far more accurate and informative than a simple quantitative tally of microbial species.
From Taxonomic Units to Functional Strains
The stability of the vaginal ecosystem depends on its genetic composition. Traditionally, healthy microbiomes are dominated by Lactobacillus crispatus or related species, which suppress the growth of pathogens by maintaining a low pH. In contrast, dysbiotic environments are overloaded with anaerobes such as Gardnerella and Prevotella.
Medicine has long used 5 primary states (CSTs) based on dominant species:
CST I: L. crispatus
CST II: L. gasseri
CST III: L. iners
CST IV: Diverse anaerobes
CST V: L. jensenii
However, within each species, there are hundreds of different strains that standard tests cannot detect. To fill this gap, the VISTA algorithm was created to analyze Vaginal Orthologous Genes (VOGs)—clusters of genes with similar functions. This approach allows us to identify mgSs (metagenomic subspecies)—the unique genetic composition of a specific species in a given environment. By synthesizing this data, 25 different mgCSTs are derived, describing not just the bacteria, but its functional role and influence on the immune response.
VISTA operates on the massive VIRGO2 database, which currently integrates 1.7 million genes from over 280 species. Research showed that primary bacterial species are actually divided into 2 to 11 mgSs. For instance, Prevotella amnii was broken down into 11 independent genetic variants, and L. crispatus into 5. Practically, this means different subspecies of the same species can have completely different clinical effects.
Global Dynamics of Strains
A study covering five different regions confirms that the functional composition of the microbiome depends on geographical location. For example, L. crispatus mgCST 1 is widely distributed in Asia, North America, and Africa, whereas mgCST 6 is specifically characteristic of the Bangladesh region. A similar picture emerges in North America, where Gardnerella swidsinskii (mgCST 21) plays a dominant role.
These data clearly show that local factors—such as host genetics, diet, and environmental conditions—shape unique genetic profiles of the microbiome. This functional diversity reinforces the necessity of creating comprehensive databases that integrate various ethnicities, geographical areas, and age groups.
Function and Activity: Who Rules Microbial Processes?
When analyzing the microbiome, it is critically important to understand that not all bacteria present in the environment are equally active. Their functional potential, which scientists call “genetic richness,” varies sharply between species. For example, protective Lactobacilli require about 20,000 to 28,000 genes to exist, while the genetic reservoir of some complex anaerobic bacteria reaches 70,000.
However, simply possessing genes does not mean they are constantly used. Therefore, scientists turn to metatranscriptomics (a method that studies functionally active genes at a given moment). This observation revealed which species are the most “influential” in the microbiome.
It turned out that Lactobacilli, despite their numerical abundance, often exhibit low genetic activity. In contrast, polymicrobial Gardnerella types expend maximum energy and most intensively change the environment according to their needs. The role of bacteria present in very small numbers is particularly impressive; for example, Finegoldia magnamight go unnoticed, yet its genes exhibit such high activity that it can influence the functioning of the entire system.
Immune Clues and “Peaceful Coexistence”
Analysis of immune markers revealed that the host organism’s reaction is determined not by the general taxonomic classification of the bacteria, but by its specific functional genome. It was found that a specific subtype of Gardnerella vaginalis (mgCST 18) and the traditionally protective L. crispatus have almost identical effects on the host immune system. In both cases, pro-inflammatory cytokine levels are at a minimum.
This “peaceful coexistence” is due to the unique genetic reservoir of mgCST 18, which distinguishes it fundamentally from other aggressive strains:
Metabolic Compatibility: This subtype can utilize lactate (lactic acid); instead of resisting the acidic environment created by Lactobacilli, it uses this resource for its own survival, establishing a stable symbiosis.
Genomic Stability: The presence of CRISPR-Cas systems (bacterial “immunity”) protects the strain from foreign genetic elements and prevents the acquisition of new, harmful virulence genes.
Virulence Deficiency: Unlike pathogenic subtypes, mgCST 18 does not express toxins and adhesins that damage tissues and trigger acute immune system reactions.
Source: American Society for Microbiology
