VISTA (Vaginal Inference of Subspecies and Typing Algorithm)

Data and code to run the VISTA and the app. Unlike other parts of the body, a healthy vaginal microbiome is usually simple, with just a few types of bacteria—mostly <i>Lactobacillus</i> species. When the vaginal microbiome becomes more diverse and includes bacteria like <i>Gardnerella</i>, <i>Sneathia</i>, <i>Prevotella</i>, or <i>“Candidatus Lachnocurva vaginae”</i>, it’s considered less optimal and can increase the risk of reproductive and urinary health problems.<br>To describe these differences, scientists often use a system called <b>Community State Types (CSTs)</b>, which groups vaginal microbiomes based on the types and amounts of lactic acid–producing bacteria they contain. For example:CST I: mostly <i>Lactobacillus crispatus</i>CST II: mostly <i>Lactobacillus gasseri</i>CST III: mostly <i>Lactobacillus iners</i>CST IV: mostly diverse anaerobic bacteriaCST V: mostly <i>Lactobacillus jensenii</i>However, this system doesn’t capture the full complexity. Many strains and species in the vaginal microbiome go undetected with traditional methods. These hidden differences can be important for understanding how the microbiome affects health.To dig deeper, researchers look at the <b>genetic makeup</b> of the bacteria—specifically, the full set of genes found in each species. These genetic groupings are called <b>metagenomic subspecies (mgSs)</b>. When you combine all the mgSs in a sample, you get a <b>metagenomic Community State Type (mgCST)</b>, which gives a more detailed picture of how the microbiome might be influencing health.<br>This software package, VISTA (Vaginal Inference of Subspecies and Typing Algorithm), allows for classification of vaginal metagenomes to mgCSTs.