Microbiome volume 8 , Article number: Cite this article. Metrics details. Taxonomic profiles of vaginal microbial communities can be sorted into a discrete number of categories termed community state types CSTs. This approach is advantageous because collapsing a hyper-dimensional taxonomic profile into a single categorical variable enables efforts such as data exploration, epidemiological studies, and statistical modeling.
Vaginal communities are typically assigned to CSTs based on the results of hierarchical clustering of the pairwise distances between samples. However, this approach is problematic because it complicates between-study comparisons and because the results are entirely dependent on the particular set of samples that were analyzed. We sought to standardize and advance the assignment of samples to CSTs.
The references were defined using a comprehensive set of 13, taxonomic profiles from women in the USA. This large dataset allowed us to comprehensively identify, define, and characterize vaginal CSTs common to reproductive age women and expand upon the CSTs that had been defined in previous studies. VALENCIA performed well on all three datasets despite the substantial variations in sequencing strategies and bioinformatics pipelines, indicating its broad application to vaginal microbiota.
This will allow unbiased analysis of both small and large vaginal microbiota datasets, comparisons between datasets and meta-analyses that combine multiple datasets. It is human nature to group objects and observations into categories based on their commonalities [ 1 ]. Doing so allows us to identify similarities and provides a unified framework for thought.
This approach is particularly useful when the underlying set of objects or observations are multidimensional and difficult to grasp through intuition. When confronted with the diversity present in the microbial communities that inhabit the human body, microbiome scientists have often turned toward categorization [ 2 ]. These communities routinely include hundreds of species with a long tail of taxonomic diversity [ 3 ]. Yet commonalities exist in the taxonomic compositions of these diverse communities and have enabled their categorization into types.
