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VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition.

Michael T France1,2, Bing Ma1,2, Pawel Gajer1,2

  • 1Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.

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|November 24, 2020
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Summary
This summary is machine-generated.

A new tool, VALENCIA, standardizes the classification of vaginal microbial communities into community state types (CSTs). This enables more reliable comparisons and analyses across different studies of the vaginal microbiota.

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Vaginal microbial communities are classified into discrete categories called community state types (CSTs).
  • Current methods for CST assignment, based on hierarchical clustering, lack standardization and hinder cross-study comparisons.
  • There is a need for a standardized approach to assign vaginal samples to CSTs for improved data analysis.

Purpose of the Study:

  • To develop and validate a standardized tool for classifying vaginal microbial communities into CSTs.
  • To create a robust method for reproducible assignment of vaginal samples to CSTs.
  • To facilitate unbiased analysis and comparison of vaginal microbiota datasets.

Main Methods:

  • Developed VALENCIA (VAginaL community state typE Nearest CentroId clAssifier), a nearest centroid-based classification tool.
  • Defined reference centroids using a comprehensive dataset of 13,160 vaginal taxonomic profiles from 1975 US women.
  • Validated VALENCIA's performance on diverse datasets including African women, adolescent girls, and postmenopausal women.

Main Results:

  • VALENCIA successfully classified vaginal microbial communities across diverse populations and datasets, irrespective of sequencing or bioinformatics variations.
  • The tool identified and characterized common CSTs in reproductive-age women and expanded upon previously defined CSTs.
  • Relationships between community characteristics (pH, Nugent score), participant demographics (race, age), and VALENCIA-defined CSTs were described.

Conclusions:

  • VALENCIA offers a standardized and reproducible method for assigning vaginal community state types.
  • This standardization will enable unbiased analysis of small and large vaginal microbiota datasets.
  • VALENCIA facilitates improved comparisons between datasets and supports meta-analyses of multiple studies.