Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals

Claire A Dubin, Chunyu Zhao, Katherine S Pollard, Tomiko Oskotsky, Jonathan L Golob, Marina Sirota

Abstract read

In one paragraph

Article in mSystems, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0cells of the map it votes in

0citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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3 · Its place in the literature

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0 citing papers in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

6 authors.

Claire A DubinMarch of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, California, USA.ORCID 0000-0003-0319-6013

Chunyu ZhaoInstitute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, California, USA.

Katherine S PollardInstitute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, California, USA.ORCID 0000-0002-9870-6196

Tomiko OskotskyMarch of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, California, USA.ORCID 0000-0001-7393-5120

Jonathan L Golob *Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, Washington, USA.ORCID 0000-0003-0009-5815

Marina Sirota *March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, California, USA.ORCID 0000-0002-7246-6083

Funding

March of Dimes Prematurity Research Center at UCSF

6 · The paper itself

Abstract

The vaginal microbiome plays a central role in reproductive health. Vaginal microbiome dysbiosis is associated with many adverse reproductive health outcomes, but most studies have focused on associations at the species level. The potential contribution of intraspecies microbial variation, especially gene content differences across bacterial strains, remains underexplored in reproductive health contexts. The Metagenomic Intra-Species Diversity Analysis (MIDAS) framework enables such analyses, but depends on comprehensive reference databases. We constructed a MIDAS-compatible pangenome database from over 18,000 genomes in the Vaginal Microbiome Genome Collection (VMGC). Compared to the Genome Taxonomy Database (GTDB)-derived reference, the VMGC-derived database expanded the pangenomes of prevalent vaginal species, better capturing vaginal-specific intraspecies diversity. Applying this database to vaginal samples from a cervical dysplasia cohort, we identified 13

Indexed as

Genome, BacterialLactobacillus crispatusMicrobiotaUterine Cervical DysplasiaVaginaDatabases, GeneticFemaleHumansMetagenomicsbioinformaticscervical dysplasiahuman microbiomeLactobacillusmetagenomicsmicrobiomepangenomereproductive healthvaginal microbiomewomen's health

Identifiers

PMID42233644

DOI10.1128/msystems.01498-25

PMCPMC13289165

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.