Work

strainshare: a standardized, contamination-aware framework for gut-cervicovaginal bacterial strain sharing

Year: 2026

Type: software

Abstract: A versioned, reference-based standard for strain-sharing analysis between the gut and the female genital tract. Packages a population-aware shared-strain call, a within-vs-between-person null, a translocation-vs-contamination discriminator, a generalist-strain filter, longitudinal-only transmission-direction inference, and a low-biomass StrainGE fallback. Includes real-read benchmarks establishing a ~10x confidence floor and a species-agnostic ~0.1% divergence resolution limit, and a validation on a public pregnancy cohort (PRJNA288562).

Source: Zenodo (CERN European Organization for Nuclear Research)

DOI: 10.5281/zenodo.22228438

Authors: Yu, Jean, Kwon, Douglas S.

Institutions: Ragon Institute of MGH, MIT and Harvard, Mass General Brigham, Massachusetts Institute of Technology

Language: English

Topic: Gut microbiota and health

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: green

OpenAlex ID: W7204904215

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