ArticleNucleic acids research2026
PRIME: a database for 16S rRNA microbiome data with phenotypic reference and comprehensive metadata.
Article in Nucleic acids research, 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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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.
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3 authors.
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Abstract
PRIME (Phenotypic Reference for Integrated Microbiome Enrichment) is a curated and standardized database of human microbiome 16S rRNA amplicon sequencing data, designed to facilitate cross-study analysis, reproducibility, and phenotype-driven discovery. PRIME aggregates 53 449 samples from 111 public studies, covering 93 body sites and 101 phenotypic categories, with detailed harmonization of sample-level metadata such as disease status, demographics, body sites, sequencing protocols, and experimental design. Each sample includes taxonomic abundance profiles generated via a consistent pipeline using both SILVA (138.2) and Greengenes2 (2024.09) reference databases, with results reported at multiple taxonomic levels as observed abundances (read counts) and relative abundances (proportions). A major strength of PRIME is its extensive manual curation, which standardizes phenotypic and contextual metadata across studies, enabling precise querying and robust phenotype-based comparisons. Users can interactively explore the database through a modern web interface, filter and visualize data by metadata fields, and download customized subsets. Programmatic access is supported via RESTful APIs and R package. PRIME aims to advance microbiome data integration and is continuously updated to incorporate new studies and features. The database is freely available at https://primedb.sjtu.edu.cn.
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Registered trials
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