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PRIME: a database for 16S rRNA microbiome data with phenotypic reference and comprehensive metadata.

Zhizhuo Zhang1, Hongyu Zhao2,3, Tao Wang1,2,4,5

  • 1Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.

Nucleic Acids Research
|October 31, 2025
PubMed
Summary
This summary is machine-generated.

The Phenotypic Reference for Integrated Microbiome Enrichment (PRIME) database standardizes human microbiome 16S rRNA data from over 53,000 samples. This enables robust, phenotype-driven discovery and cross-study analysis for researchers.

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Area of Science:

  • Microbiome Research
  • Bioinformatics
  • Genomic Data Analysis

Background:

  • Human microbiome research generates vast amounts of 16S rRNA amplicon sequencing data.
  • Lack of standardization across studies hinders data integration, reproducibility, and comparative analysis.
  • Phenotype-driven discovery requires harmonized metadata and consistent taxonomic profiling.

Purpose of the Study:

  • To create a comprehensive, curated, and standardized database of human microbiome 16S rRNA amplicon sequencing data.
  • To facilitate cross-study analysis, enhance reproducibility, and enable phenotype-driven microbiome research.
  • To provide a platform for interactive exploration and programmatic access to harmonized microbiome data.

Main Methods:

  • Aggregated 53,449 samples from 111 public studies covering 93 body sites and 101 phenotypic categories.
  • Standardized sample-level metadata including disease status, demographics, body sites, and experimental design through manual curation.
  • Generated taxonomic abundance profiles using a consistent pipeline with SILVA and Greengenes2 reference databases, reporting observed and relative abundances.

Main Results:

  • Developed the PRIME database, integrating diverse human microbiome datasets with harmonized metadata.
  • Enabled consistent taxonomic profiling across studies using standardized pipelines and reference databases.
  • Provided a web interface and APIs for interactive data exploration, filtering, visualization, and download.

Conclusions:

  • PRIME significantly advances microbiome data integration by providing a standardized, curated resource.
  • The database supports robust phenotype-based comparisons and facilitates reproducible microbiome research.
  • PRIME is continuously updated and freely available, promoting wider accessibility and future discoveries in human microbiome research.