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Published October 11, 2023 | Version 1.0.0
Dataset Open

Human Microbiome Compendium dataset

  • 1. University of Chicago
  • 2. University of Minnesota
  • 3. University of Colorado School of Medicine


The Human Microbiome Compendium is an ongoing project to build a large collection of human microbiome sequencing data processed with a uniform pipeline. Currently, the compendium contains 16S rRNA amplicon sequencing data for human gut microbiome samples retrieved from the Sequence Read Archive. Our website at has more information about the project and links to related resources. This data is freely available under a CC-BY license; if you use it in your work, please cite our preprint, "Integration of 168,000 samples reveals global patterns of the human gut microbiome" (doi: 10.1101/2023.10.11.560955).

Version history

1.0.0: Added file to the repository, and added a link to the preprint and title/author metadata for the Zenodo entry

0.2.1: "sample_metadata.tsv" was missing (Note: This was accidentally tagged "0.2.0" in the version history.)

0.2.0: Replacing "country" column in sample_metadata.tsv with an "iso" column using the country code rather than name.

0.1.0: Prepping for public release


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Preprint: 10.1101/2023.10.11.560955 (DOI)