Human Microbiome Compendium dataset

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 microbiomap.org has more information about the project and links to related resources.

This data is freely available under the Creative Commons Attribution 4.0 International license (CC BY 4.0). If you use it in your work, please cite our publication:

Abdill, Richard J., Samantha P. Graham, Vincent Rubinetti, et al. “Integration of 168,000 Samples Reveals Global Patterns of the Human Gut Microbiome.” Cell 188, no. 4 (2025): 1100–18. https://doi.org/10.1016/j.cell.2024.12.017

If you are using this dataset in combination with your own results, it's important to note that the taxonomic classifications may differ between releases, as documented in CHANGELOG.md. The most recent release (1.1.1) includes assignments made using SILVA 138.2 (SSU Ref NR 99) and Greengenes2 (2022.10 backbone).