SPIRE

SPIRE — Searchable Planetary-scale mIcrobiome REsource — is an integrated metagenomics resource encompassing ~100,000 metagenomic samples from 739 studies, 35 billion predicted protein sequences, and 1.16 million metagenome-assembled genomes (MAGs) clustered into over 100,000 species-level clusters across diverse global habitats.

Cite SPIRE

If you use SPIRE in your research, please cite:

Schmidt TSB, Fullam A, Ferretti P, Orakov A, Maistrenko OM, Ruscheweyh HJ, Letunic I, Duan Y, Van Rossum T, Sunagawa S, Mende DR, Finn RD, Kuhn M, Coelho LP, Bork P.
SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.
Nucleic Acids Research, 2024, Vol. 52, D1: D777–D783.
https://doi.org/10.1093/nar/gkad943

Contributors

Thomas S. B. Schmidt

European Molecular Biology Laboratory, Heidelberg
University College Cork

Anthony Fullam

European Molecular Biology Laboratory, Heidelberg

Michael Kuhn

European Molecular Biology Laboratory, Heidelberg

Luis Pedro Coelho

Fudan University, Shanghai
Queensland University of Technology

Peer Bork

European Molecular Biology Laboratory, Heidelberg
University of Würzburg
Max Delbrück Centre, Berlin

Tools Used to Build SPIRE

megahit

Assembly

metabat2

Binning

seqtk

Sequence processing

prodigal

Gene calling

bwa

Read mapping

samtools

BAM processing

htslib

BAM processing

ngless

QC & preprocessing

GUNC

Genome QC

CheckM2

Genome QC

metaWRAP

MAG refinement

mOTUs

Taxonomic profiling

Nextflow

Workflow management

Related Resources

Bork Group @ EMBL — Molecular Systems Biology Unit, EMBL Heidelberg
Schmidt Group @ UCC — University College Cork
Contribute — Report missing studies or data issues

Additional References

Prasoodanan PK V, Maistrenko OM, Fullam A, Mende DR, Kartal E, Coelho LP, Spang A, Bork P, Schmidt TSB.
Unbinned contigs expand known diversity in the global microbiome.
Nature Microbiology, 2026.
https://doi.org/10.1038/s41564-026-02314-6

For the planetary microbiome generalism analysis, cite:

Kim CY, Podlesny D, Schiller J, Khedkar S, Fullam A, Orakov A, Schudoma C, Robbani SM, Grekova A, Kuhn M, Rodrigues JFM, Tackmann J, Malfertheiner L, Patsch D, Perez-Molphe-Montoya E, Näpflin N, Gaio D, Rot G, Danaila M, Peluso ME, Dmitrijeva M, Schmidt TSB, von Mering C, Bork P.
Planetary microbiome structure and generalist-driven gene flow across disparate habitats.
Cell, 2026, Vol. 189, Issue 7: 2073–2091.
https://doi.org/10.1016/j.cell.2025.12.051

metaTraits — A large-scale integration of microbial phenotypic trait information
https://doi.org/10.1093/nar/gkaf1241

VIRE — Viral genome browser
https://doi.org/10.1093/nar/gkaf1225

MetaLog — Metagenomic sample metadata resource
https://doi.org/10.1093/nar/gkaf1118

proGenomes — Consistently annotated bacterial and archaeal genomes
https://doi.org/10.1093/nar/gkaf1208

GMGC — Global Microbial Gene Catalog
https://doi.org/10.1038/s41586-021-04233-4

EggNOG — Orthologous groups and functional annotation
https://doi.org/10.1093/nar/gkac1022