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

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

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

mOTUs

Taxonomic profiling

Nextflow

Workflow management

Related Resources

VIRE
Nishijima S, Fullam A, Schmidt TSB, Kuhn M, Bork P.
VIRE: a metagenome-derived, planetary-scale virome resource with environmental context.
Nucleic Acids Research, 2026, Vol. 54, D1: D902–D911.
https://doi.org/10.1093/nar/gkaf1225

proGenomes
Fullam A, Letunic I, Maistrenko OM, Castro AA, Coelho LP, Grekova A, Schudoma C, Khedkar S, Robbani M, Kuhn M, Schmidt TSB, Bork P, Mende DR.
proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes.
Nucleic Acids Research, 2026, Vol. 54, D1: D852–D857.
https://doi.org/10.1093/nar/gkaf1208

MetaLog
Kuhn M, Schmidt TSB, Ferretti P, Głazek A, Robbani SM, Akanni W, Fullam A, Schudoma C, Cetin E, Hassan M, Noack K, Schwarz A, Thielemann R, Thomas L, von Stetten M, Alves R, Iyappan A, Kartal E, Kel I, Keller MI, Maistrenko O, Mankowski A, Nishijima S, Podlesny D, Schiller J, Schulz S, Van Rossum T, Bork P.
Metalog: curated and harmonised contextual data for global metagenomics samples.
Nucleic Acids Research, 2026, Vol. 54, D1: D826–D834.
https://doi.org/10.1093/nar/gkaf1118

metaTraits
Podlesny D, Kim CY, Robbani SM, Schudoma C, Fullam A, Reimer LC, Koblitz J, Schober I, Iyappan A, Van Rossum T, Schiller J, Grekova A, Kuhn M, Bork P.
metaTraits: a large-scale integration of microbial phenotypic trait information.
Nucleic Acids Research, 2026, Vol. 54, D1: D835–D841.
https://doi.org/10.1093/nar/gkaf1241

GMGC
Coelho LP, Alves R, del Río ÁR, Myers PN, Cantalapiedra CP, Giner-Lamia J, Schmidt TS, Mende DR, Orakov A, Letunic I, Hildebrand F, Van Rossum T, Forslund SK, Khedkar S, Maistrenko OM, Pan S, Jia L, Ferretti P, Sunagawa S, Zhao XM, Nielsen HB, Huerta-Cepas J, Bork P.
Towards the biogeography of prokaryotic genes.
Nature, 2021, Vol. 601, Issue 7892: 252–256.
https://doi.org/10.1038/s41586-021-04233-4

GMSC
Duan Y, Santos-Júnior CD, Schmidt TS, Fullam A, de Almeida BLS, Zhu C, Kuhn M, Zhao XM, Bork P, Coelho LP.
A catalog of small proteins from the global microbiome.
Nature Communications, 2024, Vol. 15.
https://doi.org/10.1038/s41467-024-51894-6

AmpSphere
Santos-Júnior CD, Torres MDT, Duan Y, Rodríguez del Río Á, Schmidt TSB, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP.
Discovery of antimicrobial peptides in the global microbiome with machine learning.
Cell, 2024, Vol. 187, Issue 14: 3761–3778.
https://doi.org/10.1016/j.cell.2024.05.013

EggNOG
Hernández-Plaza A, Szklarczyk D, Botas J, Cantalapiedra CP, Giner-Lamia J, Mende DR, Kirsch R, Rattei T, Letunic I, Jensen LJ, Bork P, von Mering C, Huerta-Cepas J.
eggNOG 6.0: enabling comparative genomics across 12 535 organisms.
Nucleic Acids Research, 2023, Vol. 51, D1: D389–D394.
https://doi.org/10.1093/nar/gkac1022

Additional References

Studies that have used or relied on SPIRE data.

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

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

Fullam A, Prasoodanan PK V, Kuhn M, Bork P, Schmidt TSB.
microntology: a lightweight, data-driven controlled vocabulary to describe Earth's microbial habitats.
bioRxiv, 2026.
https://doi.org/10.64898/2026.01.12.698811

Rodríguez del Río Á, Giner-Lamia J, Cantalapiedra CP, Botas J, Deng Z, Hernández-Plaza A, Munar-Palmer M, Santamaría-Hernando S, Rodríguez-Herva JJ, Ruscheweyh HJ, Paoli L, Schmidt TSB, Sunagawa S, Bork P, López-Solanilla E, Coelho LP, Huerta-Cepas J.
Functional and evolutionary significance of unknown genes from uncultivated taxa.
Nature, 2024, Vol. 626, Issue 7998: 377–384.
https://doi.org/10.1038/s41586-023-06955-z