Searchable Planetary-scale mIcrobiome REsource.

SPIRE integrates metagenome-derived microbial data modalities across habitats, geography and phylogeny.

SPIRE is a recently published platform with the aim to provide an integrated view of microbial diversity at various taxonomic granularities, at genome and at gene level, across known microbial habitats. It is a “one-stop-shop” for microbial data, integrated and consistently processed across habitats and phylogeny, at global scales. SPIRE is derived from ~100k metagenomic samples in 739 studies encompassing ~500Tbp of publicly available raw metagenomes, and holds five main types of data:

• manually curated contextual data, including annotations against a custom “microntology”
• 16Tbp worth of metagenomic assemblies (contigs)
• 35 billion metagenomic open reading frames (ORFs) called from these contigs, functionally annotated in various ways
• 1.16 million metagenome-assembled genomes (MAGs) of medium or high quality, co-clustered with isolate genomes into ~120 thousand species-level clusters and
• custom mOTU database to allow taxonomic profiling against these species-level clusters

Publication
Nucleic Acids Research, Volume 52, Issue D1, 5 January 2024, Pages D777-D783  https://doi.org/10.1093/nar/gkad943

Collaborators

Coelho, Queensland University of Technology

Schmidt, University College Cork