Earth is teeming with microbial life, pervading all layers of the planet – from the deep subsurface to the upper atmosphere. Although characterizing this diversity remains a formidable challenge, microbial ecosystems are being explored at an unprecedented pace, continually revealing new taxa and communities. MicrobeAtlas integrates these studies into a unified, global resource for comparisons across environments, hosts, and technologies.

Here, we report on the latest updates and feature additions to MicrobeAtlas. The database now connects more than 5.3 million microbial sequencing samples into a unified dataset, substantially expanding environmental coverage and doubling community-level diversity. Using an improved, scalable workflow, these communities were clustered into tens of thousands of community types at adjustable resolution, enabling a bird's-eye view on global microbial ecosystems. Large language models now support the metadata extraction pipeline, improving environmental annotations, generating detailed keyword summaries, and enabling quantitative comparisons through semantic embeddings. Integration of the mOTUs4 and proGenomes4 databases, alongside existing links to BacDive, provides deeper functional and genomic context for lineages in MicrobeAtlas.

Ongoing efforts on reference database extension, strain-level biogeographic analyses, and microbial eukaryote integration will provide an increasingly comprehensive understanding of our microbial planet.

Co-authors: David Patsch, Daniela Gaio, Lukas Malfertheiner, Eugenio Perez-Molphe-Montoya, Matteo Eustachio Peluso, Nicolas Näpflin, Marija Dmitrijeva, Shinichi Sunagawa, Christian von Mering