Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper

2025/07/16 by Ben J. Woodcroft, Samuel T. N. Aroney, Rossen Zhao +8 · 1 voice · 7 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · #Genomics and Phylogenetic Studies #Gut microbiota and health #Microbial Community Ecology and Physiology

paper · doi:10.1038/s41587-025-02738-1

crossref issued 2025/07/16 · crossref published 2025/07/16 · crossref published-online 2025/07/16 · openalex publication_date 2025/07/16 · crossref created 2025/07/16 · openalex created_date 2025/10/10 · crossref published-print 2026/06/01 · crossref deposited 2026/06/16 · crossref indexed 2026/07/28 · openalex updated_date 2026/08/01

Citations

• Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
• A unified catalog of 204,938 reference genomes from the human gut microbiome
• Sensitive protein alignments at tree-of-life scale using DIAMOND
• GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy
• GTDB-Tk v2: memory friendly classification with the genome taxonomy database
• Bioetica - clonazione - tutela persona e della vita
• CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning
• Oenologues, qui êtes-vous?

Cited by

• Essential nucleic acid omics: a theoretical foundation for early-stage users
• Sulfurimonas lacustris sp. nov. and Sulfurimonas limnophila sp. nov. from the chemocline of a meromictic brackish lake
• Anaeroglomus insulsum gen. nov., sp. nov., anaerobic planctomycete, isolated from a thermal water stream
• Phylogenomic Analyses Reveal that Panguiarchaeum Is a Clade of Genome-Reduced Asgard Archaea Within the Njordarchaeia
• The Microflora Danica atlas of Danish environmental microbiomes
• Phenotypic and functional genome characterization of Herbivorax alkaliphila sp. nov. and Natronospora cellulosivora gen. nov., sp. nov., obligately anaerobic, cellulotrophic, endospore-forming bacteria from soda lakes in southwestern Siberia
• Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism

Discussions

• Check out our teams paper on SingleM, a metagenomic taxonomy profiler that doesn't ignore unknown species! @benjwoodcroft.bsky.social @aroneys.bsky.social doi.org/10.1038/s41587-025-02738-1 [bsky, 2 points, 0 comments]