ArticleNature biotechnology2026
Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper.
Article in Nature biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed.
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- Metagenomic insights into mechanisms of coral larval settlement induction and inhibition by marine biofilms.Environmental microbiome · 2026Article
- Urban green roofs host intrinsic resistomes shaped by management but not dominated by pathogenic resistance.BMC microbiology · 2026Article
- Genomic characteristics and geographical distribution of uncultivated soil prokaryotes.BMC genomics · 2026Article
- Within-patient gene transfer between transiently and chronically infecting bacteria causes extreme antibiotic resistance during lung infections.Nature microbiology · 2026Article
- Stop codon reassignment to tryptophan in members of the bacterial phylumMicrobial genomics · 2026Article
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- Conserved symbiosis-associated genes in the cycad Encephalartos natalensis suggest co-option for cyanobacterial symbiosis.The New phytologist · 2026Article
- Salinity-driven microbial adaptation of hydrocarbon-degrading communities in coastal sediments.mSphere · 2026Article
- Metagenomic analysis of water column samples collected from Green Canyon 233 prior to the Deepwater Horizon incident.Applied and environmental microbiology · 2026Article
- Taxonomic and Functional Comparative Metagenomics of Peruvian Salterns: Insights into Microbial Communities and Aminotransferase Potential.Microorganisms · 2026Article
- Ecological plasticity ofMicrobiology spectrum · 2026Article
- Viral modulation of sulfur-oxidizing bacteria drives organic carbon sink formation during primary succession in deglaciating ecosystems.Nature communications · 2026Article
- Complex multicellularity is linked with expanded specialized metabolite production in microorganisms.Nature microbiology · 2026Article
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- Taxonomic and functional diversity of the microbiome associated with the freshwater sponge Metania sp. (Haplosclerida: Metaniidae) from the Brazilian Cerrado, a metagenomic approach.BMC microbiology · 2026Article
- Electrogenic CH4 oxidation on a bioanode: putative extracellular electron transport system in Methylobacter sp.FEMS microbiology ecology · 2026Article
- Physiology, functional genomics, and proteomics ofApplied and environmental microbiology · 2026Article
12 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Determining the taxonomy and relative abundance of microorganisms in metagenomic data remains technically challenging. Here we present 'SingleM', which estimates community composition using conserved regions within universal marker genes. By accurately incorporating species lacking genomic representation, we show that unknown species dominate in most environmental microbial communities. Our website 'Sandpiper' collates microbial community profiles from 248,559 publicly available metagenomes.
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Registered trials
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