ArticleNature2013
Insights into the phylogeny and coding potential of microbial dark matter.
Article in Nature, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,193 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
1,193 citing papers in PubMed, 1 synthesis or guideline pooled it, 2,411 citations in OpenAlex.
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- Perseus: lineage-aware refinement of Kraken2 taxonomic classification for long read metagenomes.Bioinformatics (Oxford, England) · 2026Article
- Preparation of a new fluopyram-loaded nanocomposite with eco-environmental safety and its control effect on root-knot nematode disease.Pest management science · 2026Article
- Domain classification of archaeal proteomes reveals conserved fold repertoire.PLoS computational biology · 2026Article
- A genomic catalog of Earth's bacterial and archaeal symbionts.Nature biotechnology · 2026Article
- Deployable high-fidelity metagenome binning at scale with QuickBin.Communications biology · 2026Article
- Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages.Nature communications · 2026Article
- A Review of Rumen Biohydrogenation and Efficient, Green Production of High-Quality Ruminant Products: Mechanisms, Opportunities and Challenges.Animals : an open access journal from MDPI · 2026Review
- Microbial Diversity and Functional Potential of Keem: A Traditional Starter Culture for Alcoholic Beverage-Application of Next-Generation Amplicon and Shotgun Metagenome Sequences.Molecular biotechnology · 2026Article
- Metagenomic Insights Into Red Sea Biodiversity Across the Web of Life.Environmental microbiology · 2026Article
- Stop codon reassignment to tryptophan in members of the bacterial phylumMicrobial genomics · 2026Article
- Article
- Metagenomic analysis of water column samples collected from Green Canyon 233 prior to the Deepwater Horizon incident.Applied and environmental microbiology · 2026Article
- Eco-Geography Reverses Dominant AMR Reservoirs in Klebsiella pneumoniae: Integron-Rich Mobilomes and Cross-Niche Connectivity.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Bacterial Community Composition and Functional Potential of the Kleptoplastic Sea SlugBiomolecules · 2026Article
- Cultivation-independent high-quality microbial genome reconstruction from environmental samples with midi-metagenomics.Genome research · 2026Article
1,133 more citing papers are in PubMed but not listed here.
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Authors and funding
22 authors at 10 institutions in 5 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called 'microbial dark matter'. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20% of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.