ArticleScience advances2025
A metagenomic perspective on the microbial prokaryotic genome census.
Article in Science advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Functional-Taxonomic Scaling Resolves Conflicting Average Genome Size Estimates Across Environmental Gradients.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Revealing Functional Traits of Insect Pest Suppressive Rhizobacterial Strains Through Comparative Genomics.Environmental microbiology · 2026Article
- HaloTag-Based FACS-Compatible Assay for Intracellular Haloalkane Detection with a Potential Application to Halogenase Screening.Analytical chemistry · 2026Article
- MeioBIOME: A snakemake workflow for the parallel analysis of meiofaunal genomes and host-associated bacteria/archaea.bioRxiv : the preprint server for biology · 2026Article
- Microbe Decoder uncovers functional traits of microbes in microbiome datasets.Nucleic acids research · 2026Article
- Microbial Community and Enzymes for Biodeterioration of PVC Plastic Buried in Soil and Compost Environment.Current microbiology · 2026Article
- Unbinned contigs expand known diversity in the global microbiome.Nature microbiology · 2026Article
- Metabolite diversity of Microcystis strains shows tight correspondence to genotype and may contribute to ecotype specificities.Communications biology · 2026Article
- A multi-Omic resource for exploring microbial eukaryotes in the meromictic freshwater Lake Pavin.Scientific data · 2026Article
- Genome-resolved insights into hydrocarbon-transforming and nitrate-reducing microbial communities from deep petroleum reservoir cores of the Nashpa Oil Field, Pakistan.Frontiers in microbiology · 2026Article
- A genomic view of Earth's biomes.Nature reviews. Genetics · 2026Review
- Exploring theFrontiers in microbiology · 2026Article
- Viral Dark Matter: Illuminating Protein Function, Ecology, and Biotechnological Promises.Biochemistry · 2025Review
- The Basque Coast Estuarine Sediment Gene Catalogue.Scientific data · 2025Article
- Evidence for Trace Gas Metabolism and Widespread Antibiotic Synthesis in an Abiotically Driven, Antarctic Soil Ecosystem.Environmental microbiology reports · 2025Article
- A global soil plasmidome resource unveils functional and ecological roles of plasmids in soil microbiomes.Nature communications · 2025Article
- Augmenting microbial phylogenomic signal with tailored marker gene sets.Nature communications · 2025Article
- Article
- Microorganisms thriving together as communities.Nature reviews. Microbiology · 2025Article
- Droplet-Based Microfluidics in Single-Bacterium Analysis: Advancements in Cultivation, Detection, and Application.Biosensors · 2025Review
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Following 30 years of sequencing, we assessed the phylogenetic diversity (PD) of >1.5 million microbial genomes in public databases, including metagenome-assembled genomes (MAGs) of uncultivated microbes. As compared to the vast diversity uncovered by metagenomic sequences, cultivated taxa account for a modest portion of the overall diversity, 9.73% in bacteria and 6.55% in archaea, while MAGs contribute 48.54% and 57.05%, respectively. Therefore, a substantial fraction of bacterial (41.73%) and archaeal PD (36.39%) still lacks any genomic representation. This unrepresented diversity manifests primarily at lower taxonomic ranks, exemplified by 134,966 species identified in 18,087 metagenomic samples. Our study exposes diversity hotspots in freshwater, marine subsurface, sediment, soil, and other environments, whereas human samples yielded minimal novelty within the context of existing datasets. These results offer a roadmap for future genome recovery efforts, delineating uncaptured taxa in underexplored environments and underscoring the necessity for renewed isolation and sequencing.
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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.