ArticleMicrobiome2020
Estimate of the sequenced proportion of the global prokaryotic genome.
Article in Microbiome, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers, 1 of them a synthesis that pooled it.
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Who cites it
45 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The microbial dark matter and "wanted list" in worldwide wastewater treatment plants.Microbiome · 2023Pooled it
- Mitochondrial-Nuclear Interactions, Co-Transcription, and Adaptive Evolution in Cytoplasmic Male Sterility.Plant, cell & environment · 2026Review
- Long-read sequencing and chemical synthesis access previously hidden antibiotics.Nature biotechnology · 2026Article
- Anthropogenic climate change may reduce global diazotroph diversity.Nature communications · 2025Article
- Optimization of Mapping Tools and Investigation of Ribosomal RNA Influence for Data-Driven Gene Expression Analysis in Complex Microbiomes.Microorganisms · 2025Article
- Global biogeography and projection of antimicrobial toxin genes.Microbiome · 2025Article
- Global microbial community biodiversity increases with antimicrobial toxin abundance of rare taxa.The ISME journal · 2025Article
- High strain-level diversity of Bradyrhizobium across Australian soils.The ISME journal · 2025Article
- Unravelling Prokaryotic Codon Usage: Insights from Phylogeny, Influencing Factors and Pathogenicity.Current genomics · 2025Review
- Catalytic Enantioselective C-C Coupling of Alcohols for Polyketide Total Synthesis beyond Chiral Auxiliaries and Premetalated Reagents.Chemical reviews · 2024Review
- Quantifying functional redundancy in polysaccharide-degrading prokaryotic communities.Microbiome · 2024Article
- Mining biosynthetic gene clusters in Paenibacillus genomes to discover novel antibiotics.BMC microbiology · 2024Article
- Meta-omics assisted microbial gene and strain resources mining in contaminant environment.Engineering in life sciences · 2024Review
- Bacterial growth and environmental adaptation via thiamine biosynthesis and thiamine-mediated metabolic interactions.The ISME journal · 2024Article
- GDPF: a data resource for the distribution of prokaryotic protein families across the global biosphere.Nucleic acids research · 2024Article
- HiTaxon: a hierarchical ensemble framework for taxonomic classification of short reads.Bioinformatics advances · 2024Article
- A genomic analysis reveals the diversity of cellulosome displaying bacteria.Frontiers in microbiology · 2024Article
- CPGminer: An Interactive Dashboard to Explore the Genomic Features and Taxonomy of Complete Prokaryotic Genomes.Microorganisms · 2023Article
- Present and future outlooks on environmental DNA-based methods for antibiotic discovery.Current opinion in microbiology · 2023Review
- Germs, genes and soil: tales of pathogens past.Nature · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSequencing prokaryotic genomes has revolutionized our understanding of the many roles played by microorganisms. However, the cell and taxon proportions of genome-sequenced bacteria or archaea on earth remain unknown. This study aimed to explore this basic question using large-scale alignment between the sequences released by the Earth Microbiome Project and 155,810 prokaryotic genomes from public databases.
resultsOur results showed that the median proportions of the genome-sequenced cells and taxa (at 100% identities in the 16S-V4 region) in different biomes reached 38.1% (16.4-86.3%) and 18.8% (9.1-52.6%), respectively. The sequenced proportions of the prokaryotic genomes in biomes were significantly negatively correlated with the alpha diversity indices, and the proportions sequenced in host-associated biomes were significantly higher than those in free-living biomes. Due to a set of cosmopolitan OTUs that are found in multiple samples and preferentially sequenced, only 2.1% of the global prokaryotic taxa are represented by sequenced genomes. Most of the biomes were occupied by a few predominant taxa with a high relative abundance and much higher genome-sequenced proportions than numerous rare taxa.
conclusionsThese results reveal the current situation of prokaryotic genome sequencing for earth biomes, provide a more reasonable and efficient exploration of prokaryotic genomes, and promote our understanding of microbial ecological functions. Video Abstract.
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