ArticleNature biotechnology2017
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life.
Article in Nature biotechnology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 138 papers.
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138 citing papers in PubMed.
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- Microbial phenazines: biosynthesis, structural diversity, evolution, regulation, and biological significance.Microbiology and molecular biology reviews : MMBR · 2025Review
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- Towards a phylogenetically informed approach to solving protein-protein interactions.Biochemical Society transactions · 2025Review
- Methanogenesis inhibition remodels microbial fermentation and stimulates acetogenesis in ruminants.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Large protein databases reveal structural complementarity and functional locality.Nature communications · 2025Article
- A red algal polysaccharide influences the multicellular development of the choanoflagellate Salpingoeca rosetta.Current biology : CB · 2025Article
- Draft genome sequence ofMicrobiology resource announcements · 2025Article
- Identification of key steps in the evolution of anaerobic methanotrophy inScience advances · 2025Article
- Genome-resolved metagenomics from short-read sequencing data in the era of artificial intelligence.Functional & integrative genomics · 2025Review
- Article
- Draft genome sequence ofMicrobiology resource announcements · 2025Article
- The Alpine ibex (Capra ibex) gut microbiome, seasonal dynamics, and potential application in lignocellulose bioconversion.iScience · 2024Article
- The link between ancient microbial fluoride resistance mechanisms and bioengineering organofluorine degradation or synthesis.Nature communications · 2024Review
- Reclassification of Some Exiguobacterium Species Based on Genome Analysis.Current microbiology · 2024Article
- Genomics and physiology ofMicrobial genomics · 2024Article
- On the limits of 16S rRNA gene-based metagenome prediction and functional profiling.Microbial genomics · 2024Article
- Hound: a novel tool for automated mapping of genotype to phenotype in bacterial genomes assembled de novo.Briefings in bioinformatics · 2024Article
78 more citing papers are in PubMed but not listed here.
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Authors and funding
21 authors.
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No grant is acknowledged in the PubMed record.
Abstract
We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.
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