A genomic catalog of Earth’s microbiomes
Why is this work in the frame?
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
Full frame distilled prediction
Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
- Candidate categories
- none
- Consensus categories
- none
- Domain
- Candidate signal: noneConsensus signal: none
- Study design
- Candidate signal: Bench or experimentalConsensus signal: Bench or experimental
- Genre
- Candidate signal: EmpiricalConsensus signal: Empirical
- Teacher disagreement score
- 0.205
- Threshold uncertainty score
- 0.593
- Validation status
machine_predicted_unvalidated·codex-gemma-dda1882f352a
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
- Teacher spread
- 0.204 · how far apart the two teachers sit on this one work
- Validation status
score_only:v0-immature-baseline· verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it
Abstract
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth's continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
The record
- Venue
- Nature Biotechnology
- Topic
- Genomics and Phylogenetic Studies
- Field
- Biochemistry, Genetics and Molecular Biology
- Canadian institutions
- Concordia UniversityUniversity of WindsorUniversity of WaterlooGeological Survey of CanadaNatural Resources CanadaUniversity of CalgaryAgriculture and Agri-Food CanadaUniversity of British ColumbiaInstitut National de la Recherche ScientifiqueUniversity of TorontoMcMaster University
- Funders
- Lawrence Livermore National LaboratoryMikrobiologický Ústav, Akademie Věd České RepublikyAgriculture and Agri-Food CanadaSandia National LaboratoriesGreat Lakes Bioenergy Research CenterNatural Resources CanadaSchool of Life Sciences, Arizona State UniversityUniversity of OregonAdvanced Research Projects Agency - EnergyStockholms UniversitetCollege of Engineering, Michigan State UniversityAddis Ababa UniversityNorth Carolina State UniversityUniversity of WashingtonLinnéuniversitetetUniversidad de Buenos AiresOffice of ScienceMax-Planck-Institut für Terrestrische MikrobiologieAkademie Věd České RepublikyUniversität WienGeorgia Institute of TechnologyConsejo Nacional de Investigaciones Científicas y TécnicasBaqiyatallah University of Medical SciencesUniversity of TorontoUniversity of New South WalesNational Energy Research Scientific Computing CenterDirectorate for Biological SciencesJoint Genome InstituteUniversity of WaikatoOregon State UniversityMontana State UniversityKoninklijk Nederlands Instituut voor Onderzoek der ZeeWest Virginia UniversityUniversity of California, San DiegoUniversity of MontanaUniversity of Arkansas for Medical SciencesPennsylvania State UniversityMichigan State UniversityMcMaster UniversityUniversity of California, DavisUniversity of AkronHarvard UniversityScience for Life LaboratoryUniversiteit UtrechtUniversity of MinnesotaOklahoma State UniversityAgResearchArizona State UniversityDivision of Ocean SciencesUniversity of Wisconsin-MadisonU.S. Department of EnergySveriges LantbruksuniversitetLembaga Ilmu Pengetahuan IndonesiaAarhus UniversitetOhio State UniversityClemson UniversityLouisiana State UniversityColorado State University
- Keywords
- MetagenomicsBiologyMicrobiomePhylumGenomeMicrobial ecologyArchaeaEvolutionary biologyEcologyComputational biologyPhylogenetic treeExtant taxonHost (biology)BacteriaGeneGenetics
- Has abstract in OpenAlex
- yes