Reconstruction of 1,979 prokaryotic metagenome-assembled genomes from 37 global cave environments
Bibliographic record
Abstract
Cave microorganisms represent unique extremophiles that have evolved in isolated, nutrient-limited environments and harbor exceptional metabolic capabilities. However, knowledge of cave microbial diversity at genomic level remains limited. Previous studies have focused on individual caves and do not give a global picture. Here, we present the first prokaryotic cave metagenomic catalog from 37 geographical diverse cave environments. We employed an optimized genome reconstruction pipeline to recover 3,837 medium-to-high quality cave metagenome-assembled genomes (MAGs). These MAGs were dereplicated into 1,979 species-level representative clusters that spanned 67 phyla of Bacteria (n = 1,858) and Archaea (n = 121) domains. Classification of representative species showed that 98.7% did not match any existing genome taxonomy classification of named species at ≥ 95% average nucleotide identity (ANI). Most representative genomes harbored putative biosynthetic gene clusters (BGCs) (98.0%) and enzymatic antibiotic resistance genes (ARGs) (95.0%). This comprehensive MAGs catalog provides a foundational resource for exploring cave microbial diversity, secondary metabolism, and the evolutionary origins of antibiotic resistance in subterranean ecosystems.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. 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.
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 | 0.001 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.004 | 0.001 |
Machine scores (provisional)
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.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".