Reconstruction of 1,979 prokaryotic metagenome-assembled genomes from 37 global cave environments.

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.Data Description:MAGs_HQ.tar + MAGs_MQ.tar: 1,979 prokaryotic metagenome-assembled genomes, high quality (HQ) (≥90% completeness, ≤5% contamination) and medium quality (MQ) (≥50% completeness, ≤10% contamination) magscot.tar: 4,234 refined MAGs from 25,276 candidate binsSupplementary Files