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<p>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&#xa0;(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.</p>

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

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年12月3日

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  • Huihong Li,
  • Yuping Cao,
  • Xueke Liu,
  • Zelin Ke,
  • Liang Chen,
  • Bupe A. Siame,
  • Sima Yaron,
  • Ka Yin Leung

摘要

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.