Long-read PacBio HiFi sequencing of airborne metagenomes and physicochemical air quality data from Sudwala Caves, South Africa

The repository contains a comprehensive set of datasets generated to support the characterization of airborne microbial communities and associated environmental conditions within Sudwala Caves. It includes high-quality metagenome assemblies generated from 18 culture-enriched airborne samples using Flye, providing long-read–based genomic reconstructions suitable for downstream taxonomic, functional, and comparative analyses. Functional potential of the assembled metagenomes is captured through DRAM-based annotations, enabling systematic assessment of metabolic pathways, gene functions, and ecological roles of airborne microorganisms.
The repository also provides global sequencing and assembly statistics summarizing read quality, sequencing depth, assembly performance, and coverage across all samples. Taxonomic composition of the cave airborne metagenomes is documented through Kaiju-based taxonomic annotations, offering hierarchical classifications from kingdom to lower taxonomic ranks and facilitating comparative microbial diversity analyses. In addition, comprehensive metadata and physicochemical air quality measurements, including particulate matter fractions (PM₁.₀, PM₂.₅, PM₁₀), formaldehyde (HCHO) concentrations, temperature, and relative humidity, are provided for each sampling site and season. Together, these datasets form an integrated resource that links airborne metagenomic profiles with environmental context, supporting reuse in microbial ecology, cave microbiology, environmental monitoring, and long-read metagenomics research.