Camuy River Cave Park (CRCP) is an underground cave system located at the subtropical karst carved by the Camuy River in the subtropical moist forest of northern Puerto Rico (Nieves-Rivera, 2003) . This article contains a metagenomic dataset from the microbial and functional diversity of Clara Cave and Empalme Sinkhole water samples. The environmental DNA (eDNA) from the samples was extracted following direct Metagenomic DNA Isolation method, followed by Next-Generation-Sequencing technology (Illumina MiSeq). The sequences were submitted to MG-RAST online server for taxonomic profile generation and functional in silico description of the samples. The data consisted of domain Bacteria (96.69%), followed up by Viruses (2.87%), Eukaryotes (0.37%), and Archaea (0.02%). The data distribution by phyla showed Proteobacteria (92.61%), Bacteroidetes (1.66%), Actinobacteria (1.12%), and Firmicutes (0.48%). The subsystem functional data showed that 12.97% of genes were related to clustering-based subsystems, 11.40% to carbohydrates, and 11.0% to amino acids and derivatives. The metagenome dataset generated will provide an understanding and comparison framework of the microbial composition and functional diversity present in caves.
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