Shotgun sequencing of microbial diversity in South Korean caves

Caves host bacterial communities that have been studied in the context of antibiotic resistomes with important clinical implications (Bhullar et al., 2012). The composition variability among bacterial colonies from karstic habitats is strongly correlated to the environmental conditions inside the cave and, following a depth gradient, this variability is also dependent on surface conditions (Yun et al., 2016). In this present work, metagenomics sequence data from five South Korean caves are analyzed with the main objective of identifying microbial taxa as potential proxies for cave environmental conditions. Two independent shotgun sequencing platforms have been used targeting short and long reads through Illumina and Oxford Nanopore technologies respectively. The DNA samples come from swabs of rock surfaces or sediments inside these Korean caves that can be classified as wet, dry or seasonally wet. The internal depth gradient has also been considered for the interpretation of the composition of the internal microbiota. Dry environments like those from Baram and Simbok caves have a high abundance of species belonging to the Actinobacteria phylum, compared to wetter caves like Ondal, Sanjidang and Seodae. In dark and undisturbed sectors of the caves, the microbial colonies are dominated by Gammaproteobacteria compared to areas near the entrance.