Metagenomic-based approach to a comprehensive understanding of cave microbial diversity

When compared to other fields of ecological study, cave microbiome is still a growing research area. In recent years, considerable attention has been paid to explore cave microbiomes all over the world to achieve a better understanding of life under unfavorable conditions. With the help of advancing molecular genetic techniques and high-throughput sequencing technologies, this greatly expanded our view of taxonomic distribution from a wide range of cave samples. It is, however, worth noting that different caves have unique physicochemical and biophysical characteristics. These factors have undoubtedly contributed to the variation in taxonomic composition. In addition, with differences in metagenomic DNA extraction protocols, the choice of 16S rRNA variable regions, sequencing technologies, and bioinformatics pipelines, this makes the taxonomic distribution from different caves difficult to compare. Nonetheless, according to the previous studies, it is generally accepted that cave ecosystems usually harbor lower taxonomic diversity than their outside environments. These results strongly suggest that cave environments provide restrictive conditions that filter out nonadaptive taxa. In this review, we present recent progress in taxonomic profiling studies of cave microbiomes based on the integration of metagenomics and high-throughput sequencing. Last but not least, ecological roles of cave-dwelling taxa are also discussed.