Exploring microbial diversity and functional gene dynamics associated with the microbiome of Sof Umer cave, Ethiopia

Sof Umer Cave is the largest cave in East Africa and located in southeastern Ethiopia, is an unexplored extreme environment harboring novel microbes and potential genetic resources. However, the microbial ecology and their potential genetic resource, remain undiscovered. The purpose of this study was to employ high-throughput shotgun sequencing to explore the microbial diversity and functional gene dynamics within the microbiomes of Sof Umer Cave. High-molecular-weight DNA was extracted from homogenized sample using the GeneAll DNA Soil Mini Kit and 1% CTAB-SDS method. Purified environmental DNA was sequenced using a NovaSeq PE150. Microbial gene analysis revealed that Sof Umer Cave is primarily inhabited by Protobacteria, Actinobacteria, Bacteroidota, Verrucomicrobiota, Acidobacteiota, and Cyanobacteria, according to the Micro-RN database. The functional genes identified through the KEGG, eggNOG, and CAZy databases included 44,780 genes involved in metabolism and the biosynthesis of bioactive compounds. However, 34,716 genes related to metabolic processes remained unidentified, suggesting the presence of potentially novel genes for the discovery of natural bioactive compounds. Additionally, functional gene modeling using the FBA-built metabolic model, Model seed and MS2-prokaryotic metabolic model revealed 1,742 reactions, 1,542 compounds, and the addition of 302 new reactions during gap filling. Finally, the results revealed that the Sof Umer Cave is a reservoir for novel microbes and diverse functional genes, offering potential for the discovery of natural bioactive compounds. Article highlights Sof Umer Cave harbors a diverse range of previously unknown microbes that are potentially useful for discovering new bioactive compounds. The Sof Umer Cave microbiome is dominated by proteobacteria and actinobacteria, which play crucial roles in nutrient cycling and the production of secondary metabolites. Functional gene analysis revealed distinctive metabolic diversity, with potential genetic resources associated with novel metabolic pathways.