Microbiome of caves for bioprospecting: a critical review

Cave microbiomes, consisting of diverse and often extremophilic microorganisms, represent an underexplored reservoir for bioprospecting, which entails the systematic exploration of biological resources for commercially valuable compounds. These stable and isolated subterranean ecosystems are characterized by distinct microclimates, fostering the evolution of unique microbial consortia. The metabolic versatility of these microorganisms enables survival under oligotrophic and aphotic conditions, and this adaptability is reflected in their production of novel bioactive compounds, including antibiotics, enzymes, and secondary metabolites with significant therapeutic and industrial applications. This review aims to elucidate the distinctive characteristics of cave microbiomes, evaluate their biotechnological, medical, and industrial applications, and address the technical challenges associated with sampling and cultivating these microorganisms. The focus is extended to India’s diverse cave ecosystems, ranging from the historical Ajanta and Ellora caves to the biodiverse Meghalaya caves, which serve as critical reservoirs for microbial exploration. Special emphasis is placed on sustainable and ethical bioprospecting approaches, advocating for the conservation of cave habitats and ensuring equitable benefit-sharing with local communities. By critically analysing the influence of geological formations, climatic conditions, and nutrient availability on microbial diversity, this review highlights the immense potential of cave microbiomes for novel compound discovery. It underscores the need for further research in this promising domain while promoting practices that balance scientific exploration with environmental conservation.