Medicinal Plants as Reservoirs of Endophytic Bacterial Genes Regulating Stress Tolerance: A Metagenomic Study on Eclipta prostrata (L.) L.

Abstract Endophytic microorganisms play crucial roles in regulating host plant physiology, enhancing growth, and promoting the synthesis of bioactive metabolites. Eclipta prostrata (L.) L., an important medicinal plant widely used in Ayurveda and traditional medicine for its hepatoprotective, hair growth–promoting, and anti-inflammatory properties, was investigated to characterize its endophytic bacterial community. Plant tissues were processed for endophytic DNA extraction, followed by Illumina MiSeq metagenomic sequencing. Reads were assembled using MEGAHIT, and gene prediction was performed with MetaGeneMark. Functional annotation (KEGG, eggNOG, NCBI-nr) revealed diverse microbial genes related to stress tolerance, including heat shock proteins (GroEL, Hsp60), oxidative stress enzymes (glutathione S-transferase, superoxide dismutase), and heavy metal ATPases. These genes are integral to protecting E. prostrata from oxidative, thermal, and metal-induced stress, thereby maintaining cellular homeostasis necessary for the synthesis and stability of its secondary metabolites such as wedelolactone, luteolin, and ecliptine. The enrichment of xenobiotic degradation pathways further indicates the adaptive role of endophytes in detoxification, potentially supporting the plant’s therapeutic efficacy under environmental challenges. Sequencing data have been deposited in the NCBI Sequence Read Archive (BioProject ID: PRJNA950587). This study highlights the functional contribution of endophytic microbiota in stress tolerance, detoxification, and sustaining the medicinal potential of Eclipta prostrata .