Metagenomic insights reveal β-glucosidase-producing lactic acid bacteria from Miyamikhri with taxiphyllin degradation potential

Abstract “Miyamikhri,” a traditionally fermented bamboo shoot consumed by the Dimasa tribe of Assam, was investigated using a multi-omics approach integrating metagenomics, functional prediction, molecular docking, and probiotic evaluation. Samples (M1, M2, M3; pH: 4.03–4.52) showed Bacillota dominance (50.04–100%), with notable abundance of Cyanobacteria (M1: 32.72%) and Proteobacteria (M2: 28.85%). At the genus level, Lactobacillus (38.75–60.86%), Weissella, and Pediococcus were predominant. Diversity indices indicated M3 had the highest diversity species (Simpson: 0.7099; Evenness: 0.9199), while M1 showed the highest richness (Chao-1 = 6). Functionally, predictive KEGG analysis identified enrichment in metabolism (29.72%) and disease-related pathways (23.27%). Genes related to dopaminergic synapse (mao, comt, ddc, th), cyanoamino acid metabolism (bgl) and glycerolipid metabolism (mgll, gk, agpat1, lpin1) were detected. From 51 LAB isolates, eight showed high β-D-glucosidases activity (> 0.7 µg/mL pNP); Levilactobacillus brevis M12 exhibited the highest activity under optimal conditions (pH 5, 30 °C, 7% NaCl). Molecular docking revealed highest affinity of − 8.049 kcal/mol (M12) with taxiphyllin. MD simulations (100 ns) confirmed complex stability (RMSD: 0.27 ± 0.04 nm, avg. H-bonds: 6.86), and MM-PBSA calculations showed stronger binding for M12 (–190.28 kJ/mol) over L. plantarum WCFS1 (–49.16 kJ/mol).