Time-Dependent Metagenomic Analysis of Customized Jute Retting for Delineating Microbial Dynamics and CAZyme Profiles for Process Modernization

Abstract Jute retting is the microbial process of decomposing the plant’s non-fibrous tissues to release and separate the usable bast fibers. The lack of understanding of the taxonomic diversity and functional profiles of microbial communities during retting stages hinders the efforts to optimize the process for enhanced retting. This study employed whole metagenome shotgun sequencing to investigate the microbial diversity, temporal community dynamics, and functional gene profiles across the retting process. Proteobacteria predominated throughout all stages, with time-specific shifts noted in Bacteroidetes and Bacillota. Aerobic genera such as Acinetobacter and Pseudomonas prevailed early on, initiating pectin degradation, whereas anaerobic Clostridium species predominated later, facilitating hemicellulose and cellulose breakdown. Fungal species, particularly Aspergillus niger and Trichoderma spp., contributed to lignocellulolytic activity, further promoting fiber release. Analysis of predicted functional genes revealed stage-specific distributions of carbohydrate-active enzyme (CAZyme) families, reflecting the potential enzymatic capacity of the microbial community during retting. Glycosyl hydrolases (GH) peaked at day 5, aiding cellulose and hemicellulose hydrolysis, while glycosyl transferases showed consistent activity for polysaccharide modification. Carbohydrate esterases and carbohydrate-binding modules demonstrated activity at days 5 and 14, enhancing ester bond hydrolysis and enzyme-substrate interactions. Polysaccharide lyases (PL) and auxiliary activity enzymes, though less abundant, peaked at day 14, facilitating lignin degradation. Pectinases (PL1, PL9, GH28), xylanases (GH8, GH10), and cellulases (GH6, GH12) exhibited sequential activity throughout the retting. This study illustrates the potential of metagenomic insights for developing microbial consortia and enzymatic formulations to enhance retting efficiency for sustainable advancements in natural fiber production.