Absolute Quantification of Full-Length 16S rRNA Amplicon Sequencing and Metabolomic Profiling of Red-Stipe Disease in Morel Fruiting Bodies

Morel (<i>Morchella</i> spp.) is one of the most valuable edible and medicinal fungi globally. Red-stipe disease severely impairs morel quality and yield, although its causative pathogens remain unclear. To investigate changes in morel fruiting bodies during red-stipe disease, this study employed absolute quantification full-length sequencing and metabolomics. Red-stipe disease significantly altered bacterial communities. All α-diversity indices increased except the Pielou evenness index. Absolute abundances of <i>Pseudomonas, Carnobacterium, Stenotrophomonas,</i> and <i>Sphingobacterium</i> were elevated and identified as potential pathogenic candidates. Co-occurrence network complexity was higher in diseased samples than in healthy samples. Metabolomics revealed that red-stipe disease affected metabolite accumulation. A total of 868 metabolites were upregulated, including Anabasine, Dinoprost, 4-Nitrophenyl β-D-Glucopyranosiduronic Acid, Glucotropaeolin, and Homocamptothecin. By contrast, 928 metabolites were downregulated, including Cimifugin, Defibrotide, D-Sedoheptulose 7-Phosphate, 1-O-Feruloyl-β-D-Glucose, and Geniposide. Differential metabolites were primarily classified as amino acids, peptides and analogues, and carbohydrates and carbohydrate conjugates. They were mainly enriched in the biosynthesis of cofactors, tryptophan metabolism, ABC transporters, D-amino acid metabolism, and nucleotide metabolism KEGG pathways. This study revealed distinct bacterial and metabolic alterations associated with red-stipe disease in morel fruiting bodies. The findings provide foundational data for identifying causative agents and elucidating metabolic mechanisms underlying nutrient composition changes in diseased morels.