Omics Analysis of Lignin Degradation by the Gut Microbiomes of Wood-Eating Hypomeces squamosus Fabricius.

Microbial degradation of lignin is important to carbon cycling. The gut microbiome of wood-feeding Hypomeces squamosus Fabricius has been shown to degrade lignin efficiently. However, the specific degradation mechanisms remain incompletely understood. In this study, we investigated the mechanism of lignin degradation using omics comparative analysis, focusing on differentially expressed genes and metabolic pathways in the gut microbiome of insects fed with a lignin-rich diet. The dominant genus taxon was Pantoea (29.82%), which was predominant in insects fed with high lignin-containing Iris ensata Thunberg, whereas Wolbachia and Enterobacter were predominant in insects fed with cabbage leaves (MHS_K group). Furthermore, expression levels of carbohydrate-active enzymes from the auxiliary activities (AAs) families in the MHS_I group were 1.18 times higher than those in the MHS_K group. These mainly included lignin peroxidase and manganese peroxidase of the AA2 family, vanillyl-alcohol oxygenase of the AA4 family, and 1,4-benzoquinone reductase of the AA6 family. Expression levels of multiple genes encoding aromatic compound-degrading genes (2303 accounted for 75.76% of the total upregulated genes) were found, including about 0.03% was related to lignin degradation. Genes MHS-HN_11398_2 (protocatechuate 2,3-dioxygenase) and MHS-HN_4821_1 (muconolactone d-isomerase) were enriched in the MHS_I group. Three lignin-degrading pathways were found: ortho-cleavage and meta-cleavage of catechol, as well as ring-opening of protocatechuate. This study provides a comprehensive and theoretical evidence of the gut microbiome roles of H. squamosus Fabricius in lignin degradation.