Comparative genomic and transcriptome analysis of Bacillus velezensis CL-4 fermented corn germ meal

Abstract

Bacillus, an excellent organic-degrading agent, can degrade lignocellulose. Notably, some B. velezensis strains encode lignocellulases. However, their ability to degrade lignocellulose in fermented feed is not much appreciated. This study performed a comparative genomic analysis of twenty-three B. velezensis strains to find common carbohydrate-active enzymes (CAZymes) encoding genes and evaluated their potential to degrade lignocellulose. The comparative genomic and CAZyme database-based analyses identified several potential CAZymes genes that degrade cellulose (GH1, GH4, GH5, GH13, GH16, GH32, PL1, and PL9), hemicellulose (GH11, GH26, GH43, GH51, and CE3) and lignin (AA4, AA6, AA7, and AA10). Furthermore, Illumina RNA-seq transcriptome analysis revealed the expression of more than 1794 genes in B. velezensis CL-4 fermented corn germ meal at 48 h (FCGM 48 h). Gene ontology analysis of expressed genes revealed their enrichment in hydrolase activity (breaking the glycosyl bonds during carbohydrate metabolism), indicating the upregulation of CAZymes. In total, 58 differentially upregulated CAZymes-encoding genes were identified in FCGM 48 h compared to FCGM 0 h. The upregulated CAZymes-encoding genes were related to cellulose (6-phospho-β-galactosidase and 6-phospho-α-glucosidase), starch (α-glucosidase and α-amylase), pectin (pectin lyase), and hemicellulose (arabinan endo-1,5-α-L-arabinosidase, xylan 1,4-beta-xylosidase, α-N-arabinofuranosidase, and acetyl xylan esterase). Importantly, arabinoxylan degradation mainly occurred in FCGM 48 h, followed by partial degradation of cellulose, pectin, and starch. This study can support the development of enzymatic cocktails for the solid-state fermented feed (SFF).

Whole-Genome Analysis of Termite-Derived Bacillus velezensis BV-10 and Its Application in King Grass Silage

“…Similarly, we sequenced the whole genome of B. velezensis BV-10 and found that B. velezensis BV-10 has numerous genes encoding cellulose-, hemicellulose-, and lignin-degrading enzymes in the CAZy database, including β-glucosidase, xylanase, laccase, and amylase. These results were similar to the findings of Chen et al [20]. Common genes from the GH1, GH3, GH4, GH5 and GH16 families participate in cellulose degradation.…”

“…At least one bacterial species of the genus Bacillus, Bacillus velezensis (B. velezensis), can degrade crude fiber, degrade cellulose into reducing sugars, increase soluble carbohydrates, and improve the fermentation substrate content [19]. B. velezensis may not be able to directly hydrolyze cellobiose because it lacks exocellulase, limiting its cellulose-degrading activity; thus, it is necessary to add appropriate exogenous enzymes for synergistic treatment [20]. To the best of our knowledge, no studies adding B. velezensis to silage in combination with other additives have been conducted to date.…”

Analyzing Current Trends and Possible Strategies to Improve Sucrose Isomerases’ Thermostability

“…Furthermore, the architecture of the active site of SIase places them within the glycoside hydrolase family, family 13 (GH13) [61]. Established in the early 1990s, the GH13 family [62] represents the largest family of polysaccharide metabolizing enzymes [63,64], grouping enzymes with hydrolytic [65], transferase [66,67], and isomerase activities [68]. Specifically, differences in substrate specificity and/or enzymatic activities among the GH13 family members led to its subdivision into subfamilies.…”

Cellulase with Bacillus velezensis improves physicochemical characteristics, microbiota and metabolites of corn germ meal during two-stage co-fermentation

“…In addition, B. velezensis fermentation signi cantly improved the overall nutritional level of CGM. Furthermore, the study of differential metabolites and differentially expressed genes during the B. velezensis fermentation showed that CAZymes enzyme genes mainly involved the degradation of cellulose, starch, pectin, and hemicellulose were signi cantly upregulated (Chen et al 2023). However, from the results of comparative genomics, enzyme activity assays, and cellulose degradation rate of fermented CGM, we found that B. velezensis lacks cellulase and cannot directly hydrolyze cellulose in CGM.…”