Characterization of a Bacterium Isolated from Hydrolyzed Instant Sea Cucumber Using Whole-Genome Sequencing and Metabolomics

Overview

Journal Foods

Specialty Biotechnology

Date 2024 Nov 27

PMID 39594079

Authors

Xin Luo

Zhixuan Zhang

Zhangyi Zheng

Wenwen Zhang

Tinghong Ming

Lefei Jiao

Xiurong Su

Jiajie Xu

Fei Kong

Affiliations

Soon will be listed here.

Abstract

Autolysis in the sea cucumber is typically triggered by degradation caused by microorganisms within their bodies. However, information on this topic remains limited. Recently, we isolated and purified a bacterial strain from hydrolyzed instant sea cucumber samples. To investigate its potential role in the autolysis process, this study employed whole-genome sequencing and metabolomics to explore its genetic and metabolic characteristics. The identified strain was classified as and designated with the number XL-2024. Its genome size is 5,075,210 bp with a GC content of 37.33%, encoding 5275 genes. Functional database comparisons revealed that the protein-coding genes were distributed among glucose metabolism hydrolase, metal hydrolase, lysozyme, cell wall hydrolase, and CAZymes. Compared to 20 closely related strains, XL-2024 shared 1502 core homologous genes and had 707 specific genes. These specific genes were mainly involved in the carbohydrate metabolism pathway and exhibited glycosyl bond hydrolase activity. Metabolomic analysis showed that XL-2024 produced several metabolites related to polysaccharide degradation, including peptidase, glucanase, and pectinase. Additionally, the presence of antibacterial metabolites such as propionic acid and ginkgo acid among its metabolites may enhance the stability of the sea cucumber hydrolysate. In summary, XL-2024 may play a pivotal role in the autolysis of . The results of this study provide a strong foundation for understanding how to prevent autolysis in and for better utilizing XL-2024.

References

Barrangou R, Doudna J . Applications of CRISPR technologies in research and beyond. Nat Biotechnol. 2016; 34(9):933-941. DOI: 10.1038/nbt.3659. View

Berdy J . Bioactive microbial metabolites. J Antibiot (Tokyo). 2005; 58(1):1-26. DOI: 10.1038/ja.2005.1. View

Primo E, Otero L, Ruiz F, Klinke S, Giordano W . The disruptive effect of lysozyme on the bacterial cell wall explored by an in-silico structural outlook. Biochem Mol Biol Educ. 2017; 46(1):83-90. DOI: 10.1002/bmb.21092. View

Ma J, Wang J, Mahfuz S, Long S, Wu D, Gao J . Supplementation of Mixed Organic Acids Improves Growth Performance, Meat Quality, Gut Morphology and Volatile Fatty Acids of Broiler Chicken. Animals (Basel). 2021; 11(11). PMC: 8614297. DOI: 10.3390/ani11113020. View

Benson D, Karsch-Mizrachi I, Lipman D, Ostell J, Wheeler D . GenBank: update. Nucleic Acids Res. 2003; 32(Database issue):D23-6. PMC: 308779. DOI: 10.1093/nar/gkh045. View

Finlay B, McFadden G . Anti-immunology: evasion of the host immune system by bacterial and viral pathogens. Cell. 2006; 124(4):767-82. DOI: 10.1016/j.cell.2006.01.034. View

Huang X, Wang H, Tu Z . A comprehensive review of the control and utilization of aquatic animal products by autolysis-based processes: Mechanism, process, factors, and application. Food Res Int. 2023; 164:112325. DOI: 10.1016/j.foodres.2022.112325. View

De Masi R, Orlando S . GANAB and -Glycans Substrates Are Relevant in Human Physiology, Polycystic Pathology and Multiple Sclerosis: A Review. Int J Mol Sci. 2022; 23(13). PMC: 9266668. DOI: 10.3390/ijms23137373. View

Drula E, Garron M, Dogan S, Lombard V, Henrissat B, Terrapon N . The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res. 2021; 50(D1):D571-D577. PMC: 8728194. DOI: 10.1093/nar/gkab1045. View

10.

Li Y, Lei L, Zheng L, Xiao X, Tang H, Luo C . Genome sequencing of gut symbiotic LC1 for bioethanol production from bamboo shoots. Biotechnol Biofuels. 2020; 13:34. PMC: 7048129. DOI: 10.1186/s13068-020-1671-9. View

11.

Judge A, Dodd M . Metabolism. Essays Biochem. 2020; 64(4):607-647. PMC: 7545035. DOI: 10.1042/EBC20190041. View

12.

Simpson J, Wong K, Jackman S, Schein J, Jones S, Birol I . ABySS: a parallel assembler for short read sequence data. Genome Res. 2009; 19(6):1117-23. PMC: 2694472. DOI: 10.1101/gr.089532.108. View

13.

Chen L, Xiong Z, Sun L, Yang J, Jin Q . VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res. 2011; 40(Database issue):D641-5. PMC: 3245122. DOI: 10.1093/nar/gkr989. View

14.

Ge X, Wang H, Yin M, Wang X . Effect of Different Thawing Methods on the Physicochemical Properties and Microstructure of Frozen Instant Sea Cucumber. Foods. 2022; 11(17). PMC: 9455729. DOI: 10.3390/foods11172616. View

15.

You Y, Kong H, Li C, Gu Z, Ban X, Li Z . Carbohydrate binding modules: Compact yet potent accessories in the specific substrate binding and performance evolution of carbohydrate-active enzymes. Biotechnol Adv. 2024; 73:108365. DOI: 10.1016/j.biotechadv.2024.108365. View

16.

Lin S, Liao Y . CISA: contig integrator for sequence assembly of bacterial genomes. PLoS One. 2013; 8(3):e60843. PMC: 3610655. DOI: 10.1371/journal.pone.0060843. View

17.

Kozlova M, Shalaeva D, Dibrova D, Mulkidjanian A . Common Patterns of Hydrolysis Initiation in P-loop Fold Nucleoside Triphosphatases. Biomolecules. 2022; 12(10). PMC: 9599529. DOI: 10.3390/biom12101345. View

18.

Fischer S, Brunk B, Chen F, Gao X, Harb O, Iodice J . Using OrthoMCL to assign proteins to OrthoMCL-DB groups or to cluster proteomes into new ortholog groups. Curr Protoc Bioinformatics. 2011; Chapter 6:6.12.1-6.12.19. PMC: 3196566. DOI: 10.1002/0471250953.bi0612s35. View

19.

Wang X, Deng T, Zhou X, Chu L, Zeng X, Zhang S . A Mixture of Formic Acid, Benzoic Acid, and Essential Oils Enhanced Growth Performance via Modulating Nutrient Uptake, Mitochondrion Metabolism, and Immunomodulation in Weaned Piglets. Antioxidants (Basel). 2024; 13(2). PMC: 10886008. DOI: 10.3390/antiox13020246. View

20.

Shleeva M, Kondratieva D, Kaprelyants A . : A Producer of Antimicrobial Substances, including Antimycobacterials, Which Are Feasible for Medical Applications. Pharmaceutics. 2023; 15(7). PMC: 10383908. DOI: 10.3390/pharmaceutics15071893. View