Whole-genome Sequencing and Assessment of a Novel Protein- and Gossypol-degrading Bacillus Subtilis Strain Isolated from Intestinal Digesta of Tibetan Pigs

Overview

Journal BMC Microbiol

Publisher Biomed Central

Specialty Microbiology

Date 2024 Oct 22

PMID 39438803

Authors

Xiangyue Guo

Zhenda Shang

Qianxi Li

Lixue Wang

Ying Zhang

Suozhu Liu

Yunhe Cao

Bing Dong

Affiliations

Soon will be listed here.

Abstract

Background: With the rapid development of animal husbandry, the demand for protein feed resources is increasing. Cottonseed meal (CSM) and soybean meal (SBM) are rich sources of protein. However, their application is limited due to the existence of anti-nutrients, which can be harmful to the digestion and absorption. A strain of Bacillus subtilis (Mafic-Y7) was isolated from digesta of intestines of Tibetan pigs. The strain showed high protease activity, which helps in degrading proteinic anti-nutritional factors in grain meal and in vitro degradation of free gossypol. In order to better understand this isolated strain, whole genome of Mafic-Y7 strain was sequenced and analyzed. Different effects on various grain meals were identified.

Result: The GC-depth Poisson distributions showed no bias suggesting high-quality genome assembly of Mafic-Y7. The whole genome sequencing showed that one chromosome with 4,248,845 base pairs(bp)and the genes total length with 3,736,524 bp was predicted in Mafic-Y7. Additionally, Mafic-Y7 possessed 4,254 protein-coding genes, and several protease genes were annotated by aligning them with databases. There are 55 protease genes, one phytase gene and one laccase gene were annotated in the gene sequence of Mafic-Y7. The average nucleotide identity between Mafic-Y7 and the GCA-000009045.1 homologous genome was 0.9938, suggesting a close genetic relationship between them at the species level. Compared with the closest four whole genomes, Mafic-Y7 was annotated the most abundant of protease genes (55 genes). The fermentation supernatant of Mafic-Y7 could increase the content of small peptides, water-soluble proteins, and acid-soluble proteins in vitro by 411%, 281% and 317% in SBM and 420%, 257% and 338% in CSM. After fermentation in grain meal by Mafic-Y7, the degradation rate of anti-nutritional factors in SBM, such as trypsin inhibitor, glycinin, and β-conglycinin was greater than 70%, and lectin was greater than 30%. The degradation rates of anti-nutritional factors in CSM, such as gossypol and phytic acid, were 82% and 26%, respectively.

References

Santibanez N, Vega M, Perez T, Yanez A, Gonzalez-Stegmaier R, Figueroa J . Biofilm Produced In Vitro by Generates Differential Cytotoxicity Levels and Expression Patterns of Immune Genes in the Atlantic Salmon Cell Line SHK-1. Microorganisms. 2020; 8(10). PMC: 7594049. DOI: 10.3390/microorganisms8101609. View

Chen L, Zhao Z, Yu W, Zheng L, Li L, Gu W . Nutritional quality improvement of soybean meal by Bacillus velezensis and Lactobacillus plantarum during two-stage solid- state fermentation. AMB Express. 2021; 11(1):23. PMC: 7865068. DOI: 10.1186/s13568-021-01184-x. View

Kaleda A, Talvistu K, Tamm M, Viirma M, Rosend J, Tanilas K . Impact of Fermentation and Phytase Treatment of Pea-Oat Protein Blend on Physicochemical, Sensory, and Nutritional Properties of Extruded Meat Analogs. Foods. 2020; 9(8). PMC: 7465559. DOI: 10.3390/foods9081059. View

Goel G, Makkar H, Francis G, Becker K . Phorbol esters: structure, biological activity, and toxicity in animals. Int J Toxicol. 2007; 26(4):279-88. DOI: 10.1080/10915810701464641. View

Jabbar A, Tahir M, A Alhidary I, Abdelrahman M, Albadani H, Khan R . Impact of Microbial Protease Enzyme and Dietary Crude Protein Levels on Growth and Nutrients Digestibility in Broilers over 15-28 Days. Animals (Basel). 2021; 11(9). PMC: 8471728. DOI: 10.3390/ani11092499. View

Zheng L, Li D, Li Z, Kang L, Jiang Y, Liu X . Effects of Bacillus fermentation on the protein microstructure and anti-nutritional factors of soybean meal. Lett Appl Microbiol. 2017; 65(6):520-526. DOI: 10.1111/lam.12806. View

Zhang Y, Zhang Z, Dai L, Liu Y, Cheng M, Chen L . Isolation and characterization of a novel gossypol-degrading bacteria strain Rumen Bacillus Subtilis. Asian-Australas J Anim Sci. 2017; 31(1):63-70. PMC: 5756925. DOI: 10.5713/ajas.17.0018. View

Tong M, Liu W, He H, Hu H, Ding Y, Li X . Identification and functional analysis of the CorA/MGT/MRS2-type magnesium transporter in banana. PLoS One. 2020; 15(10):e0239058. PMC: 7529347. DOI: 10.1371/journal.pone.0239058. View

Shen J, Zhang J, Zhao Y, Lin Z, Ji L, Ma X . Tibetan Pig-Derived Probiotic SLZX20-1 Improved Intestinal Function Producing Enzymes and Regulating Intestinal Microflora. Front Nutr. 2022; 9:846991. PMC: 9002122. DOI: 10.3389/fnut.2022.846991. View

10.

Zhang R, Huang Y, Qin W, Quan Z . The complete genome of extracellular protease-producing Deinococcus sp. D7000 isolated from the hadal region of Mariana Trench Challenger Deep. Mar Genomics. 2021; 57:100832. DOI: 10.1016/j.margen.2020.100832. View

11.

Khan U, Selamoglu Z . Use of Enzymes in Dairy Industry: A Review of Current Progress. Arch Razi Inst. 2020; 75(1):131-136. PMC: 8410156. DOI: 10.22092/ari.2019.126286.1341. View

12.

Ezoe A, Shirai K, Hanada K . Degree of Functional Divergence in Duplicates Is Associated with Distinct Roles in Plant Evolution. Mol Biol Evol. 2020; 38(4):1447-1459. PMC: 8042753. DOI: 10.1093/molbev/msaa302. View

13.

Grasso G . THE USE OF MASS SPECTROMETRY TO STUDY ZN-METALLOPROTEASE-SUBSTRATE INTERACTIONS. Mass Spectrom Rev. 2020; 39(5-6):574-585. DOI: 10.1002/mas.21621. View

14.

Averina E, Konnerth J, van Herwijnen H . Protein Adhesives: Investigation of Factors Affecting Wet Strength of Alkaline Treated Proteins Crosslinked with Glyoxal. Polymers (Basel). 2022; 14(20). PMC: 9612214. DOI: 10.3390/polym14204351. View

15.

Iemura Y, Takahashi T, Yamada T, Furukawa K, Hara S . Properties of TCA-insoluble peptides in kimoto (traditional seed mash for sake brewing) and conditions for liberation of the peptides from rice protein. J Biosci Bioeng. 2005; 88(5):531-5. DOI: 10.1016/s1389-1723(00)87671-9. View

16.

Chen F, Dong G, Zhang D, Liu X, Jia X, An C . Agriculture facilitated permanent human occupation of the Tibetan Plateau after 3600 B.P. Science. 2015; 347(6219):248-50. DOI: 10.1126/science.1259172. View

17.

Li X, Wang J, Jia Y, Reheman A, Yan Y . The Genome Analysis of YC-XJ1 with Diverse Xenobiotics Biodegrading Capacity and Degradation Characteristics of Related Hydrolase. Int J Mol Sci. 2020; 21(12). PMC: 7352507. DOI: 10.3390/ijms21124436. View

18.

Tripathi A, Saxena P, Thakur P, Rauniyar S, Samanta D, Gopalakrishnan V . Transcriptomics and Functional Analysis of Copper Stress Response in the Sulfate-Reducing Bacterium G20. Int J Mol Sci. 2022; 23(3). PMC: 8836040. DOI: 10.3390/ijms23031396. View

19.

Sulthana A, Lakshmi S, Madempudi R . Genome Sequencing and Annotation of UBBS-14 to Ensure Probiotic Safety. J Genomics. 2019; 7:14-17. PMC: 6389496. DOI: 10.7150/jgen.31170. View

20.

Zhu X, Li S, Liu L, Li S, Luo Y, Lv C . Genome Sequencing and Analysis of sp. SZU445 Provides Novel Insights into the Polyunsaturated Fatty Acid Biosynthesis Pathway. Mar Drugs. 2020; 18(2). PMC: 7073664. DOI: 10.3390/md18020118. View