Molecular Identification and Phylogenetic Characterization of Lignocellulose-Degrading Gut Bacteria Isolated From the Eri Silkworm (Samia Cynthia Ricini)
DOI:
https://doi.org/10.22159/ijcr.2026v10i4.360Keywords:
16S rRNA gene, Phylogenetic analysis, Gut microbiota, Lignocellulose degradation, Eri silkworm, Bacillus, PaenibacillusAbstract
Objective: The present study was aimed at identifying and characterising lignocellulose-degrading bacterial isolates from the gut of the eri silkworm, Samia cynthia ricini, by 16S rRNA gene sequencing and phylogenetic analysis.
Methods: Genomic DNA was isolated from six bacterial isolates and PCR amplified for the 16S rRNA gene. The amplified products were sequenced and aligned with reference sequences available in the NCBI GenBank database using BLAST analysis. Multiple sequence alignment was performed, and phylogenetic relationships were deduced using the Neighbour-Joining method with 1000 bootstrap replicates in MEGA11.
Results: Sequence analysis revealed that the isolates are Bacillus paralicheniformis (BUBSL1, 99.2%), Bacillus subtilis (BUBSL2, 99.5%), Bacillus licheniformis (BUBSL3, 98.9%), Paenibacillus sp. (BUBSL4, 97.8%), Bacillus velezensis (BUBSL5, 99.3%) and Paenibacillus lactis (BUBSL6, 99.0%). Phylogenetic analysis grouped the isolates into the genera Bacillus and Paenibacillus, supporting their taxonomic position and evolutionary relationship, and the clustering pattern showed that the isolates were closely related to the reference strains obtained from GenBank.
Conclusion: The gut microbiota of Samia cynthia ricini is composed of diverse bacterial species predominantly from the genera Bacillus and Paenibacillus. The isolated strains are potential lignocellulose-degrading bacteria, which can be used for future biofuel-related studies and may assist in biomass conversion.
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1. Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS. Microbial cellulose utilisation: fun-damentals and biotechnology. Microbiol Mol Biol Rev. 2002;66(3):506-577. doi:10.1128/MMBR.66.3.506-577.2002.
2. Kumar R, Singh S, Singh OV. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind MicrobiolBiotechnol. 2009;36(3):377-391. doi:10.1007/s10295-008-0414-7.
3. Bugg TDH, Ahmad M, Hardiman EM, Rahmanpour R. Pathways for degradation of lignin in bacteria and fungi. Nat Prod Rep. 2011;28(12):1883 1896.doi:10.1039/C1NP00042J.
4. Engel P, Moran NA. The gut microbiota of insects: diversity in structure and function. FEMS Microbiol Rev. 2013;37(5):699-735. doi:10.1111/1574-6976.12025.
5. Brune A. Symbiotic digestion of lignocellulose in termite guts. Nat Rev Microbiol. 2014;12(3):168-180. doi:10.1038/nrmicro3182.
6. Schallmey M, Singh A, Ward OP. Developments in the use of Bacillus species for in-dustrial production. Can J Microbiol. 2004;50(1):1-17. doi:10.1139/W03-076.
7. de Souza WR, de Siqueira FG, Bon EPS. Lignocellulose degradation by bacteria: strat-egies and applications. FEMS Microbiol Rev. 2013;37(6):859-887. doi:10.1111/1574-6976.12006.
8. Lane DJ. 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M, editors. Nu-cleic acid techniques in bacterial systematics. New York: Wiley; 1991. p. 115-175.
9. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J SystBacteriol. 1994;44(4):846-849.
10. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J SystEvolMicrobiol. 2018;68(1):461-466. doi:10.1099/ijsem.0.002516.
11. Cappuccino JG, Sherman N. Microbiology: a laboratory manual. 10th ed. Boston: Pearson; 2014.
12. Pointing SB. Qualitative methods for the determination of lignocellulolytic enzyme production by fungi. Fungal Divers. 1999;2:17-33.
13. Green MR, Sambrook J. Molecular cloning: a laboratory manual. 4th ed. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2012.
14. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nu-cleic Acids Res. 1997;25(17):3389-3402. doi:10.1093/nar/25.17.3389.
15. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22(22):4673-4680. doi:10.1093/nar/22.22.4673.
16. Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbour-joining method. Proc Natl Acad Sci U S A. 2004;101(30):11030-11035. doi:10.1073/pnas.0404206101.
17. Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Mol BiolEvol. 2021;38(7):3022-3027. doi:10.1093/molbev/msab120.
18. Saitou N, Nei M. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol BiolEvol. 1987;4(4):406-425. doi:10.1093/oxfordjournals.molbev.a040454.
19. Gupta RS, Patel S. Phylogenomic analysis of the family Bacillaceae. Front Microbiol. 2019;10:1971. doi:10.3389/fmicb.2019.01971.
20. Kumar V, Chhabra D, Shukla P. Advances in microbial cellulases and their industrial applications. Enzyme Res. 2012;2012:280696. doi:10.1155/2012/280696.
21. Singh R, Kumar M, Mittal A, Mehta PK. Microbial enzymes: industrial progress in the 21st century. 3 Biotech. 2016;6(2):174. doi:10.1007/s13205-016-0485-8.
22. Wang Y, Li H, Chen X. Microbial degradation of lignocellulosic biomass and its bio-technological applications. Microorganisms. 2023;11(5):1248.
23. Vojnovic S, Vorkapic D, Vlahovic M, Radisavljevic M. Bacillus and Streptomyces spp. as hosts for production of industrially relevant enzymes and proteins. Appl Mi-crobiolBiotechnol. 2024;108:110. doi:10.1007/s00253-023-12900-x.
24. Grady EN, MacDonald J, Liu L, Richman A, Yuan ZC. Current knowledge and per-spectives of Paenibacillus: a review. Microb Cell Fact. 2016;15:203. doi:10.1186/s12934-016-0603-7.
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