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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References
1. Lynd LR, Weimer PJ, Van Zyl WH, Pretorius IS. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev. 2002;66(3):506-77. doi: 10.1128/MMBR.66.3.506-577.2002, PMID 12209002.
2. Kumar R, Singh S, Singh OV. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 2008;35(5):377-91. doi: 10.1007/s10295-008-0327-8, PMID 18338189.
3. Bugg TD, Ahmad M, Hardiman EM, Rahmanpour R. Pathways for degradation of lignin in bacteria and fungi. Nat Prod Rep. 2011;28(12):1883-96. doi: 10.1039/C1NP00042J, PMID 21918777.
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, PMID 23692388.
5. Brune A. Symbiotic digestion of lignocellulose in termite guts. Nat Rev Microbiol. 2014;12(3):168-80. doi: 10.1038/nrmicro3182, PMID 24487819.
6. Schallmey M, Singh A, Ward OP. Developments in the use of Bacillus species for industrial production. Can J Microbiol. 2004;50(1):1-17. doi: 10.1139/W03-076, PMID 15052317.
7. Catalao MJ, Gil F, Moniz-Pereira J, Sao-Jose C, Pimentel M. Diversity in bacterial lysis systems: bacteriophages show the way. FEMS Microbiol Rev. 2013;37(4):554-71. doi: 10.1111/1574-6976.12006, PMID 23043507.
8. Lane DJ. 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M, editors. Nucleic acid techniques in bacterial systematics. New York: John Wiley & Sons; 1991. p. 115-75.
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 Syst Evol Microbiol. 1994;44(4):846-9. doi: 10.1099/00207713-44-4-846.
10. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, Da Costa MS. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol. 2018;68(1):461-6. doi: 10.1099/ijsem.0.002516, PMID 29292687.
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: Cold Spring Harbor Laboratory Press; 2012.
14. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25(17):3389-402. doi: 10.1093/nar/25.17.3389, PMID 9254694.
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):4673-80. doi: 10.1093/nar/22.22.4673, PMID 7984417.
16. Tamura K, Nei M, Kumar S. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc Natl Acad Sci USA. 2004;101(30):11030-5. doi: 10.1073/pnas.0404206101, PMID 15258291.
17. Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11. Mol Biol Evol. 2021;38(7):3022-7. doi: 10.1093/molbev/msab120, PMID 33892491.
18. Saitou N, Nei M. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4(4):406-25. doi: 10.1093/oxfordjournals.molbev.a040454.
19. Espadinha D, Sobral RG, Mendes CI, Meric G, Sheppard SK, Carrico JA. Distinct phenotypic and genomic signatures underlie contrasting patho-genic potential of Staphylococcus epidermidis clonal lineages. Front Microbiol. 2019;10:1971. doi: 10.3389/fmicb.2019.01971, PMID 31507574.
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 21st century. 3 Biotech. 2016;6(2):174. doi: 10.1007/s13205-016-0485-8, PMID 28330246.
22. Masmoudi F, Alsafran M, Jabri HA, Hosseini H, Trigui M, Sayadi S. Halobacteria-based biofertilizers: a promising alternative for enhancing soil fertility and crop productivity under biotic and abiotic stresses-a review. Microorganisms. 2023;11(5):1248. doi: 10.3390/microorganisms11051248, PMID 37317222.
23. Vojnovic S, Aleksic I, Ilic-Tomic T, Stevanovic M, Nikodinovic-Runic J. Bacillus and Streptomyces spp. as hosts for production of industrially relevant enzymes. Appl Microbiol Biotechnol. 2024;108(1):185. doi: 10.1007/s00253-023-12900-x, PMID 38289383.
24. Grady EN, Mac Donald J, Liu L, Richman A, Yuan ZC. Current knowledge and perspectives of Paenibacillus: a review. Microb Cell Fact. 2016;15(1):203. doi: 10.1186/s12934-016-0603-7, PMID 27905924.
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