Whole genome sequence and LC-Mass for identifying antimicrobial metabolites of Bacillus licheniformis endophyte

Nourhan K Soliman; Ahmad M Abbas; Wafaa N El Tayeb; Mohammad Y Alshahrani; Khaled M Aboshanab

doi:10.1186/s13568-024-01789-y

Whole genome sequence and LC-Mass for identifying antimicrobial metabolites of Bacillus licheniformis endophyte

AMB Express. 2024 Dec 20;14(1):139. doi: 10.1186/s13568-024-01789-y.

Authors

Nourhan K Soliman¹, Ahmad M Abbas^{1

2}, Wafaa N El Tayeb³, Mohammad Y Alshahrani⁴, Khaled M Aboshanab⁵

Affiliations

¹ Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, 11566, Egypt.
² Department of Microbiology and Immunology, Faculty of Pharmacy, King Salman International University (KSIU), Ras Sudr, South Sinai, Egypt.
³ Department of Microbiology, Faculty of Pharmacy, Misr International University (MIU), Cairo, 19648, Egypt.
⁴ Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, P.O. Box 61413, 9088, Abha, Saudi Arabia.
⁵ Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo, 11566, Egypt. aboshanab2012@pharma.asu.edu.eg.

Abstract

Antimicrobial resistance (AMR) represents a critical public health issue that requiring immediate action. Wild halophytic plants can be the solution for the AMR crisis because they harbor unique endophytes capable of producing potent antimicrobial metabolites. This study aimed at identifying promising and antimicrobial metabolites produced by endophytic/epiphytic bacteria recovered from the wild Bassia scoparia plant. Standard methods were employed for the isolation of endophytes/epiphytes. Whole genome sequence (WGS) using Oxford Nanopore technology followed by antiSMASH analysis coupled with advanced LC-MS spectroscopic analysis were used for identification of the active antimicrobial metabolites. This study identified Bacillus licheniformis strain CCASU-B18 as a promising endophytic bacterium from the Bassia scoparia plant. In addition, the strain showed broad-spectrum antibacterial activity against three standard and five MDR clinical Gram-positive and Gram-negative isolates, and antifungal activity against the standard C. albicans strain. Six main antimicrobial metabolites-thermoactinoamide A, bacillibactins, lichenysins, lichenicidins, fengycin, and bacillomycin-were verified to exist by whole genome sequencing for identifying the respective conserved biosynthetic gene clusters in conjunction with LC/MS-MS analysis. The complete genomic DNA (4125835) and associated plasmid (205548 bp) of the promising endophytic isolate were sequenced, assembled, annotated, and submitted into the NCBI GenBank database under the accession codes, CP157373. In conclusion, Bacillus licheniformis strain CCASU-B18, a promising endophytic bacterium exhibiting broad-spectrum antimicrobial activities, was isolated. Future research is highly recommended to optimize the culture conditions that will be employed to enhance the production of respective antimicrobial metabolites, as well as testing these compounds against a broader range of MDR-resistant pathogens.

Keywords: Enterococcus faceium; Enterococcus fecalis; Antibiotic resistance; Bacteriophage; Stability; Virulence factor.