Mining the nanotube-forming Bacillus amyloliquefaciens MR14M3 genome for determining anti- Candida auris and anti- Candida albicans potential by pathogenicity and comparative genomics analysis

J Francis Borgio; Rahaf Alhujaily; Rahaf Alquwaie; Maryam Jawad Alabdullah; Eman AlHasani; Wojod Alothman; Rawan Khalid Alaqeel; Aqeelah Salman Alfaraj; Ayidah Kaabi; Norah F Alhur; Sultan Akhtar; Reem AlJindan; Sarah Almofty; Noor B Almandil; Sayed AbdulAzeez

doi:10.1016/j.csbj.2023.08.031

Mining the nanotube-forming Bacillus amyloliquefaciens MR14M3 genome for determining anti- Candida auris and anti- Candida albicans potential by pathogenicity and comparative genomics analysis

Comput Struct Biotechnol J. 2023 Sep 1:21:4261-4276. doi: 10.1016/j.csbj.2023.08.031. eCollection 2023.

Authors

J Francis Borgio^{1

2}, Rahaf Alhujaily³, Rahaf Alquwaie⁴, Maryam Jawad Alabdullah³, Eman AlHasani⁴, Wojod Alothman³, Rawan Khalid Alaqeel³, Aqeelah Salman Alfaraj³, Ayidah Kaabi³, Norah F Alhur¹, Sultan Akhtar⁵, Reem AlJindan⁶, Sarah Almofty⁷, Noor B Almandil⁸, Sayed AbdulAzeez¹

Affiliations

¹ Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
² Department of Epidemic Diseases Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
³ Summer Research Program, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
⁴ Master Program of Biotechnology, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
⁵ Department of Biophysics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
⁶ Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 40017, Saudi Arabia).
⁷ Department of Stem Cell Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.
⁸ Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia.

Abstract

There is a global health concern associated with the emergence of the multidrug-resistant (MDR) fungus Candida auris, which has significant mortality rates. Finding innovative and distinctive anti-Candida compounds is essential for treating infections caused by MDR C. auris. A bacterial strain with anti-Candida activity was isolated and identified using 16 S rRNA gene sequencing. The whole genome was sequenced to identify biosynthesis-related gene clusters. The pathogenicity and cytotoxicity of the isolate were analyzed in Candida and HFF-1 cell lines, respectively. This study set out to show that whole-genome sequencing, cytotoxicity testing, and pathogenicity analysis combined with genome mining and comparative genomics can successfully identify biosynthesis-related gene clusters in native bacterial isolates that encode antifungal natural compounds active against Candida albicans and C. auris. The native isolate MR14M3 has the ability to inhibit C. auris (zone of inhibition 25 mm) and C. albicans (zone of inhibition 25 mm). The 16 S rRNA gene sequence of MR14M3 aligned with Bacillus amyloliquefaciens with similarity (100%). Bacillus amyloliquefaciens MR14M3 establishes bridges of intercellular nanotubes (L 258.56 ± 35.83 nm; W 25.32 ± 6.09 nm) connecting neighboring cells. Candida cell size was reduced significantly, and crushed phenotypes were observed upon treatment with the defused metabolites of B. amyloliquefaciens MR14M3. Furthermore, the pathogenicity of B. amyloliquefaciens MR14M3 on Candida cells was observed through cell membrane disruption and lysed yeast cells. The whole-genome alignment of the MR14M3 genome (3981,643 bp) using 100 genes confirmed its affiliation with Bacillus amyloliquefaciens. Genome mining analysis revealed that MR14M3-coded secondary metabolites are involved in the biosynthesis of polyketides (PKs) and nonribosomal peptide synthases (NRPSs), including 11 biosynthesis-related gene clusters with one hundred percent similarity. Highly conserved biosynthesis-related gene clusters with anti-C. albicans and anti-C. auris potentials and cytotoxic-free activity of B. amyloliquefaciens MR14M3 proposes the utilization of Bacillus amyloliquefaciens MR14M3 as a biofactory for an anti-Candida auris and anti-C. albicans compound synthesizer.

Keywords: Antifungal activity; Bacillus; Biofactory; Biosynthesis-related gene clusters; Candida albicans; Candida auris; Comparative genomics; Cytotoxicity; Genome mining.