A Metagenomic Nanopore Sequence Analysis Combined with Conventional Screening and Spectroscopic Methods for Deciphering the Antimicrobial Metabolites Produced by <i>Alcaligenes faecalis</i> Soil Isolate MZ921504
The continuous development of multidrug resistance pathogens with limited therapeutic options has become a great problem globally that impose sever health hazards. Accordingly, searching for of new antimicrobials became an urgent demand and great challenge. Soil significantly have been associated wi...
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| Format: | Article |
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MDPI AG
2021-11-01
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| Series: | Antibiotics |
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| Online Access: | https://www.mdpi.com/2079-6382/10/11/1382 |
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| author | Mohamed A. Eltokhy Bishoy T. Saad Wafaa N. Eltayeb Mona R. El-Ansary Khaled M. Aboshanab Mohamed S. E. Ashour |
| author_facet | Mohamed A. Eltokhy Bishoy T. Saad Wafaa N. Eltayeb Mona R. El-Ansary Khaled M. Aboshanab Mohamed S. E. Ashour |
| author_sort | Mohamed A. Eltokhy |
| collection | DOAJ |
| description | The continuous development of multidrug resistance pathogens with limited therapeutic options has become a great problem globally that impose sever health hazards. Accordingly, searching for of new antimicrobials became an urgent demand and great challenge. Soil significantly have been associated with several species that are antibiotic producers. In this study, combination of conventional screening methods with Liquid chromatography- Mass spectroscopy (LC/MS) and metagenomic nanopore sequence analysis have been conducted for the deciphering the active metabolites produced by soil isolate(s). Preliminary soil screening resulted in a Gram-negative isolate identified via 16S ribosomal RNA as <i>Alcaligenes faecalis</i> isolate MZ921504 with promising antimicrobial activities against wide range of MDR gram-positive and gram-negative pathogens. The LC/MS analysis of the metabolites of <i>A. faecalis</i> isolate MZ921504 confirmed the presence of ectoine, bacillibactin, quinolobactin and burkholderic acid. Metagenomics sequence analysis of the soil sample (NCBI GenBank accession PRJNA771993) revealed the presence of conserved biosynthetic gene clusters of ectoine, bacteriocin, bacillibactin, quinolobactin, terpene and burkholderic acid of <i>A. faecalis</i>. In conclusion, <i>A. faecalis</i> isolate MZ921504 is a promising source for antimicrobial metabolites. LC/MS spectral analysis and third generation sequencing tools followed by secondary metabolite gene clusters analysis are useful methods to predict the nature of the antimicrobial metabolites. |
| first_indexed | 2024-03-10T05:45:05Z |
| format | Article |
| id | doaj.art-5358392bc66947c2a44dd30a4335f674 |
| institution | Directory Open Access Journal |
| issn | 2079-6382 |
| language | English |
| last_indexed | 2024-03-10T05:45:05Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Antibiotics |
| spelling | doaj.art-5358392bc66947c2a44dd30a4335f6742023-11-22T22:10:49ZengMDPI AGAntibiotics2079-63822021-11-011011138210.3390/antibiotics10111382A Metagenomic Nanopore Sequence Analysis Combined with Conventional Screening and Spectroscopic Methods for Deciphering the Antimicrobial Metabolites Produced by <i>Alcaligenes faecalis</i> Soil Isolate MZ921504Mohamed A. Eltokhy0Bishoy T. Saad1Wafaa N. Eltayeb2Mona R. El-Ansary3Khaled M. Aboshanab4Mohamed S. E. Ashour5Department of Microbiology, Faculty of Pharmacy, Misr International University (MIU), Cairo 19648, EgyptDepartment of Bioinformatics, HITS Solutions Co., Cairo 11765, EgyptDepartment of Microbiology, Faculty of Pharmacy, Misr International University (MIU), Cairo 19648, EgyptDepartment of Biochemistry, Modern University for Technology and Information (MTI), Cairo 12055, EgyptDepartment of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Organization of African Unity St., Cairo 11566, EgyptDepartment of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo 11651, EgyptThe continuous development of multidrug resistance pathogens with limited therapeutic options has become a great problem globally that impose sever health hazards. Accordingly, searching for of new antimicrobials became an urgent demand and great challenge. Soil significantly have been associated with several species that are antibiotic producers. In this study, combination of conventional screening methods with Liquid chromatography- Mass spectroscopy (LC/MS) and metagenomic nanopore sequence analysis have been conducted for the deciphering the active metabolites produced by soil isolate(s). Preliminary soil screening resulted in a Gram-negative isolate identified via 16S ribosomal RNA as <i>Alcaligenes faecalis</i> isolate MZ921504 with promising antimicrobial activities against wide range of MDR gram-positive and gram-negative pathogens. The LC/MS analysis of the metabolites of <i>A. faecalis</i> isolate MZ921504 confirmed the presence of ectoine, bacillibactin, quinolobactin and burkholderic acid. Metagenomics sequence analysis of the soil sample (NCBI GenBank accession PRJNA771993) revealed the presence of conserved biosynthetic gene clusters of ectoine, bacteriocin, bacillibactin, quinolobactin, terpene and burkholderic acid of <i>A. faecalis</i>. In conclusion, <i>A. faecalis</i> isolate MZ921504 is a promising source for antimicrobial metabolites. LC/MS spectral analysis and third generation sequencing tools followed by secondary metabolite gene clusters analysis are useful methods to predict the nature of the antimicrobial metabolites.https://www.mdpi.com/2079-6382/10/11/1382<i>Alcaligenes faecalis</i>LC/MSmetagenomicsectoinebacillibactinquinolobactin |
| spellingShingle | Mohamed A. Eltokhy Bishoy T. Saad Wafaa N. Eltayeb Mona R. El-Ansary Khaled M. Aboshanab Mohamed S. E. Ashour A Metagenomic Nanopore Sequence Analysis Combined with Conventional Screening and Spectroscopic Methods for Deciphering the Antimicrobial Metabolites Produced by <i>Alcaligenes faecalis</i> Soil Isolate MZ921504 Antibiotics <i>Alcaligenes faecalis</i> LC/MS metagenomics ectoine bacillibactin quinolobactin |
| title | A Metagenomic Nanopore Sequence Analysis Combined with Conventional Screening and Spectroscopic Methods for Deciphering the Antimicrobial Metabolites Produced by <i>Alcaligenes faecalis</i> Soil Isolate MZ921504 |
| title_full | A Metagenomic Nanopore Sequence Analysis Combined with Conventional Screening and Spectroscopic Methods for Deciphering the Antimicrobial Metabolites Produced by <i>Alcaligenes faecalis</i> Soil Isolate MZ921504 |
| title_fullStr | A Metagenomic Nanopore Sequence Analysis Combined with Conventional Screening and Spectroscopic Methods for Deciphering the Antimicrobial Metabolites Produced by <i>Alcaligenes faecalis</i> Soil Isolate MZ921504 |
| title_full_unstemmed | A Metagenomic Nanopore Sequence Analysis Combined with Conventional Screening and Spectroscopic Methods for Deciphering the Antimicrobial Metabolites Produced by <i>Alcaligenes faecalis</i> Soil Isolate MZ921504 |
| title_short | A Metagenomic Nanopore Sequence Analysis Combined with Conventional Screening and Spectroscopic Methods for Deciphering the Antimicrobial Metabolites Produced by <i>Alcaligenes faecalis</i> Soil Isolate MZ921504 |
| title_sort | metagenomic nanopore sequence analysis combined with conventional screening and spectroscopic methods for deciphering the antimicrobial metabolites produced by i alcaligenes faecalis i soil isolate mz921504 |
| topic | <i>Alcaligenes faecalis</i> LC/MS metagenomics ectoine bacillibactin quinolobactin |
| url | https://www.mdpi.com/2079-6382/10/11/1382 |
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