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Yang A, Hong Y, Zhou F, Zhang L, Zhu Y, Wang C, Hu Y, Yu L, Chen L, Wang X. Endophytic Microbes from Medicinal Plants in Fenghuang Mountain as a Source of Antibiotics. Molecules 2023; 28:6301. [PMID: 37687129 PMCID: PMC10488465 DOI: 10.3390/molecules28176301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/22/2023] [Accepted: 08/26/2023] [Indexed: 09/10/2023] Open
Abstract
One of the largest concerns with world health today is still antibiotic resistance, which is making it imperative to find efficient alternatives as soon as possible. It has been demonstrated that microbes are reliable sources for the creation of therapeutic antibiotics. This research intends to investigate the endophytic microorganisms from several medicinal plants in Fenghuang Mountain (Jiangsu Province, China) and to discover new antibiotics from their secondary metabolites. A total of 269 endophytic strains were isolated from nine distinct medicinal plants. Taxonomic analysis revealed that there were 20 distinct species among these endophytes, with Streptomyces being the most common genus. Three of the target strains were chosen for scale-up fermentation after preliminary screening of antibacterial activities and the metabolomics investigation using LC-MS. These strains were Penicillium sp. NX-S-6, Streptomyces sp. YHLB-L-2 and Streptomyces sp. ZLBB-S-6. Twenty-three secondary metabolites (1-23), including a new sorbicillin analogue (1), were produced as a result of antibacterial activity-guided isolation. Through spectroscopic analysis using MS and NMR, the structures of yield compounds were clarified. According to antibacterial data, S. aureus or B. subtilis were inhibited to varying degrees by sorrentanone (3), emodic acid (8), GKK1032 B (10), linoleic acid (14), toyocamycin (17) and quinomycin A (21). The most effective antimicrobial agent against S. aureus, B. subtilis, E. coli and A. baumannii was quinomycin A (21). In addition, quinomycin A showed strong antifungal activity against Aspergillus fumigatus, Cryptococcus neoformans, and two clinical isolated strains Aspergillus fumigatus #176 and #339, with MIC as 16, 4, 16 and 16 µg/mL, respectively. This is the first time that bioprospecting of actinobacteria and their secondary metabolites from medicinal plants in Fenghuang Mountain was reported. The finding demonstrates the potential of endophytic microbes in medical plants to produce a variety of natural products. Endophytic microbes will be an important source for new antibiotics.
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Affiliation(s)
- Aiping Yang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yu Hong
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Fujian Province Key Laboratory for the Development of Bioactive Material from Marine Algae, College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou 362000, China
| | - Fengjuan Zhou
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ling Zhang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Youjuan Zhu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Chang Wang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yang Hu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Li Yu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Level 3 Laboratory of Molecular Biology (Epidemic and Febrile Diseases) of National TCM Administrator, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Lihong Chen
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Xiachang Wang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Fujian Province Key Laboratory for the Development of Bioactive Material from Marine Algae, College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou 362000, China
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Hintersatz C, Singh S, Rojas LA, Kretzschmar J, Wei STS, Khambhati K, Kutschke S, Lehmann F, Singh V, Jain R, Pollmann K. Halomonas gemina sp. nov. and Halomonas llamarensis sp. nov., two siderophore-producing organisms isolated from high-altitude salars of the Atacama Desert. Front Microbiol 2023; 14:1194916. [PMID: 37378283 PMCID: PMC10291192 DOI: 10.3389/fmicb.2023.1194916] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Introduction This study aimed to identify and characterize novel siderophore-producing organisms capable of secreting high quantities of the iron-binding compounds. In the course of this, two not yet reported halophilic strains designated ATCHAT and ATCH28T were isolated from hypersaline, alkaline surface waters of Salar de Llamará and Laguna Lejía, respectively. The alkaline environment limits iron bioavailability, suggesting that native organisms produce abundant siderophores to sequester iron. Methods Both strains were characterized by polyphasic approach. Comparative analysis of the 16S rRNA gene sequences revealed their affiliation with the genus Halomonas. ATCHAT showed close similarity to Halomonas salicampi and Halomonas vilamensis, while ATCH28T was related closest to Halomonas ventosae and Halomonas salina. The ability of both strains to secrete siderophores was initially assessed using the chromeazurol S (CAS) liquid assay and subsequently further investigated through genomic analysis and NMR. Furthermore, the effect of various media components on the siderophore secretion by strain ATCH28T was explored. Results The CAS assay confirmed the ability of both strains to produce iron-binding compounds. Genomic analysis of strain ATCHAT revealed the presence of a not yet reported NRPS-dependant gene cluster responsible for the secretion of siderophore. However, as only small amounts of siderophore were secreted, further investigations did not lie within the scope of this study. Via NMR and genomic analysis, strain ATCH28T has been determined to produce desferrioxamine E (DFOE). Although this siderophore is common in various terrestrial microorganisms, it has not yet been reported to occur within Halomonas, making strain ATCH28T the first member of the genus to produce a non-amphiphilic siderophore. By means of media optimization, the produced quantity of DFOE could be increased to more than 1000 µM. Discussion Phenotypic and genotypic characteristics clearly differentiated both strains from other members of the genus Halomonas. Average nucleotide identity (ANI) values and DNA-DNA relatedness indicated that the strains represented two novel species. Therefore, both species should be added as new representatives of the genus Halomonas, for which the designations Halomonas llamarensis sp. nov. (type strain ATCHAT = DSM 114476 = LMG 32709) and Halomonas gemina sp. nov. (type strain ATCH28T = DSM 114418 = LMG 32708) are proposed.
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Affiliation(s)
- Christian Hintersatz
- Department of Biotechnology, Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Shalini Singh
- Department of Biotechnology, Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Luis Antonio Rojas
- Department of Chemistry, Universidad Católica del Norte, Antofagasta, Chile
| | - Jerome Kretzschmar
- Department of Actinide Thermodynamics, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Sean Ting-Shyang Wei
- Department of Biogeochemistry, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Khushal Khambhati
- Department of Biosciences, School of Science, Indrashil University, Mehsana, India
| | - Sabine Kutschke
- Department of Biotechnology, Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Falk Lehmann
- Department of Biotechnology, Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Mehsana, India
| | - Rohan Jain
- Department of Biotechnology, Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Katrin Pollmann
- Department of Biotechnology, Helmholtz Institute Freiberg for Resource Technology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
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Exploring Micromonospora as Phocoenamicins Producers. Mar Drugs 2022; 20:md20120769. [PMID: 36547916 PMCID: PMC9782249 DOI: 10.3390/md20120769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022] Open
Abstract
Over the past few years, new technological and scientific advances have reinforced the field of natural product discovery. The spirotetronate class of natural products has recently grown with the discovery of phocoenamicins, natural actinomycete derived compounds that possess different antibiotic activities. Exploring the MEDINA's strain collection, 27 actinomycete strains, including three marine-derived and 24 terrestrial strains, were identified as possible phocoenamicins producers and their taxonomic identification by 16S rDNA sequencing showed that they all belong to the Micromonospora genus. Using an OSMAC approach, all the strains were cultivated in 10 different media each, resulting in 270 fermentations, whose extracts were analyzed by LC-HRMS and subjected to High-throughput screening (HTS) against methicillin-resistant Staphylococcus aureus (MRSA), Mycobacterium tuberculosis H37Ra and Mycobacterium bovis. The combination of LC-UV-HRMS analyses, metabolomics analysis and molecular networking (GNPS) revealed that they produce several related spirotetronates not disclosed before. Variations in the culture media were identified as the most determining factor for phocoenamicin production and the best producer strains and media were established. Herein, we reported the chemically diverse production and metabolic profiling of Micromonospora sp. strains, including the known phocoenamicins and maklamicin, reported for the first time as being related to this family of compounds, as well as the bioactivity of their crude extracts. Although our findings do not confirm previous statements about phocoenamicins production only in unique marine environments, they have identified marine-derived Micromonospora species as the best producers of phocoenamicins in terms of both the abundance in their extracts of some major members of the structural class and the variety of molecular structures produced.
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González D, Robas M, Fernández V, Bárcena M, Probanza A, Jiménez PA. Comparative Metagenomic Study of Rhizospheric and Bulk Mercury-Contaminated Soils in the Mining District of Almadén. Front Microbiol 2022; 13:797444. [PMID: 35330761 PMCID: PMC8940170 DOI: 10.3389/fmicb.2022.797444] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/17/2022] [Indexed: 12/22/2022] Open
Abstract
Soil contamination by heavy metals, particularly mercury (Hg), is a problem that can seriously affect the environment, animals, and human health. Hg has the capacity to biomagnify in the food chain. That fact can lead to pathologies, of those which affect the central nervous system being the most severe. It is convenient to know the biological environmental indicators that alert of the effects of Hg contamination as well as the biological mechanisms that can help in its remediation. To contribute to this knowledge, this study conducted comparative analysis by the use of Shotgun metagenomics of the microbial communities in rhizospheric soils and bulk soil of the mining region of Almadén (Ciudad Real, Spain), one of the most affected areas by Hg in the world The sequences obtained was analyzed with MetaPhlAn2 tool and SUPER-FOCUS. The most abundant taxa in the taxonomic analysis in bulk soil were those of Actinobateria and Alphaproteobacteria. On the contrary, in the rhizospheric soil microorganisms belonging to the phylum Proteobacteria were abundant, evidencing that roots have a selective effect on the rhizospheric communities. In order to analyze possible indicators of biological contamination, a functional potential analysis was performed. The results point to a co-selection of the mechanisms of resistance to Hg and the mechanisms of resistance to antibiotics or other toxic compounds in environments contaminated by Hg. Likewise, the finding of antibiotic resistance mechanisms typical of the human clinic, such as resistance to beta-lactams and glycopeptics (vancomycin), suggests that these environments can behave as reservoirs. The sequences involved in Hg resistance (operon mer and efflux pumps) have a similar abundance in both soil types. However, the response to abiotic stress (salinity, desiccation, and contaminants) is more prevalent in rhizospheric soil. Finally, sequences involved in nitrogen fixation and metabolism and plant growth promotion (PGP genes) were identified, with higher relative abundances in rhizospheric soils. These findings can be the starting point for the targeted search for microorganisms suitable for further use in bioremediation processes in Hg-contaminated environments.
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Affiliation(s)
- Daniel González
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
| | - Marina Robas
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
| | - Vanesa Fernández
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
| | - Marta Bárcena
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
| | - Agustín Probanza
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
| | - Pedro A Jiménez
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
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Singh P, Khan A, Kumar R, Kumar R, Singh VK, Srivastava A. Recent developments in siderotyping: procedure and application. World J Microbiol Biotechnol 2020; 36:178. [PMID: 33128090 DOI: 10.1007/s11274-020-02955-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/27/2020] [Indexed: 12/31/2022]
Abstract
Siderophores are metal chelating secondary metabolites secreted by almost all organisms. Beside iron starvation, the ability to produce siderophores depends upon several other factors. Chemical structure of siderophore is very complex with vast structural diversity, thus the principle challenge involves its detection, quantification, purification and characterisation. Metal chelation is its most fascinating attribute. This metal chelation property is now forming the basis of its application as molecular markers, siderotyping tool for taxonomic clarification, biosensors and bioremediation agents. This has led researchers to develop and continuously modify previous techniques in order to provide accurate and reproducible methods of studying siderophores. Knowledge obtained via computational approaches provides a new horizon in the field of siderophore biosynthetic gene clusters and their interaction with various proteins/peptides. This review illustrates various techniques, bioinformatics tools and databases employed in siderophores' studies, the principle of analytical methods and their recent applications.
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Affiliation(s)
- Pratika Singh
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, 824236, India
| | - Azmi Khan
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, 824236, India
| | - Rakesh Kumar
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, 824236, India
| | - Ravinsh Kumar
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, 824236, India
| | - Vijay Kumar Singh
- Department of Bioinformatics, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, 824236, India
| | - Amrita Srivastava
- Department of Life Science, School of Earth, Biological and Environmental Sciences, Central University of South Bihar, Gaya, 824236, India.
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