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Zhang S, Shu M, Gong Z, Liu X, Zhang C, Liang Y, Lin Q, Zhou B, Guo T, Liu J. Enhancing extracellular monascus pigment production in submerged fermentation with engineered microbial consortia. Food Microbiol 2024; 121:104499. [PMID: 38637070 DOI: 10.1016/j.fm.2024.104499] [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: 10/15/2023] [Revised: 12/13/2023] [Accepted: 02/21/2024] [Indexed: 04/20/2024]
Abstract
In this study, we investigated the impact of microbial interactions on Monascus pigment (MP) production. We established diverse microbial consortia involving Monascus purpureus and Lactobacillus fermentum. The addition of Lactobacillus fermentum (4% at 48 h) to the submerged fermentation of M. purpureus resulted in a significantly higher MP production compared to that achieved using the single-fermentation system. Co-cultivation with immobilized L. fermentum led to a remarkable increase of 59.18% in extracellular MP production, while mixed fermentation with free L. fermentum caused a significant decrease of 66.93% in intracellular MPs, contrasting with a marginal increase of 4.52% observed during co-cultivation with immobilized L. fermentum and the control group respectively. The findings indicate an evident enhancement in cell membrane permeability of M. purpureus when co-cultivated with immobilized L. fementum. Moreover, integrated transcriptomic and metabolomic analyses were conducted to elucidate the regulatory mechanisms underlying MP biosynthesis and secretion following inoculation with immobilized L. fementum, with specific emphasis on glycolysis, steroid biosynthesis, fatty acid biosynthesis, and energy metabolism.
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Affiliation(s)
- Song Zhang
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Meng Shu
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Zihan Gong
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Xinyi Liu
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Chenyu Zhang
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Ying Liang
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Qinlu Lin
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Bo Zhou
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
| | - Ting Guo
- Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China
| | - Jun Liu
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Hunan Key Laboratory of Grain-Oil Deep Process and Quality Control, National Engineering Research Center of Rice and Byproduct Deep Processing, College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China.
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Hu Z, Cui H, Wang Q, Li C, Chen S, Gao Z, Liu L, Peng B, Li J. Induced production of defensive secondary metabolites from Aspergillus fumigatiaffinis by co-culture with Aspergillus alabamensis. PHYTOCHEMISTRY 2024; 225:114187. [PMID: 38889845 DOI: 10.1016/j.phytochem.2024.114187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024]
Abstract
Seven previously undescribed compounds, including four diketomorpholine alkaloids (1‒4), one indole diketopiperazine alkaloid (9), one chromone (10), and one benzoic acid derivative (13), and nine known compounds (5-8, 11, 12, and 14-16) were isolated from two different fungal sources. Nine of these metabolites (1-9) were obtained from a seagrass-derived Aspergillus alabamensis SYSU-6778, while the others were obtained from a mixed culture of A. alabamensis SYSU-6778 and a co-isolated fungus A. fumigatiaffinis SYSU-6786. The chemical structures of the compounds were deduced via spectroscopic techniques (including HRESIMS, 1D and 2D NMR), chemical reactions, and ECD calculations. It is worth noting that compound 10 was identified as a defensive secondary metabolite of strain SYSU-6786, produced through the induction of compound 8 under co-culture conditions. Compounds 3 and 4 possessed a naturally rare isotryptophan core. Moreover, compounds 1 and 2 exhibited potent inhibitory activities against fish pathogenic bacterium Edwardsiella ictalurid, with minimum inhibitory concentration values of 10.0 μg/mL for both compounds.
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Affiliation(s)
- Zhibo Hu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, PR China
| | - Haishan Cui
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, PR China
| | - Qiang Wang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, PR China
| | - Cheng Li
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, PR China
| | - Senhua Chen
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, PR China
| | - Zhizeng Gao
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, PR China
| | - Lan Liu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, PR China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519082, PR China
| | - Bo Peng
- Institute for Environmental and Climate Research, Jinan University, Guangzhou, 511443, PR China
| | - Jing Li
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, PR China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai, 519082, PR China.
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Samia ALKHALILS. EFFECT OF PENICILLIUM SPECIES ON THE ANTIBIOTIC RESISTANCE PROFILE OF ALCALIGENES FAECALIS. Afr J Infect Dis 2024; 18:8-18. [PMID: 38606189 PMCID: PMC11004782 DOI: 10.21010/ajidv18i2.2] [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: 08/30/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 04/13/2024] Open
Abstract
Background Infectious diseases due to antibiotic resistant pathogens are a global public health problem. This study aimed at determining the potential effect of bacterial-fungal interaction on the antibiotic susceptibility profile of Alcaligenes faecalis. Materials and Methods Alcaligenes faecalis was isolated from water samples. The isolate was identified using the conventional biochemical tests and the 16S rRNA molecular sequencing technique. Additionally, Penicillium species was isolated and identified based on colony morphological characteristics and microscopic features. Standardized isolates were co-cultured in broth medium. Antibiotic susceptibility evaluation of the Alcaligenes faecalis from the co-culture and the original Alcaligenes faecalis was carried out using the Kirby bauer disk diffusion method. Results The antibiotic susceptibility profile of Alcaligenes faecalis before and after co-culture remained largely unchanged except in the case of chloramphenicol, where the isolate showed reduced susceptibility. Molecular analysis of resistance gene revealed the absence of tested gene encoding antibiotic resistance, including the streptomycin resistance (str) genes (stra and strb) and the erythromycin resistance methylase (erm) gene. Conclusion The result of this study showed that there is a minimal influence of Penicillium cultures on the susceptibility of A. faecalis. Further research involving a wide spectrum of microorganisms and their interactions should be conducted to acquire a thorough understanding of the influence of microbial interactions on antibiotic susceptibility profiles in order to pave way for novel strategies to combat antimicrobial resistance.
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Affiliation(s)
- ALKHALIL S. Samia
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Alquwayiyah, Riyadh, Saudi Arabia
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Geris R, Teles de Jesus VE, Ferreira da Silva A, Malta M. Exploring Culture Media Diversity to Produce Fungal Secondary Metabolites and Cyborg Cells. Chem Biodivers 2024; 21:e202302066. [PMID: 38335028 DOI: 10.1002/cbdv.202302066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/12/2024]
Abstract
Fungi are microorganisms of significant biotechnological importance due to their ability to provide food and produce several value-added secondary metabolites and enzymes. Its products move billions of dollars in the pharmaceutical, cosmetics, and additives sectors. These microorganisms also play a notable role in bionanotechnology, leading to the production of hybrid biological-inorganic materials (such as cyborg cells) and the use of their enzyme complex in the biosynthesis of nanoparticles. In this sense, optimizing the fungal growth process is necessary, with selecting the cultivation medium as one of the essential factors for the microorganism to reach its maximum metabolic expression. The culture medium's composition can also impact the nanomaterial's stability and prevent the incorporation of nanoparticles into fungal cells. Therefore, our main objectives are the following: (1) compile and discuss the most commonly employed culture media for the production of fungal secondary metabolites and the formation of cyborg cells, accompanied by preparation methods; (2) provide a six-step guide to investigating the fungal metabolomic profile and (3) discuss the main procedures of microbial cultivation to produce fungal cyborg cells.
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Affiliation(s)
- Regina Geris
- Laboratório de Biotecnologia e Química de Microrganismos (LBQM), Departamento de Química Orgânica, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo S/n, 40170-115, Salvador, Brasil
| | - Vitória Evelyn Teles de Jesus
- Laboratório de Biotecnologia e Química de Microrganismos (LBQM), Departamento de Química Orgânica, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo S/n, 40170-115, Salvador, Brasil
| | - Antonio Ferreira da Silva
- Laboratório de Biotecnologia e Química de Microrganismos (LBQM), Departamento de Química Orgânica, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo S/n, 40170-115, Salvador, Brasil
| | - Marcos Malta
- Laboratório de Biotecnologia e Química de Microrganismos (LBQM), Departamento de Química Orgânica, Instituto de Química, Universidade Federal da Bahia, Rua Barão de Jeremoabo S/n, 40170-115, Salvador, Brasil
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Sabotič J, Bayram E, Ezra D, Gaudêncio SP, Haznedaroğlu BZ, Janež N, Ktari L, Luganini A, Mandalakis M, Safarik I, Simes D, Strode E, Toruńska-Sitarz A, Varamogianni-Mamatsi D, Varese GC, Vasquez MI. A guide to the use of bioassays in exploration of natural resources. Biotechnol Adv 2024; 71:108307. [PMID: 38185432 DOI: 10.1016/j.biotechadv.2024.108307] [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: 07/24/2023] [Revised: 12/05/2023] [Accepted: 01/01/2024] [Indexed: 01/09/2024]
Abstract
Bioassays are the main tool to decipher bioactivities from natural resources thus their selection and quality are critical for optimal bioprospecting. They are used both in the early stages of compounds isolation/purification/identification, and in later stages to evaluate their safety and efficacy. In this review, we provide a comprehensive overview of the most common bioassays used in the discovery and development of new bioactive compounds with a focus on marine bioresources. We present a comprehensive list of practical considerations for selecting appropriate bioassays and discuss in detail the bioassays typically used to explore antimicrobial, antibiofilm, cytotoxic, antiviral, antioxidant, and anti-ageing potential. The concept of quality control and bioassay validation are introduced, followed by safety considerations, which are critical to advancing bioactive compounds to a higher stage of development. We conclude by providing an application-oriented view focused on the development of pharmaceuticals, food supplements, and cosmetics, the industrial pipelines where currently known marine natural products hold most potential. We highlight the importance of gaining reliable bioassay results, as these serve as a starting point for application-based development and further testing, as well as for consideration by regulatory authorities.
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Affiliation(s)
- Jerica Sabotič
- Department of Biotechnology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia.
| | - Engin Bayram
- Institute of Environmental Sciences, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - David Ezra
- Department of Plant Pathology and Weed Research, ARO, The Volcani Institute, P.O.Box 15159, Rishon LeZion 7528809, Israel
| | - Susana P Gaudêncio
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal; UCIBIO - Applied Biomolecular Sciences Unit, Department of Chemistry, Blue Biotechnology & Biomedicine Lab, NOVA School of Science and Technology, NOVA University of Lisbon, 2819-516 Caparica, Portugal
| | - Berat Z Haznedaroğlu
- Institute of Environmental Sciences, Bogazici University, Bebek, Istanbul 34342, Turkey
| | - Nika Janež
- Department of Biotechnology, Jožef Stefan Institute, 1000 Ljubljana, Slovenia
| | - Leila Ktari
- B3Aqua Laboratory, National Institute of Marine Sciences and Technologies, Carthage University, Tunis, Tunisia
| | - Anna Luganini
- Department of Life Sciences and Systems Biology, University of Turin, 10123 Turin, Italy
| | - Manolis Mandalakis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500 Heraklion, Greece
| | - Ivo Safarik
- Department of Nanobiotechnology, Biology Centre, ISBB, CAS, Na Sadkach 7, 370 05 Ceske Budejovice, Czech Republic; Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacky University, Slechtitelu 27, 783 71 Olomouc, Czech Republic
| | - Dina Simes
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, 8005-139 Faro, Portugal; 2GenoGla Diagnostics, Centre of Marine Sciences (CCMAR), Universidade do Algarve, Faro, Portugal
| | - Evita Strode
- Latvian Institute of Aquatic Ecology, Agency of Daugavpils University, Riga LV-1007, Latvia
| | - Anna Toruńska-Sitarz
- Department of Marine Biology and Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, 81-378 Gdynia, Poland
| | - Despoina Varamogianni-Mamatsi
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500 Heraklion, Greece
| | | | - Marlen I Vasquez
- Department of Chemical Engineering, Cyprus University of Technology, 3036 Limassol, Cyprus
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Li Q, Li S, Li S, Hao X, Wang A, Si S, Xu Y, Shu J, Gan M. Antimicrobial and Anti-inflammatory Cyclic Tetrapeptides from the Co-cultures of Two Marine-Derived Fungi. JOURNAL OF NATURAL PRODUCTS 2024; 87:365-370. [PMID: 38276888 DOI: 10.1021/acs.jnatprod.3c01115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Violaceotides B-E (1-4), four new cyclic tetrapeptides, along with seven known compounds, were identified from the sponge-associated Aspergillus insulicola IMB18-072 co-cultivated with the marine-derived Alternaria angustiovoidea IMB20-805. Their structures were elucidated by extensive analysis of spectroscopic data, including HRESIMS, 1D and 2D NMR, and MS/MS data. The absolute configurations were determined by the advanced Marfey's method. Compounds 2, 3, and violaceotide A (5) displayed selective antimicrobial activities against the aquatic pathogenic bacteria Edwardsiella tarda and E. ictaluri. In addition, compounds 1-5 showed inhibitory activities against the LPS-induced expression of the inflammatory mediator IL-6 in RAW264.7 cells at a concentration of 10 μM.
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Affiliation(s)
- Qin Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
- Key Laboratory of Modern Preparation of Traditional Chinese Medicines, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, People's Republic of China
| | - Shasha Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Shunwang Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Xiaomeng Hao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Anqi Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Shuyi Si
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Yanni Xu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Jicheng Shu
- Key Laboratory of Modern Preparation of Traditional Chinese Medicines, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, People's Republic of China
| | - Maoluo Gan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
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Song YP, Ji NY. Chemistry and biology of marine-derived Trichoderma metabolites. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:14. [PMID: 38302800 PMCID: PMC10834931 DOI: 10.1007/s13659-024-00433-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
Marine-derived fungi of the genus Trichoderma have been surveyed for pharmaceuticals and agrochemicals since 1993, with various new secondary metabolites being characterized from the strains of marine animal, plant, sediment, and water origin. Chemical structures and biological activities of these metabolites are comprehensively reviewed herein up to the end of 2022 (covering 30 years). More than 70 strains that belong to at least 18 known Trichoderma species have been chemically investigated during this period. As a result, 445 new metabolites, including terpenes, steroids, polyketides, peptides, alkaloids, and others, have been identified, with over a half possessing antimicroalgal, zooplankton-toxic, antibacterial, antifungal, cytotoxic, anti-inflammatory, and other activities. The research is highlighted by the molecular diversity and antimicroalgal potency of terpenes and steroids. In addition, metabolic relevance along with co-culture induction in the production of new compounds is also concluded. Trichoderma strains of marine origin can transform and degrade heterogeneous molecules, but these functions need further exploration.
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Affiliation(s)
- Yin-Ping Song
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, People's Republic of China
| | - Nai-Yun Ji
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, People's Republic of China.
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Neuhoff D, Neumann G, Weinmann M. Testing plant growth promoting microorganisms in the field - a proposal for standards. FRONTIERS IN PLANT SCIENCE 2024; 14:1324665. [PMID: 38293625 PMCID: PMC10824932 DOI: 10.3389/fpls.2023.1324665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/11/2023] [Indexed: 02/01/2024]
Abstract
In the European Union and worldwide there are a burgeoning markets for plant growth promoting microorganisms (PGPM) and other biological agents as soil improvers, bio-fertilizers, plant bio-stimulants, and biological control agents or bio-pesticides. Microbial agents have a major share in this development. The use of such products is often advertised with the promise of contributing to sustainable agricultural practices by increasing crop growth and yield and offering an alternative or substitute to decrease the dependency of agriculture on hazardeous agrochemicals. In contrast to registered microbial plant protection products, PGPM that are marketed in the EU as soil improvers or plant biostimulants, are not strictly required to have proven minimum efficacy levels under field conditions. Manufacturers only have to ensure that these products do not pose unacceptable risks to human, animal or plant health, safety or the environment. Uniform guidelines comparable to the EPPO - standards (European and Mediterranean Plant Protection Organisation) to test the efficacy in field trials are not available. This paper attempts to fill the gap. It proposes guidelines for PGPM field trial design and implementation, as well as recommendations for the type and scope of data collection and evaluation. Selected research papers from literature were evaluated to analyze, whether and to what extent the requirements are already met. The majority of the papers had a clear experimental design followed by proper data evaluation. Frequent deficiencies were the low number of tested environments and crop species, insufficient site and agronomic management description and missing data on soil humidity and temperature. Using the suggested standards is assumed to increase the expressive power of tested microbial products.
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Affiliation(s)
- Daniel Neuhoff
- Department Agroecology & Organic Farming, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Günter Neumann
- Department of Nutritional Crop Physiology (340h), Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
| | - Markus Weinmann
- Department of Nutritional Crop Physiology (340h), Institute of Crop Science, University of Hohenheim, Stuttgart, Germany
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Lee Y, Hwang S, Kim W, Kim JH, Palsson BO, Cho BK. CRISPR-aided genome engineering for secondary metabolite biosynthesis in Streptomyces. J Ind Microbiol Biotechnol 2024; 51:kuae009. [PMID: 38439699 PMCID: PMC10949845 DOI: 10.1093/jimb/kuae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/02/2024] [Indexed: 03/06/2024]
Abstract
The demand for discovering novel microbial secondary metabolites is growing to address the limitations in bioactivities such as antibacterial, antifungal, anticancer, anthelmintic, and immunosuppressive functions. Among microbes, the genus Streptomyces holds particular significance for secondary metabolite discovery. Each Streptomyces species typically encodes approximately 30 secondary metabolite biosynthetic gene clusters (smBGCs) within its genome, which are mostly uncharacterized in terms of their products and bioactivities. The development of next-generation sequencing has enabled the identification of a large number of potent smBGCs for novel secondary metabolites that are imbalanced in number compared with discovered secondary metabolites. The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system has revolutionized the translation of enormous genomic potential into the discovery of secondary metabolites as the most efficient genetic engineering tool for Streptomyces. In this review, the current status of CRISPR/Cas applications in Streptomyces is summarized, with particular focus on the identification of secondary metabolite biosynthesis gene clusters and their potential applications.This review summarizes the broad range of CRISPR/Cas applications in Streptomyces for natural product discovery and production. ONE-SENTENCE SUMMARY This review summarizes the broad range of CRISPR/Cas applications in Streptomyces for natural product discovery and production.
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Affiliation(s)
- Yongjae Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Bernhard O Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Graduate school of Engineering Biology, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
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10
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Zhu X, Wang A, Zheng Y, Li D, Wei Y, Gan M, Li Y, Si S. Anti-Biofilm Activity of Cocultimycin A against Candida albicans. Int J Mol Sci 2023; 24:17026. [PMID: 38069349 PMCID: PMC10707031 DOI: 10.3390/ijms242317026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/19/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
Candida albicans (C. albicans), the most common fungal pathogen, has the ability to form a biofilm, leading to enhanced virulence and antibiotic resistance. Cocultimycin A, a novel antifungal antibiotic isolated from the co-culture of two marine fungi, exhibited a potent inhibitory effect on planktonic C. albicans cells. This study aimed to evaluate the anti-biofilm activity of cocultimycin A against C. albicans and explore its underlying mechanism. Crystal violet staining showed that cocultimycin A remarkably inhibited biofilm formation in a dose-dependent manner and disrupted mature biofilms at higher concentrations. However, the metabolic activity of mature biofilms treated with lower concentrations of cocultimycin A significantly decreased when using the XTT reduction method. Cocultimycin A could inhibit yeast-to-hypha transition and mycelium formation of C. albicans colonies, which was observed through the use of a light microscope. Scanning electron microscopy revealed that biofilms treated with cocultimycin A were disrupted, yeast cells increased, and hypha cells decreased and significantly shortened. The adhesive ability of C. albicans cells treated with cocultimycin A to the medium and HOEC cells significantly decreased. Through the use of a qRT-PCR assay, the expression of multiple genes related to adhesion, hyphal formation and cell membrane changes in relation to biofilm cells treated with cocultimycin A. All these results suggested that cocultimycin A may be considered a potential novel molecule for treating and preventing biofilm-related C. albicans infections.
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Affiliation(s)
| | | | | | | | | | - Maoluo Gan
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China; (X.Z.); (A.W.); (Y.Z.); (D.L.); (Y.W.); (S.S.)
| | - Yan Li
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China; (X.Z.); (A.W.); (Y.Z.); (D.L.); (Y.W.); (S.S.)
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Yang K, Li H, Li L, Zhao Z, Hu J, Wei Y, Yang H, Li J. Metabolomics reveal metabolic variation caused by co-culture of Arthrobacter ureafaciens and Trichoderma harzianum and their impacts on wheat germination. Int Microbiol 2023; 26:723-739. [PMID: 36564574 DOI: 10.1007/s10123-022-00302-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/26/2022] [Accepted: 11/17/2022] [Indexed: 12/24/2022]
Abstract
Arthrobacter ureafaciens DnL1-1 is a bacterium used for atrazine degradation, while Trichoderma harzianum LTR-2 is a widely used biocontrol fungus. In this study, a liquid co-cultivation of these two organisms was initially tested. The significant changes in the metabolome of fermentation liquors were investigated based on cultivation techniques (single-cultured and co-cultured DnL1-1 and LTR-2) using an UPLC-QTOF-MS in an untargeted metabolomic approach. Principle components analysis (PCA) and partial least squares discriminant analysis (PLS-DA) supervised modelling revealed modifications of the metabolic profiles in fermentation liquors as a function of interactions between different strains. Compared with pure-cultivation of DnL1-1, 51 compounds were altered during the cocultivation, with unique and significant differences in the abundance of organic nitrogen compounds (e.g. carnitine, acylcarnitine 4:0, acylcarnitine 5:0, 3-dehydroxycarnitine and O-acetyl-L-carnitine) and trans-zeatin riboside. Nevertheless, compared with pure-cultivation of LTR-2, the abundance of 157 compounds, including amino acids, soluble sugars, organic acids, indoles and derivatives, nucleosides, and others, changed significantly in the cocultivation. Among them, the concentration of tryptophan, which is a precursor to indoleacetic acid, indoleacetic acid, aspartic acid, and L-glutamic acid increased while that of most soluble sugars decreased upon cocultivation. The fermentation filtrates of co-cultivation of LTR-2 and DnL1-1 showed significant promoting effects on germination and radicle length of wheat. A subsequent experiment demonstrated synergistic effects of differential metabolites caused by co-cultivation of DnL1-1 and LTR-2 on wheat germination. Comprehensive metabolic profiling may provide valuable information on the effects of DnL1-1 and LTR-2 on wheat growth.
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Affiliation(s)
- Kai Yang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute of Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250013, China
| | - Hongmei Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute of Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250013, China
| | - Ling Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute of Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250013, China
| | - Zhongjuan Zhao
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute of Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250013, China
| | - Jindong Hu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute of Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250013, China
| | - Yanli Wei
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute of Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250013, China
| | - Hetong Yang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute of Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250013, China
| | - Jishun Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute of Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250013, China.
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12
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Takishita Y, Subramanian S, Souleimanov A, Smith DL. Interactive effects of Pseudomonas entomophila strain 23S and Clavibacter michiganensis subsp. michiganensis on proteome and anti-Cmm compound production. J Proteomics 2023; 289:105006. [PMID: 37717723 DOI: 10.1016/j.jprot.2023.105006] [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: 02/11/2023] [Revised: 09/03/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
Pseudomonas entomophila strain 23S is an effective biocontrol bacterium for tomato bacterial canker caused by Clavibacter michiganensis subsp. michiganensis (Cmm); it produces an inhibitory compound affecting the growth of Cmm. In this study, the interactions between pure cultures of P. entomophila 23S and Cmm were investigated. First, the population dynamics of each bacterium during the interaction was determined using the selective media. Second, the amount of anti-Cmm compound produced by P. entomophila 23S in the presence of Cmm was quantified using HPLC. Lastly, a label-free shotgun proteomics study of P. entomophila 23S, Cmm, and a co-culture was conducted to understand the effects of the interaction of each bacterium at the proteomic level. Compared with the pure culture grown, the total number of proteins decreased in the interaction for both bacteria. P. entomophila 23S secreted stress-related proteins, such as chaperonins, peptidases, ABC-transporters and elongation factors. The bacterium also produced more proteins related with purine, pyrimidine, carbon and nitrogen metabolisms in the presence of Cmm. The population enumeration study revealed that the Cmm population declined dramatically during the interaction, while the population of P. entomophila 23S maintained. The quantification of anti-Cmm compound indicated that P. entomophila 23S produced significantly higher amount of anti-Cmm compound when it was cultured with Cmm. Overall, the study suggested that P. entomophila 23S, although is cidal to Cmm, was also negatively affected by the presence of Cmm, while trying to adapt to the stress condition, and that such an environment favored increased production of the anti-Cmm compound by P. entomophila 23S. SIGNIFICANCE: Pseudomonas entomophila strain 23S is an effective biocontrol bacterium for tomato bacterial canker caused by Clavibacter michiganensis subsp. michiganensis (Cmm); it produces an inhibitory compound affecting the growth of Cmm. In this study, secreted proteome of pure cultures of P. entomophila 23S and Cmm, and also of a co-culture was first time identified. Furthermore, the study found that P. entomophila strain 23S produced significantly higher amount of anti-Cmm compound when the bacterium was grown together with Cmm. Co-culture enhancing anti-Cmm compound production by P. entomophila 23S is useful information, particularly from a commercial point of view of biocontrol application, and for scale-up of anti-Cmm compound production.
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Affiliation(s)
- Yoko Takishita
- Department of Plant Science, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Sowmyalakshmi Subramanian
- Department of Plant Science, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Alfred Souleimanov
- Department of Plant Science, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Donald L Smith
- Department of Plant Science, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada.
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Santamaría RI, Martínez-Carrasco A, Tormo JR, Martín J, Genilloud O, Reyes F, Díaz M. Interactions of Different Streptomyces Species and Myxococcus xanthus Affect Myxococcus Development and Induce the Production of DK-Xanthenes. Int J Mol Sci 2023; 24:15659. [PMID: 37958645 PMCID: PMC10649082 DOI: 10.3390/ijms242115659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
The co-culturing of microorganisms is a well-known strategy to study microbial interactions in the laboratory. This approach facilitates the identification of new signals and molecules produced by one species that affects other species' behavior. In this work, we have studied the effects of the interaction of nine Streptomyces species (S. albidoflavus, S. ambofaciens, S. argillaceus, S. griseus, S. lividans, S. olivaceus, S. parvulus, S. peucetius, and S. rochei) with the predator bacteria Myxococcus xanthus, five of which (S. albidoflavus, S. griseus, S. lividans, S. olivaceus, and S. argillaceus) induce mound formation of M. xanthus on complex media (Casitone Yeast extract (CYE) and Casitone tris (CTT); media on which M. xanthus does not form these aggregates under normal culture conditions. An in-depth study on S. griseus-M. xanthus interactions (the Streptomyces strain producing the strongest effect) has allowed the identification of two siderophores produced by S. griseus, demethylenenocardamine and nocardamine, responsible for this grouping effect over M. xanthus. Experiments using pure commercial nocardamine and different concentrations of FeSO4 show that iron depletion is responsible for the behavior of M. xanthus. Additionally, it was found that molecules, smaller than 3 kDa, produced by S. peucetius can induce the production of DK-xanthenes by M. xanthus.
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Affiliation(s)
- Ramón I. Santamaría
- Instituto de Biología Funcional y Genómica (IBFG), Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, C/Zacarías González, nº 2, 37007 Salamanca, Spain;
| | - Ana Martínez-Carrasco
- Instituto de Biología Funcional y Genómica (IBFG), Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, C/Zacarías González, nº 2, 37007 Salamanca, Spain;
| | - José R. Tormo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (J.R.T.); (J.M.); (O.G.); (F.R.)
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (J.R.T.); (J.M.); (O.G.); (F.R.)
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (J.R.T.); (J.M.); (O.G.); (F.R.)
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (J.R.T.); (J.M.); (O.G.); (F.R.)
| | - Margarita Díaz
- Instituto de Biología Funcional y Genómica (IBFG), Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, C/Zacarías González, nº 2, 37007 Salamanca, Spain;
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14
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Tsipinana S, Husseiny S, Alayande KA, Raslan M, Amoo S, Adeleke R. Contribution of endophytes towards improving plant bioactive metabolites: a rescue option against red-taping of medicinal plants. FRONTIERS IN PLANT SCIENCE 2023; 14:1248319. [PMID: 37771494 PMCID: PMC10522919 DOI: 10.3389/fpls.2023.1248319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/11/2023] [Indexed: 09/30/2023]
Abstract
Medicinal plants remain a valuable source for natural drug bioprospecting owing to their multi-target spectrum. However, their use as raw materials for novel drug synthesis has been greatly limited by unsustainable harvesting leading to decimation of their wild populations coupled with inherent low concentrations of constituent secondary metabolites per unit mass. Thus, adding value to the medicinal plants research dynamics calls for adequate attention. In light of this, medicinal plants harbour endophytes which are believed to be contributing towards the host plant survival and bioactive metabolites through series of physiological interference. Stimulating secondary metabolite production in medicinal plants by using endophytes as plant growth regulators has been demonstrated to be one of the most effective methods for increasing metabolite syntheses. Use of endophytes as plant growth promotors could help to ensure continuous supply of medicinal plants, and mitigate issues with fear of extinction. Endophytes minimize heavy metal toxicity in medicinal plants. It has been hypothesized that when medicinal plants are exposed to harsh conditions, associated endophytes are the primary signalling channels that induce defensive reactions. Endophytes go through different biochemical processes which lead to activation of defence mechanisms in the host plants. Thus, through signal transduction pathways, endophytic microorganisms influence genes involved in the generation of secondary metabolites by plant cells. Additionally, elucidating the role of gene clusters in production of secondary metabolites could expose factors associated with low secondary metabolites by medicinal plants. Promising endophyte strains can be manipulated for enhanced production of metabolites, hence, better probability of novel bioactive metabolites through strain improvement, mutagenesis, co-cultivation, and media adjustment.
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Affiliation(s)
- Sinawo Tsipinana
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Samah Husseiny
- Department of Biotechnology and Life Sciences, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, Beni-Suef, Egypt
| | - Kazeem A. Alayande
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Mai Raslan
- Department of Biotechnology and Life Sciences, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, Beni-Suef, Egypt
| | - Stephen Amoo
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
- Agricultural Research Council – Vegetables, Industrial and Medicinal Plants, Roodeplaat, Pretoria, South Africa
| | - Rasheed Adeleke
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
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15
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Verma A, Tiwari H, Singh S, Gupta P, Rai N, Kumar Singh S, Singh BP, Rao S, Gautam V. Epigenetic manipulation for secondary metabolite activation in endophytic fungi: current progress and future directions. Mycology 2023; 14:275-291. [PMID: 38187885 PMCID: PMC10769123 DOI: 10.1080/21501203.2023.2241486] [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: 05/11/2023] [Accepted: 07/21/2023] [Indexed: 01/09/2024] Open
Abstract
Fungal endophytes have emerged as a promising source of secondary metabolites with significant potential for various applications in the field of biomedicine. The biosynthetic gene clusters of endophytic fungi are responsible for encoding several enzymes and transcriptional factors that are involved in the biosynthesis of secondary metabolites. The investigation of fungal metabolic potential at genetic level faces certain challenges, including the synthesis of appropriate amounts of chemicals, and loss of the ability of fungal endophytes to produce secondary metabolites in an artificial culture medium. Therefore, there is a need to delve deeper into the field of fungal genomics and transcriptomics to explore the potential of fungal endophytes in generating secondary metabolites governed by biosynthetic gene clusters. The silent biosynthetic gene clusters can be activated by modulating the chromatin structure using chemical compounds. Epigenetic modification plays a significant role by inducing cryptic gene responsible for the production of secondary metabolites using DNA methyl transferase and histone deacetylase. CRISPR-Cas9-based genome editing emerges an effective tool to enhance the production of desired metabolites by modulating gene expression. This review primarily focuses on the significance of epigenetic elicitors and their capacity to boost the production of secondary metabolites from endophytes. This article holds the potential to rejuvenate the drug discovery pipeline by introducing new chemical compounds.
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Affiliation(s)
- Ashish Verma
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Harshita Tiwari
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Swati Singh
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Priyamvada Gupta
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Nilesh Rai
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Santosh Kumar Singh
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Bhim Pratap Singh
- Department of Agriculture & Environmental Sciences (AES), National Institute of Food Technology Entrepreneurship & Management (NIFTEM), Sonepat, India
| | - Sombir Rao
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Vibhav Gautam
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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16
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Jagels A, Adpressa DA, Kaweesa EN, McCauley M, Philmus B, Strother JA, Loesgen S. Metabolomics-Guided Discovery, Isolation, Structure Elucidation, and Bioactivity of Myropeptins C-E from Myrothecium inundatum. JOURNAL OF NATURAL PRODUCTS 2023; 86:1723-1735. [PMID: 37411007 DOI: 10.1021/acs.jnatprod.3c00148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
The saprotrophic filamentous fungus Myrothecium inundatum represents a chemically underexplored ascomycete with a high number of putative biosynthetic gene clusters in its genome. Here, we present new linear lipopeptides from nongenetic gene activation experiments using nutrient and salt variations. Metabolomics studies revealed four myropeptins, and structural analyses by NMR, HRMS, Marfey's analysis, and ECD assessment for their helical properties established their absolute configuration. A myropeptin biosynthetic gene cluster in the genome was identified. The myropeptins exhibit general nonspecific toxicity against all cancer cell lines in the NCI-60 panel, larval zebrafish with EC50 concentrations of 5-30 μM, and pathogenic bacteria and fungi (MICs of 4-32 μg/mL against multidrug-resistant S. aureus and C. auris). In vitro hemolysis, cell viability, and ionophore assays indicate that the myropeptins target mitochondrial and cellular membranes, inducing cell depolarization and cell death. The toxic activity is modulated by the length of the lipid side chain, which provides valuable insight into their structure-activity relationships.
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Affiliation(s)
- Annika Jagels
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, United States
| | | | - Elizabeth N Kaweesa
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, United States
| | - Mark McCauley
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, United States
| | - Benjamin Philmus
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon 97331, United States
| | - James A Strother
- Department of Biology, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, United States
| | - Sandra Loesgen
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, Florida 32080, United States
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17
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Schultz J, Modolon F, Peixoto RS, Rosado AS. Shedding light on the composition of extreme microbial dark matter: alternative approaches for culturing extremophiles. Front Microbiol 2023; 14:1167718. [PMID: 37333658 PMCID: PMC10272570 DOI: 10.3389/fmicb.2023.1167718] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/09/2023] [Indexed: 06/20/2023] Open
Abstract
More than 20,000 species of prokaryotes (less than 1% of the estimated number of Earth's microbial species) have been described thus far. However, the vast majority of microbes that inhabit extreme environments remain uncultured and this group is termed "microbial dark matter." Little is known regarding the ecological functions and biotechnological potential of these underexplored extremophiles, thus representing a vast untapped and uncharacterized biological resource. Advances in microbial cultivation approaches are key for a detailed and comprehensive characterization of the roles of these microbes in shaping the environment and, ultimately, for their biotechnological exploitation, such as for extremophile-derived bioproducts (extremozymes, secondary metabolites, CRISPR Cas systems, and pigments, among others), astrobiology, and space exploration. Additional efforts to enhance culturable diversity are required due to the challenges imposed by extreme culturing and plating conditions. In this review, we summarize methods and technologies used to recover the microbial diversity of extreme environments, while discussing the advantages and disadvantages associated with each of these approaches. Additionally, this review describes alternative culturing strategies to retrieve novel taxa with their unknown genes, metabolisms, and ecological roles, with the ultimate goal of increasing the yields of more efficient bio-based products. This review thus summarizes the strategies used to unveil the hidden diversity of the microbiome of extreme environments and discusses the directions for future studies of microbial dark matter and its potential applications in biotechnology and astrobiology.
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Affiliation(s)
- Júnia Schultz
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Flúvio Modolon
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Raquel Silva Peixoto
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Alexandre Soares Rosado
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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18
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Gasparek M, Steel H, Papachristodoulou A. Deciphering mechanisms of production of natural compounds using inducer-producer microbial consortia. Biotechnol Adv 2023; 64:108117. [PMID: 36813010 DOI: 10.1016/j.biotechadv.2023.108117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/22/2023]
Abstract
Living organisms produce a wide range of metabolites. Because of their potential antibacterial, antifungal, antiviral, or cytostatic properties, such natural molecules are of high interest to the pharmaceutical industry. In nature, these metabolites are often synthesized via secondary metabolic biosynthetic gene clusters that are silent under the typical culturing conditions. Among different techniques used to activate these silent gene clusters, co-culturing of "producer" species with specific "inducer" microbes is a particularly appealing approach due to its simplicity. Although several "inducer-producer" microbial consortia have been reported in the literature and hundreds of different secondary metabolites with attractive biopharmaceutical properties have been described as a result of co-cultivating inducer-producer consortia, less attention has been devoted to the understanding of the mechanisms and possible means of induction for production of secondary metabolites in co-cultures. This lack of understanding of fundamental biological functions and inter-species interactions significantly limits the diversity and yield of valuable compounds using biological engineering tools. In this review, we summarize and categorize the known physiological mechanisms of production of secondary metabolites in inducer-producer consortia, and then discuss approaches that could be exploited to optimize the discovery and production of secondary metabolites.
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Affiliation(s)
- Miroslav Gasparek
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom.
| | - Harrison Steel
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
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19
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Mohamed NZ, Shaban L, Safan S, El-Sayed ASA. Physiological and metabolic traits of Taxol biosynthesis of endophytic fungi inhabiting plants: Plant-microbial crosstalk, and epigenetic regulators. Microbiol Res 2023; 272:127385. [PMID: 37141853 DOI: 10.1016/j.micres.2023.127385] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/08/2023] [Accepted: 04/09/2023] [Indexed: 05/06/2023]
Abstract
Attenuating the Taxol productivity of fungi with the subculturing and storage under axenic conditions is the challenge that halts the feasibility of fungi to be an industrial platform for Taxol production. This successive weakening of Taxol productivity by fungi could be attributed to the epigenetic down-regulation and molecular silencing of most of the gene clusters encoding Taxol biosynthetic enzymes. Thus, exploring the epigenetic regulating mechanisms controlling the molecular machinery of Taxol biosynthesis could be an alternative prospective technology to conquer the lower accessibility of Taxol by the potent fungi. The current review focuses on discussing the different molecular approaches, epigenetic regulators, transcriptional factors, metabolic manipulators, microbial communications and microbial cross-talking approaches on restoring and enhancing the Taxol biosynthetic potency of fungi to be industrial platform for Taxol production.
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Affiliation(s)
- Nabil Z Mohamed
- Enzymology and Fungal Biotechnology Lab, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt
| | - Lamis Shaban
- Enzymology and Fungal Biotechnology Lab, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt.
| | - Samia Safan
- Enzymology and Fungal Biotechnology Lab, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt
| | - Ashraf S A El-Sayed
- Enzymology and Fungal Biotechnology Lab, Botany and Microbiology Department, Faculty of Science, Zagazig University, Zagazig 44519, Egypt.
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20
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Müller M, Spiers AJ, Tan A, Mujahid A. Investigating quorum-quenching marine bacilli as potential biocontrol agents for protection of shrimps against Early Mortality Syndrome (EMS). Sci Rep 2023; 13:4095. [PMID: 36907954 PMCID: PMC10008827 DOI: 10.1038/s41598-023-31197-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 03/07/2023] [Indexed: 03/14/2023] Open
Abstract
Early Mortality Syndrome (EMS) has been a major problem for shrimp aquaculture in Southeast Asia due to its epizootic prevalence within the region since the first reported case in 2009. This study explores the application of halophilic marine bacilli isolated from coral mucus and their quorum-quenching abilities as potential biocontrol agents in aquaculture systems to combat the causative agent of EMS, Vibrio parahaemolyticus. N-acylhomoserine lactone (AHL)-degrading (AiiA) activity was first screened by PCR then confirmed by bio-reporter assay, and a combination of 16S rDNA sequence analysis and quantitative phenotype assays including biofilm-formation and temperature-growth responses were used to demonstrate diversity amongst these quorum-quenching isolates. Three phenotypically distinct strains showing notable potential were chosen to undergo co-cultivation as a method for strain improvement via long term exposure to the pathogenic V. parahaemolyticus. The novel approach taken led to significant improvements in antagonism and quorum quenching activities as compared to the ancestral wild-type strains and offers a potential solution as well as pathway to improve existing beneficial microbes for one of the most pressing issues in shrimp aquacultures worldwide.
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Affiliation(s)
- Moritz Müller
- Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak, 93350, Kuching, Malaysia.
| | - Andrew J Spiers
- School of Science, Engineering and Technology, Abertay University, Dundee, DD1 1HG, UK
| | - Angelica Tan
- Faculty of Engineering, Computing and Science, Swinburne University of Technology Sarawak, 93350, Kuching, Malaysia
| | - Aazani Mujahid
- Institute of Biodiversity and Environmental Conservation (IBEC), Universiti Malaysia Sarawak, 93400, Kota Samarahan, Sarawak, Malaysia
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21
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The Potential Use of Fungal Co-Culture Strategy for Discovery of New Secondary Metabolites. Microorganisms 2023; 11:microorganisms11020464. [PMID: 36838429 PMCID: PMC9965835 DOI: 10.3390/microorganisms11020464] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Fungi are an important and prolific source of secondary metabolites (SMs) with diverse chemical structures and a wide array of biological properties. In the past two decades, however, the number of new fungal SMs by traditional monoculture method had been greatly decreasing. Fortunately, a growing number of studies have shown that co-culture strategy is an effective approach to awakening silent SM biosynthetic gene clusters (BGCs) in fungal strains to produce cryptic SMs. To enrich our knowledge of this approach and better exploit fungal biosynthetic potential for new drug discovery, this review comprehensively summarizes all fungal co-culture methods and their derived new SMs as well as bioactivities on the basis of an extensive literature search and data analysis. Future perspective on fungal co-culture study, as well as its interaction mechanism, is supplied.
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Selegato DM, Castro-Gamboa I. Enhancing chemical and biological diversity by co-cultivation. Front Microbiol 2023; 14:1117559. [PMID: 36819067 PMCID: PMC9928954 DOI: 10.3389/fmicb.2023.1117559] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023] Open
Abstract
In natural product research, microbial metabolites have tremendous potential to provide new therapeutic agents since extremely diverse chemical structures can be found in the nearly infinite microbial population. Conventionally, these specialized metabolites are screened by single-strain cultures. However, owing to the lack of biotic and abiotic interactions in monocultures, the growth conditions are significantly different from those encountered in a natural environment and result in less diversity and the frequent re-isolation of known compounds. In the last decade, several methods have been developed to eventually understand the physiological conditions under which cryptic microbial genes are activated in an attempt to stimulate their biosynthesis and elicit the production of hitherto unexpressed chemical diversity. Among those, co-cultivation is one of the most efficient ways to induce silenced pathways, mimicking the competitive microbial environment for the production and holistic regulation of metabolites, and has become a golden methodology for metabolome expansion. It does not require previous knowledge of the signaling mechanism and genome nor any special equipment for cultivation and data interpretation. Several reviews have shown the potential of co-cultivation to produce new biologically active leads. However, only a few studies have detailed experimental, analytical, and microbiological strategies for efficiently inducing bioactive molecules by co-culture. Therefore, we reviewed studies applying co-culture to induce secondary metabolite pathways to provide insights into experimental variables compatible with high-throughput analytical procedures. Mixed-fermentation publications from 1978 to 2022 were assessed regarding types of co-culture set-ups, metabolic induction, and interaction effects.
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Munusamy M, Tan K, Nge CE, Gakuubi MM, Crasta S, Kanagasundaram Y, Ng SB. Diversity and Biosynthetic Potential of Fungi Isolated from St. John's Island, Singapore. Int J Mol Sci 2023; 24:ijms24021033. [PMID: 36674548 PMCID: PMC9861175 DOI: 10.3390/ijms24021033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/01/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Adaptation to a wide variety of habitats allows fungi to develop unique abilities to produce diverse secondary metabolites with diverse bioactivities. In this study, 30 Ascomycetes fungi isolated from St. John's Island, Singapore were investigated for their general biosynthetic potential and their ability to produce antimicrobial secondary metabolites (SMs). All the 30 fungal isolates belong to the Phylum Ascomycota and are distributed into 6 orders and 18 genera with Order Hypocreales having the highest number of representative (37%). Screening for polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes using degenerate PCR led to the identification of 23 polyketide synthases (PKSs) and 5 nonribosomal peptide synthetases (NRPSs) grouped into nine distinct clades based on their reduction capabilities. Some of the identified PKSs genes share high similarities between species and known reference genes, suggesting the possibility of conserved biosynthesis of closely related compounds from different fungi. Fungal extracts were tested for their antimicrobial activity against S. aureus, Methicillin-resistant S. aureus (MRSA), and Candida albicans. Bioassay-guided fractionation of the active constituents from two promising isolates resulted in the isolation of seven compounds: Penilumamides A, D, and E from strain F4335 and xanthomegnin, viomellein, pretrichodermamide C and vioxanthin from strain F7180. Vioxanthin exhibited the best antibacterial activity with IC50 values of 3.0 μM and 1.6 μM against S. aureus and MRSA respectively. Viomellein revealed weak antiproliferative activity against A549 cells with an IC50 of 42 μM. The results from this study give valuable insights into the diversity and biosynthetic potential of fungi from this unique habitat and forms a background for an in-depth analysis of the biosynthetic capability of selected strains of interest with the aim of discovering novel fungal natural products.
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Affiliation(s)
- Madhaiyan Munusamy
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Kenneth Tan
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Choy Eng Nge
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Martin Muthee Gakuubi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Sharon Crasta
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore
- Correspondence:
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Havryliuk O, Hovorukha V, Bida I, Gladka G, Tymoshenko A, Kyrylov S, Mariychuk R, Tashyrev O. Anaerobic Degradation of the Invasive Weed Solidago canadensis L. ( goldenrod) and Copper Immobilization by a Community of Sulfate-Reducing and Methane-Producing Bacteria. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12010198. [PMID: 36616327 PMCID: PMC9824853 DOI: 10.3390/plants12010198] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/12/2022] [Accepted: 12/23/2022] [Indexed: 06/01/2023]
Abstract
The weed Solidago canadensis L. poses a global threat to the environment as it spreads uncontrollably on roadsides, in forests, fields, meadows, and farmland. Goldenrod emits toxic substances that suppress other plants on the site, displacing wild ones. Thus, goldenrod conquers huge areas very quickly. The use of herbicides and mechanical methods does not solve the problem of the spontaneous spread of goldenrod. On the other hand, many scientists consider goldenrod as a valuable source of biologically active substances: flavonoids, phenolic compounds, vitamins, etc. In this study, we consider Solidago plants as a promising, free (cheap), and renewable substrate for the production of methane gas. The goal of the study was to identify the main patterns of degradation of the Solidago canadensis L. plant by methane-producing and sulfate-reducing bacteria with methane gas production and simultaneous detoxification of toxic copper. The composition of the gas phase was monitored by gas chromatography. The pH and redox potential parameters were determined potentiometrically; metal concentrations were measured by photometry. The concentration of flavonoids, sugars and phenolic compounds in plant biomass was determined according to well-known protocols. As a result of the study, high efficiencies of methane degradation in the Solidago plant and copper detoxification were obtained. Methane yield has reached the value of 68.2 L kg-1 TS of Solidago canadensis L. biomass. The degradation coefficient (Kd) was also high at 21.4. The Cu(II) was effectively immobilized by methanogens and sulfate reducers during the goldenrod degradation at the initial concentrations of 500 mg L-1. Thus, a new method of beneficial application of invasive plants was presented. The result confirms the possibility of using methanogenic microorganisms to produce methane gas from invasive weeds and detoxification of toxic metals.
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Affiliation(s)
- Olesia Havryliuk
- Department of Extremophilic Microorganisms Biology, Zabolotny Institute of Microbiology and Virology of the National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Vira Hovorukha
- Department of Extremophilic Microorganisms Biology, Zabolotny Institute of Microbiology and Virology of the National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Iryna Bida
- Department of Extremophilic Microorganisms Biology, Zabolotny Institute of Microbiology and Virology of the National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Galyna Gladka
- Department of Extremophilic Microorganisms Biology, Zabolotny Institute of Microbiology and Virology of the National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Artem Tymoshenko
- Department of Biotechnology, Faculty of Environmental Safety, Engineering and Technologies, National Aviation University, 03058 Kyiv, Ukraine
| | - Semen Kyrylov
- Department of Biotechnology, Faculty of Environmental Safety, Engineering and Technologies, National Aviation University, 03058 Kyiv, Ukraine
| | - Ruslan Mariychuk
- Department of Ecology, Faculty of Humanities and Natural Sciences, Presov Universityin Presov, 08116 Presov, Slovakia
| | - Oleksandr Tashyrev
- Department of Extremophilic Microorganisms Biology, Zabolotny Institute of Microbiology and Virology of the National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
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Exploring Potential of Aspergillus sclerotiorum: Secondary Metabolites and Biotechnological Relevance. Mycol Prog 2023. [DOI: 10.1007/s11557-022-01856-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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26
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González-Salazar LA, Quezada M, Rodríguez-Orduña L, Ramos-Aboites H, Capon RJ, Souza-Saldívar V, Barona-Gomez F, Licona-Cassani C. Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments. Microb Genom 2023; 9:mgen000921. [PMID: 36748531 PMCID: PMC9973853 DOI: 10.1099/mgen.0.000921] [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] [Indexed: 01/21/2023] Open
Abstract
Calculations predict that testing of 5 000-10 000 molecules and >1 billion US dollars (£0.8 billion, £1=$1.2) are required for one single drug to come to the market. A solution to this problem is to establish more efficient protocols that reduce the high rate of re-isolation and continuous rediscovery of natural products during early stages of the drug development process. The study of 'rare actinobacteria' has emerged as a possible approach for increasing the discovery rate of drug leads from natural sources. Here, we define a simple genomic metric, defined as biosynthetic novelty index (BiNI), that can be used to rapidly rank strains according to the novelty of the subset of encoding biosynthetic clusters. By comparing a subset of high-quality genomes from strains of different taxonomic and ecological backgrounds, we used the BiNI score to support the notion that rare actinobacteria encode more biosynthetic gene cluster (BGC) novelty. In addition, we present the isolation and genomic characterization, focused on specialized metabolites and phenotypic screening, of two isolates belonging to genera Lentzea and Actinokineospora from a highly oligotrophic environment. Our results show that both strains harbour a unique subset of BGCs compared to other members of the genera Lentzea and Actinokineospora. These BGCs are responsible for potent antimicrobial and cytotoxic bioactivity. The experimental data and analysis presented in this study contribute to the knowledge of genome mining analysis in rare actinobacteria and, most importantly, can serve to direct sampling efforts to accelerate early stages of the drug discovery pipeline.
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Affiliation(s)
- Luz A González-Salazar
- Industrial Genomics Laboratory, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, Mexico
| | - Michelle Quezada
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lorena Rodríguez-Orduña
- Industrial Genomics Laboratory, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, Mexico
| | - Hilda Ramos-Aboites
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanza (LANGEBIO), Cinvestav-IPN, Irapuato, Mexico
| | - Robert J Capon
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland 4072, Australia
| | - Valeria Souza-Saldívar
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Francisco Barona-Gomez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanza (LANGEBIO), Cinvestav-IPN, Irapuato, Mexico.,Present address: Microbial Diversity and Specialized Metabolism Laboratory, Institute of Biology, Leiden University, Leiden, Netherlands
| | - Cuauhtémoc Licona-Cassani
- Industrial Genomics Laboratory, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, Mexico.,Division of Integrative Biology, Institute for Obesity Research, Tecnológico de Monterrey, Nuevo León, Mexico
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27
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Testing the Biocontrol Ability of a Trichoderma-Streptomycetes Consortium against Pyrrhoderma noxium (Corner) L.W. Zhou and Y.C. Dai in Soil. J Fungi (Basel) 2022; 9:jof9010067. [PMID: 36675888 PMCID: PMC9864159 DOI: 10.3390/jof9010067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/14/2022] [Accepted: 12/14/2022] [Indexed: 01/03/2023] Open
Abstract
The Brown root rot pathogen Pyrrhoderma noxium (Corner) L.W. Zhou and Y.C. Dai is known to infect a large number of culturally and economically important plant species across the world. Although chemical control measures have been effective in managing this pathogen, their adverse effects on the ecosystem have limited their use. The use of biological control agents (BCAs) thus is generally accepted as an environmentally friendly way of managing various pathogens. Testing various consortia of the BCAs with different antagonistic mechanisms may even provide better disease protection than the use of a single BCA against aggressive plant pathogens such as the P. noxium. In the presented study, the wood decay experiment and the pot trial confirmed that the consortium of Trichoderma strains (#5029 and 5001) and streptomycetes (#USC-6914 and #USC-595-B) used was effective in protecting wood decay and plant disease caused by P. noxium. Among the treatments, complete elimination of the pathogen was observed when the BCAs were applied as a consortium. In addition, the BCAs used in this study promoted the plant growth. Therefore, Trichoderma and streptomycetes consortium could be used as a potential biocontrol measure to manage P. noxium infections in the field over the application of hazardous chemical control measures.
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Ntemafack A, Chouhan R, Kapoor N, Kumar A, Dhiman SK, Manhas RS, Chaubey A, Hassan QP, Gandhi SG. Protective effect of Bacillus species associated with Rumex dentatus against postharvest soil borne disease in potato tubers and GC-MS metabolite profile. Arch Microbiol 2022; 204:583. [PMID: 36042050 DOI: 10.1007/s00203-022-03213-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/02/2022] [Accepted: 08/22/2022] [Indexed: 11/02/2022]
Abstract
Potato is constantly exposed to various kinds of phytopathogens which cause diseases during the developmental stage and post-harvest storage. This investigation was designed to assay the anti-phytopathogen activity of bacterial endophytes and their suppressive effects on rot disease in potato. The study also aimed to screen isolates for their plant growth-promoting traits and establish GC-MS-based metabolite profile of the potent isolate. Endophytes were isolated from Rumex dentatus and identified based on 16S rRNA gene. They were screened in dual culture assay against fungal phytopathogens and the potent isolate was tested for its capability to suppress Fusarium rot disease in potato tubers. The mechanism of action of endophytes on the phytopathogens was assessed using scanning electron microcopy. Isolates were also screened in vitro to assay their capability to produce phytohormones, hydrolytic enzymes, and to solubilize phosphates. Endophytic isolates produced proteases with a diameter of halo zone ranging from 7 to 32 mm. Bacillus sp. KL5 exhibited the highest production of indole acetic acid (IAA) with the amount of 104.28 µg/mL and was the most potent antagonist of Fusarium oxysporum and Verticillium dahliae with an inhibitory percentage of 61.53 and 100%, respectively. It showed a reduction of potato rot disease severity by more than 50%. GC-MS of active fractions of KL5 showed the presence of dibutylphthalate and 2,4-di-tert-butylphenol as major metabolites. From this study, it is evident that endophytic Bacillus species from R. dentatus are potent antagonists of F. oxysporum and V. dahliae. Bacillus sp. KL5 is a potent inhibitor of pathogenic F. oxysporum in potato tubers and can be developed as a biocontrol agent.
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Affiliation(s)
- Augustin Ntemafack
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.,Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Rekha Chouhan
- Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.,Guru Nanak Dev University, Amritsar, India
| | - Nitika Kapoor
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.,Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Amit Kumar
- Instrumentation Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Shakti Kumar Dhiman
- Instrumentation Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Ravi Singh Manhas
- Fermentation Technology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Asha Chaubey
- Fermentation Technology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India
| | - Qazi Parvaiz Hassan
- Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Sanat Nagar, Srinagar, India.
| | - Sumit G Gandhi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India. .,Plant Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, India.
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Abstract
The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and in situ diffusion devices) that could be applied to retrieve the CAM "dark matter" (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics.
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30
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Zahroh EW, Ningsih F, Sjamsuridzal W. DETECTION OF ANTIMICROBIAL COMPOUNDS FROM THERMOPHILIC ACTINOMYCETES USING ONE STRAIN MANY COMPOUNDS (OSMAC) APPROACH. BIOLINK (JURNAL BIOLOGI LINGKUNGAN INDUSTRI KESEHATAN) 2022. [DOI: 10.31289/biolink.v9i1.6438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Actinomycetes are a group of filamentous bacteria with high biosynthetic potential that can produce secondary metabolites. Actinomycetes are known to produce secondary metabolites which are potential as antimicrobial, antitumor, and others. Actinomycetes can be found abundantly in diverse environments, including environments with extremely high temperatures such as hot springs, deserts, geothermal areas, and hydrothermal vents. They can survive in high temperatures due to their membrane lipids containing straight-chains and more saturated fatty acids that protect the membrane's fluidity to maintain membrane function. Thermophilic actinomycetes are potential producers of thermostable enzymes and bioactive compounds, which are important in the pharmaceutical, health, and industrial fields. Thermophilic actinomycetes are still less explored for novel metabolites and antimicrobial compounds due to the difficulty in isolation, maintenance, and preservation in pure culture. Novel bioactive compounds produced by actinomycetes are conventionally discovered by isolating potential strains and screening the compound bioactivity through various bioassays. A sequence-independent approach, termed the OSMAC (one strain many compounds), has been widely used in natural product research for activating cryptic biosynthetic gene clusters (BGCs) by modifying the growth conditions of a bacterial culture. This approach aims to optimize the number of secondary metabolites produced by one single microorganism. The application of the OSMAC method has been proven successful in revealing the biosynthetic potential of bacteria.
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Li J, Zhang L, Yao G, Zhu L, Lin J, Wang C, Du B, Ding Y, Mei X. Synergistic effect of co-culture rhizosphere Streptomyces: A promising strategy to enhance antimicrobial activity and plant growth-promoting function. Front Microbiol 2022; 13:976484. [PMID: 36033877 PMCID: PMC9403869 DOI: 10.3389/fmicb.2022.976484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
Rhizosphere Streptomyces is one of the important types of rhizosphere microorganisms that plays an important role in promoting plant growth and controlling plant diseases to maintain agricultural ecosystem balance and green ecological agriculture development as beneficial bacteria. Microbial co-culture simulates the complex biocommunity in nature, which has more advantages than the monoculture with a synergistic effect. As the key signal mediums of microorganisms, plants, and their interactions, microbial metabolites are of great significance in revealing their functional mechanism. In this study, two potential plant growth-promoting rhizobacteria, Streptomyces albireticuli MDJK11, and Streptomyces alboflavus MDJK44, were selected to explore the effects of co-culture and monoculture on plant growth promotion and disease prevention, and the metabolic material basis was analyzed by metabonomics. Results showed that Streptomyces MDJK11, MDJK44 monoculture, and co-culture condition all showed good growth promoting and antimicrobial effects. Moreover, as compared to the monoculture, the co-culture showed the advantage of a synergistic enhancement effect. LC-MS-based metabonomics analysis showed the metabolic material bases of Streptomyces for plant growth promotion and disease prevention were mainly plant hormone and antibiotics and the co-culture condition could significantly stimulate the production of plant hormone promoters and macrolide, cyclic peptide, and aminoglycoside antibiotics. The study proved that the co-cultures of S. albireticuli MDJK11 and S. alboflavus MDJK44 have great potential in crop growth promotion and disease prevention.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Lin Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Gan Yao
- College of life sciences, Shandong Agricultural University, Tai’an, China
| | - Lixiang Zhu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Jingling Lin
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
| | - Chengqiang Wang
- College of life sciences, Shandong Agricultural University, Tai’an, China
| | - Binghai Du
- College of life sciences, Shandong Agricultural University, Tai’an, China
| | - Yanqin Ding
- College of life sciences, Shandong Agricultural University, Tai’an, China
- *Correspondence: Yanqin Ding,
| | - Xiangui Mei
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai’an, China
- Xiangui Mei,
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Mohamed H, Awad MF, Shah AM, Sadaqat B, Nazir Y, Naz T, Yang W, Song Y. Coculturing of Mucor plumbeus and Bacillus subtilis bacterium as an efficient fermentation strategy to enhance fungal lipid and gamma-linolenic acid (GLA) production. Sci Rep 2022; 12:13111. [PMID: 35908106 PMCID: PMC9338991 DOI: 10.1038/s41598-022-17442-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 07/25/2022] [Indexed: 11/29/2022] Open
Abstract
This study aimed to improve lipid and gamma-linolenic acid (GLA) production of an oleaginous fungus, Mucor plumbeus, through coculturing with Bacillus subtilis bacteria, optimising the environmental and nutritional culture conditions, and scaling them for batch fermentation. The maximum levels of biomass, lipid, fatty acid, and GLA in a 5 L bioreactor containing cellobiose and ammonium sulfate as the optimal carbon and nitrogen sources, respectively, achieved during the coculturing processes were 14.5 ± 0.4 g/L, 41.5 ± 1.3, 24 ± 0.8, and 20 ± 0.5%, respectively. This strategy uses cellobiose in place of glucose, decreasing production costs. The nutritional and abiotic factor results suggest that the highest production efficiency is achieved at 6.5 pH, 30 °C temperature, 10% (v/v) inoculum composition, 200 rpm agitation speed, and a 5-day incubation period. Interestingly, the GLA concentration of cocultures (20.0 ± 0.5%) was twofold higher than that of monocultures (8.27 ± 0.11%). More importantly, the GC chromatograms of cocultures indicated the presence of one additional peak corresponding to decanoic acid (5.32 ± 0.20%) that is absent in monocultures, indicating activation of silent gene clusters via cocultivation with bacteria. This study is the first to show that coculturing of Mucor plumbeus with Bacillus subtilis is a promising strategy with industrialisation potential for the production of GLA-rich microbial lipids and prospective biosynthesis of new products.
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Affiliation(s)
- Hassan Mohamed
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255000, China. .,Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut, 71524, Egypt.
| | - Mohamed F Awad
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Assiut, 71524, Egypt.,Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Aabid Manzoor Shah
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255000, China
| | - Beenish Sadaqat
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255000, China
| | - Yusuf Nazir
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255000, China.,Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Tahira Naz
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255000, China
| | - Wu Yang
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255000, China
| | - Yuanda Song
- Colin Ratledge Center of Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255000, China.
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Cui D, Kong L, Wang Y, Zhu Y, Zhang C. In situ identification of environmental microorganisms with Raman spectroscopy. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2022; 11:100187. [PMID: 36158754 PMCID: PMC9488013 DOI: 10.1016/j.ese.2022.100187] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/13/2022] [Accepted: 05/15/2022] [Indexed: 05/28/2023]
Abstract
Microorganisms in natural environments are crucial in maintaining the material and energy cycle and the ecological balance of the environment. However, it is challenging to delineate environmental microbes' actual metabolic pathways and intraspecific heterogeneity because most microorganisms cannot be cultivated. Raman spectroscopy is a culture-independent technique that can collect molecular vibration profiles from cells. It can reveal the physiological and biochemical information at the single-cell level rapidly and non-destructively in situ. The first part of this review introduces the principles, advantages, progress, and analytical methods of Raman spectroscopy applied in environmental microbiology. The second part summarizes the applications of Raman spectroscopy combined with stable isotope probing (SIP), fluorescence in situ hybridization (FISH), Raman-activated cell sorting and genomic sequencing, and machine learning in microbiological studies. Finally, this review discusses expectations of Raman spectroscopy and future advances to be made in identifying microorganisms, especially for uncultured microorganisms.
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Affiliation(s)
- Dongyu Cui
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Lingchao Kong
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science & Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yi Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuanqing Zhu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, 200062, China
| | - Chuanlun Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, University of Southern University of Science and Technology, Shenzhen, 518055, China
- Shanghai Sheshan National Geophysical Observatory, Shanghai Earthquake Agency, Shanghai, 200062, China
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Pira H, Risdian C, Müsken M, Schupp PJ, Wink J. Photobacterium arenosum WH24, Isolated from the Gill of Pacific Oyster Crassostrea gigas from the North Sea of Germany: Co-cultivation and Prediction of Virulence. Curr Microbiol 2022; 79:219. [PMID: 35704100 PMCID: PMC9200695 DOI: 10.1007/s00284-022-02909-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 05/20/2022] [Indexed: 11/28/2022]
Abstract
Cream colored bacteria from marine agar, strain WH24, WH77, and WH80 were isolated from the gill of the Crassostrea gigas a Pacific oyster with a filter-feeding habit that compels accompanying bacteria to demonstrate a high metabolic capacity, has proven able to colonize locations with changing circumstances. Based on the 16S rRNA gene sequence, all strains had high similarity to Photobacterium arenosum CAU 1568T (99.72%). This study involved phenotypic traits, phylogenetic analysis, antimicrobial activity evaluation, genome mining, Co-cultivation experiments, and chemical studies of crude extracts using HPLC and LC-HRESIMS. Photobacterium arenosum WH24 and Zooshikella harenae WH53Twere co-cultivated for 3 days in a rotary shaker at 160 rpm at 30 °C, and LC-MS monitored the chemical profiles of the co-cultures on the third day. The UV chromatograms of the extracts of the co-cultivation experiments show that Zooshikella harenae WH53T could be inhibited by strain WH24. The high virulence of Photobacterium arenosum WH24 was confirmed by genome analysis. Gene groups with high virulence potential were detected: tssA (ImpA), tssB (ImpB/vipA), tssC (ImpC/vipB), tssE, tssF (ImpG/vasA), tssG (ImpH/vasB), tssM (IcmF/vasK), tssJ (vasD), tssK (ImpJ/vasE), tssL (ImpK/vasF), clpV (tssH), vasH, hcp, lapP, plpD, and tpsB family.
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Affiliation(s)
- Hani Pira
- Microbial Strain Collection (MISG), Helmholtz Centre for Infection Research (HZI), 38124, Brunswick, Germany
| | - Chandra Risdian
- Microbial Strain Collection (MISG), Helmholtz Centre for Infection Research (HZI), 38124, Brunswick, Germany
- Research Unit for Clean Technology, National Research and Innovation Agency (BRIN), Bandung, 40135, Indonesia
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Centre for Infection Research (HZI), 38124, Brunswick, Germany
| | - Peter J Schupp
- Institute for Chemistry and Biology of the Marine Environment, University Oldenburg, Oldenburg, Germany
| | - Joachim Wink
- Microbial Strain Collection (MISG), Helmholtz Centre for Infection Research (HZI), 38124, Brunswick, Germany.
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Lu Q, Jia L, Awasthi MK, Jing G, Wang Y, He L, Zhao N, Chen Z, Zhang Z, Shi X. Variations in lignin monomer contents and stable hydrogen isotope ratios in methoxy groups during the biodegradation of garden biomass. Sci Rep 2022; 12:8734. [PMID: 35610354 PMCID: PMC9130509 DOI: 10.1038/s41598-022-12689-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Lignin, a highly polymerized organic component of plant cells, is one of the most difficult aromatic substances to degrade. Selective biodegradation under mild conditions is a promising method, but the dynamic variations in lignin monomers during the biodegradation of lignocellulose are not fully understood. In this study, we evaluated the differences in lignin degradation under different microbial inoculation based on the lignin monomer content, monomer ratio, and stable hydrogen isotope ratio of lignin methoxy groups (δ2HLM). The weight loss during degradation and the net loss of lignocellulosic components improved dramatically with fungal inoculation. Syringyl monolignol (S-lignin), which contains two methoxy groups, was more difficult to degrade than guaiacyl (G-lignin), which contains only one methoxy group. The co-culture of Pseudomonas mandelii and Aspergillus fumigatus produced the greatest decrease in the G/S ratio, but δ2HLM values did not differ significantly among the three biodegradation experiments, although the enrichment was done within the fungal inoculation. The fluctuation of δ2HLM values during the initial phase of biodegradation may be related to the loss of pectic polysaccharides (another methoxy donor), which mainly originate from fallen leaves. Overall, the relative δ2HLM signals were preserved despite decreasing G/S ratios in the three degradation systems. Nevertheless, some details of lignin δ2HLM as a biomarker for biogeochemical cycles need to be explored further.
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Affiliation(s)
- Qiangqiang Lu
- Key Laboratory of Soil Resource and Biotech Applications, Shaanxi Academy of Sciences, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), No.17, Cuihua South Road, Xi'an, 710061, China
- School of Geography and Tourism, Shaanxi Normal University, Xi'an, 710119, China
| | - Lili Jia
- College of Forestry, Northwest A&F University, Yangling, 712100, China
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Guanghua Jing
- Key Laboratory of Soil Resource and Biotech Applications, Shaanxi Academy of Sciences, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), No.17, Cuihua South Road, Xi'an, 710061, China
| | - Yabo Wang
- School of Geography and Tourism, Shaanxi Normal University, Xi'an, 710119, China
| | - Liyan He
- Key Laboratory of Soil Resource and Biotech Applications, Shaanxi Academy of Sciences, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), No.17, Cuihua South Road, Xi'an, 710061, China
| | - Ning Zhao
- Key Laboratory of Soil Resource and Biotech Applications, Shaanxi Academy of Sciences, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), No.17, Cuihua South Road, Xi'an, 710061, China
| | - Zhikun Chen
- Key Laboratory of Soil Resource and Biotech Applications, Shaanxi Academy of Sciences, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), No.17, Cuihua South Road, Xi'an, 710061, China
| | - Zhao Zhang
- Key Laboratory of Soil Resource and Biotech Applications, Shaanxi Academy of Sciences, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), No.17, Cuihua South Road, Xi'an, 710061, China
| | - Xinwei Shi
- Key Laboratory of Soil Resource and Biotech Applications, Shaanxi Academy of Sciences, Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), No.17, Cuihua South Road, Xi'an, 710061, China.
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Fifani B, Steels S, Helmus C, Delacuvellerie A, Deracinois B, Phalip V, Delvigne F, Jacques P. Coculture of Trichoderma harzianum and Bacillus velezensis Based on Metabolic Cross-Feeding Modulates Lipopeptide Production. Microorganisms 2022; 10:microorganisms10051059. [PMID: 35630500 PMCID: PMC9148127 DOI: 10.3390/microorganisms10051059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 01/27/2023] Open
Abstract
Cocultures have been widely explored for their use in deciphering microbial interaction and its impact on the metabolisms of the interacting microorganisms. In this work, we investigate, in different liquid coculture conditions, the compatibility of two microorganisms with the potential for the biocontrol of plant diseases: the fungus Trichoderma harzianum IHEM5437 and the bacterium Bacillus velezensis GA1 (a strong antifungal lipopeptide producing strain). While the Bacillus overgrew the Trichoderma in a rich medium due to its antifungal lipopeptide production, a drastically different trend was observed in a medium in which a nitrogen nutritional dependency was imposed. Indeed, in this minimum medium containing nitrate as the sole nitrogen source, cooperation between the bacterium and the fungus was established. This is reflected by the growth of both species as well as the inhibition of the expression of Bacillus genes encoding lipopeptide synthetases. Interestingly, the growth of the bacterium in the minimum medium was enabled by the amendment of the culture by the fungal supernatant, which, in this case, ensures a high production yield of lipopeptides. These results highlight, for the first time, that Trichoderma harzianum and Bacillus velezensis are able, in specific environmental conditions, to adapt their metabolisms in order to grow together.
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Affiliation(s)
- Barbara Fifani
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, ICV—Charles Viollette Institute, 59000 Lille, France; (B.D.); (V.P.)
| | - Sebastien Steels
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
| | - Catherine Helmus
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
| | | | - Barbara Deracinois
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, ICV—Charles Viollette Institute, 59000 Lille, France; (B.D.); (V.P.)
| | - Vincent Phalip
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, ICV—Charles Viollette Institute, 59000 Lille, France; (B.D.); (V.P.)
| | - Frank Delvigne
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
| | - Philippe Jacques
- UMR Transfrontalière BioEcoAgro No 1158, University Lille, INRAE, University Liège, UPJV, YNCREA, University Artois, University Littoral Côte d’Opale, TERRA—Teaching and Research Centre, Gembloux Agro-Bio Tech, University Liège, 5030 Gembloux, Belgium; (B.F.); (S.S.); (C.H.); (F.D.)
- Correspondence:
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Wang Y, Glukhov E, He Y, Liu Y, Zhou L, Ma X, Hu X, Hong P, Gerwick WH, Zhang Y. Secondary Metabolite Variation and Bioactivities of Two Marine Aspergillus Strains in Static Co-Culture Investigated by Molecular Network Analysis and Multiple Database Mining Based on LC-PDA-MS/MS. Antibiotics (Basel) 2022; 11:antibiotics11040513. [PMID: 35453264 PMCID: PMC9031932 DOI: 10.3390/antibiotics11040513] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/30/2022] [Accepted: 04/06/2022] [Indexed: 12/11/2022] Open
Abstract
Co-culture is known as an efficient way to explore the metabolic potential of fungal strains for new antibiotics and other therapeutic agents that could counter emerging health issues. To study the effect of co-culture on the secondary metabolites and bioactivities of two marine strains, Aspergillus terreus C23-3 and Aspergillus. unguis DLEP2008001, they were co-cultured in live or inactivated forms successively or simultaneously. The mycelial morphology and high-performance thin layer chromatography (HPTLC) including bioautography of the fermentation extracts were recorded. Furthermore, the agar cup-plate method was used to compare the antimicrobial activity of the extracts. Based on the above, liquid chromatography-photodiode array-tandem mass spectrometry (LC-PDA-MS/MS) together with Global Natural Products Social molecular networking (GNPS) and multiple natural products database mining were used to further analyze their secondary metabolite variations. The comprehensive results showed the following trends: (1) The strain first inoculated will strongly inhibit the growth and metabolism of the latter inoculated one; (2) Autoclaved A. unguis exerted a strong inducing effect on later inoculated A. terreus, while the autoclaved A. terreus showed high stability of its metabolites and still potently suppressed the growth and metabolism of A. unguis; (3) When the two strains are inoculated simultaneously, they both grow and produce metabolites; however, the A. terreus seemed to be more strongly induced by live A. unguis and this inducing effect surpassed that of the autoclaved A. unguis. Under some of the conditions, the extracts showed higher antimicrobial activity than the axenic cultures. Totally, A. unguis was negative in response but potent in stimulating its rival while A. terreus had the opposite effect. Fifteen MS detectable and/or UV active peaks showed different yields in co-cultures vs. the corresponding axenic culture. GNPS analysis assisted by multiple natural products databases mining (PubChem, Dictionary of Natural Products, NPASS, etc.) gave reasonable annotations for some of these peaks, including antimicrobial compounds such as unguisin A, lovastatin, and nidulin. However, some of the peaks were correlated with antagonistic properties and remain as possible novel compounds without mass or UV matching hits from any database. It is intriguing that the two strains both synthesize chemical ‘weapons’ for antagonism, and that these are upregulated when needed in competitive co-culture environment. At the same time, compounds not useful in this antagonistic setting are downregulated in their expression. Some of the natural products produced during antagonism are unknown chlorinated metabolites and deserve further study for their antimicrobial properties. In summary, this study disclosed the different responses of two Aspergillus strains in co-culture, revealed their metabolic variation, and displayed new opportunities for antibiotic discovery.
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Affiliation(s)
- Yuan Wang
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; (E.G.); (Y.H.); (W.H.G.)
| | - Yifan He
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; (E.G.); (Y.H.); (W.H.G.)
| | - Yayue Liu
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Longjian Zhou
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Xiaoxiang Ma
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - Xueqiong Hu
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
| | - Pengzhi Hong
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
| | - William H. Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; (E.G.); (Y.H.); (W.H.G.)
| | - Yi Zhang
- College of Food Science and Technology, Guangdong Ocean University, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Shenzhen Institute of Guangdong Ocean University, Zhanjiang Municipal Key Laboratory of Marine Drugs and Nutrition for Brain Health, Research Institute for Marine Drugs and Nutrition, Guangdong Ocean University, Zhanjiang 524088, China; (Y.W.); (Y.L.); (L.Z.); (X.M.); (X.H.); (P.H.)
- Collaborative Innovation Center of Seafood Deep Processing, Dalian Polytechnic University, Dalian 116034, China
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, and the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; (E.G.); (Y.H.); (W.H.G.)
- Correspondence: or ; Tel.: +86-759-2396046
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Progress Report: Antimicrobial Drug Discovery in the Resistance Era. Pharmaceuticals (Basel) 2022; 15:ph15040413. [PMID: 35455410 PMCID: PMC9030565 DOI: 10.3390/ph15040413] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 02/05/2023] Open
Abstract
Antibiotic resistance continues to be a most serious threat to public health. This situation demands that the scientific community increase their efforts for the discovery of alternative strategies to circumvent the problems associated with conventional small molecule therapeutics. The Global Antimicrobial Resistance and Use Surveillance System (GLASS) Report (published in June 2021) discloses the rapidly increasing number of bacterial infections that are mainly caused by antimicrobial-resistant bacteria. These concerns have initiated various government agencies and other organizations to educate the public regarding the appropriate use of antibiotics. This review discusses a brief highlight on the timeline of antimicrobial drug discovery with a special emphasis on the historical development of antimicrobial resistance. In addition, new antimicrobial targets and approaches, recent developments in drug screening, design, and delivery were covered. This review also discusses the emergence and roles of various antibiotic adjuvants and combination therapies while shedding light on current challenges and future perspectives. Overall, the emergence of resistant microbial strains has challenged drug discovery but their efforts to develop alternative technologies such as nanomaterials seem to be promising for the future.
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Pellicciaro M, Padoan E, Lione G, Celi L, Gonthier P. Pyoluteorin Produced by the Biocontrol Agent Pseudomonas protegens Is Involved in the Inhibition of Heterobasidion Species Present in Europe. Pathogens 2022; 11:pathogens11040391. [PMID: 35456066 PMCID: PMC9027871 DOI: 10.3390/pathogens11040391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 02/01/2023] Open
Abstract
Pseudomonas protegens (strain DSMZ 13134) is a biocontrol agent with promising antagonistic activity hinging on antibiosis against the fungal forest pathogens Heterobasidion spp. Here, by using High-Performance Liquid Chromatography coupled to Mass Spectrometry (HPLC-MS), we assessed whether monocultures of P. protegens (strain DSMZ 13134) produce the three major determinants of biocontrol activity known for the genus Pseudomonas: 2,4-diacetylphloroglucinol (2,4-DAPG), pyoluteorin (PLT), and pyrrolnitrin (PRN). At the tested culture conditions, we observed the production of PLT at concentrations ranging from 0.01 to 10.21 mg/L and 2,4-DAPG at a concentration not exceeding 0.5 mg/L. Variations of culture conditions involving culture medium, incubation temperature, and incubation period had no consistent influence on PLT production by the bacterium. Assays using culture medium amended with PLT at the same concentration of that present in cell-free filtrate of the bacterium, i.e., 3.77 mg/L, previously documented as effective against Heterobasidion spp., showed a remarkable activity of PLT against genotypes of all the four Heterobasidion species present in Europe, including the non-native invasive H. irregulare. However, such antifungal activity decreased over time, and this may be a constraint for using this molecule as a pesticide against Heterobasidion spp. When the bacterium was co-cultured in liquid medium with genotypes of the different Heterobasidion species, an increased production of PLT was observed at 4 °C, suggesting the bacterium may perform better as a PLT producer in field applications under similar environmental conditions, i.e., at low temperatures. Our results demonstrated the role of PLT in the inhibition of Heterobasidion spp., although all lines of evidence suggest that antibiosis does not rely on a single constitutively produced metabolite, but rather on a plethora of secondary metabolites. Findings presented in this study will help to optimize treatments based on Pseudomonas protegens (strain DSMZ 13134) against Heterobasidion spp.
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Caudal F, Tapissier-Bontemps N, Edrada-Ebel RA. Impact of Co-Culture on the Metabolism of Marine Microorganisms. Mar Drugs 2022; 20:md20020153. [PMID: 35200682 PMCID: PMC8879974 DOI: 10.3390/md20020153] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/19/2022] [Accepted: 02/19/2022] [Indexed: 01/21/2023] Open
Abstract
Natural products from plants have been listed for hundreds of years as a source of biologically active molecules. In recent years, the marine environment has demonstrated its ability to provide new structural entities. More than 70% of our planet’s surface is covered by oceans, and with the technical advances in diving and remotely operated vehicles, it is becoming easier to collect samples. Although the risk of rediscovery is significant, the discovery of silent gene clusters and innovative analytical techniques has renewed interest in natural product research. Different strategies have been proposed to activate these silent genes, including co-culture, or mixed fermentation, a cultivation-based approach. This review highlights the potential of co-culture of marine microorganisms to induce the production of new metabolites as well as to increase the yields of respective target metabolites with pharmacological potential, and moreover to indirectly improve the biological activity of a crude extract.
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Affiliation(s)
- Flore Caudal
- Laboratoire Biotechnologie et Chimie Marines, Université Bretagne Sud, EA3884, LBCM, IUEM, CEDEX, 56321 Lorient, France;
| | - Nathalie Tapissier-Bontemps
- CRIOBE, USR3278-EPHE/CNRS/UPVD/PSL, University of Perpignan via Domitia, 52 Avenue Paul Alduy, 66860 Perpignan, France;
- Laboratoire d’Excellence ‘CORAIL’, Moorea 98729, French Polynesia
| | - Ru Angelie Edrada-Ebel
- The Natural Products Metabolomics Group, Strathclyde Institute of Pharmacy and Biomedical Sciences, Faculty of Science, University of Strathclyde, The John Arbuthnott Building, 161 Cathedral Street, Glasgow G4 0RE, UK
- Correspondence:
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Understanding Interaction Patterns within Deep-Sea Microbial Communities and Their Potential Applications. Mar Drugs 2022; 20:md20020108. [PMID: 35200637 PMCID: PMC8874374 DOI: 10.3390/md20020108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 11/17/2022] Open
Abstract
Environmental microbes living in communities engage in complex interspecies interactions that are challenging to decipher. Nevertheless, the interactions provide the basis for shaping community structure and functioning, which is crucial for ecosystem service. In addition, microbial interactions facilitate specific adaptation and ecological evolution processes particularly essential for microbial communities dwelling in resource-limiting habitats, such as the deep oceans. Recent technological and knowledge advancements provide an opportunity for the study of interactions within complex microbial communities, such as those inhabiting deep-sea waters and sediments. The microbial interaction studies provide insights into developing new strategies for biotechnical applications. For example, cooperative microbial interactions drive the degradation of complex organic matter such as chitins and celluloses. Such microbiologically-driven biogeochemical processes stimulate creative designs in many applied sciences. Understanding the interaction processes and mechanisms provides the basis for the development of synthetic communities and consequently the achievement of specific community functions. Microbial community engineering has many application potentials, including the production of novel antibiotics, biofuels, and other valuable chemicals and biomaterials. It can also be developed into biotechniques for waste processing and environmental contaminant bioremediation. This review summarizes our current understanding of the microbial interaction mechanisms and emerging techniques for inferring interactions in deep-sea microbial communities, aiding in future biotechnological and therapeutic applications.
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Sanitá Lima M, Coutinho de Lucas R. Co-cultivation, Co-culture, Mixed Culture, and Microbial Consortium of Fungi: An Understudied Strategy for Biomass Conversion. Front Microbiol 2022; 12:837685. [PMID: 35126339 PMCID: PMC8811191 DOI: 10.3389/fmicb.2021.837685] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 12/29/2021] [Indexed: 11/24/2022] Open
Affiliation(s)
- Matheus Sanitá Lima
- Department of Biology, University of Western Ontario, London, ON, Canada
- *Correspondence: Matheus Sanitá Lima
| | - Rosymar Coutinho de Lucas
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
- Department of Parasitology, Microbiology and Immunology, Institute of Biological Sciences, Federal University of Juiz de Fora, Juiz de Fora, Brazil
- Rosymar Coutinho de Lucas
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Screening of Antimicrobial Activities and Lipopeptide Production of Endophytic Bacteria Isolated from Vetiver Roots. Microorganisms 2022; 10:microorganisms10020209. [PMID: 35208667 PMCID: PMC8876289 DOI: 10.3390/microorganisms10020209] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/11/2022] [Accepted: 01/17/2022] [Indexed: 02/05/2023] Open
Abstract
The exploration of certain microbial resources such as beneficial endophytic microorganisms is considered a promising strategy for the discovery of new antimicrobial compounds for the pharmaceutical industries and agriculture. Thirty-one endophytic bacterial strains affiliated with Bacillus, Janthinobacterium, Yokenella, Enterobacter, Pseudomonas, Serratia, and Microbacterium were previously isolated from vetiver (Chrysopogon zizanioides (L.) Roberty) roots. These endophytes showed antifungal activity against Fusarium graminearum and could be a source of antimicrobial metabolites. In this study, in particular, using high-throughput screening, we analyzed their antagonistic activities and those of their cell-free culture supernatants against three species of Fusarium plant pathogens, a bacterial strain of Escherichia coli, and a yeast strain of Saccharomyces cerevisiae, as well as their capacity to produce lipopeptides. The results showed that the culture supernatants of four strains close to B. subtilis species exhibited antimicrobial activities against Fusarium species and E. coli. Using mass spectrometry analyses, we identified two groups of lipopeptides (surfactins and plipastatins) in their culture supernatants. Whole-genome sequencing confirmed that these bacteria possess NRPS gene clusters for surfactin and plipastatin. In vitro tests confirmed the inhibitory effect of plipastatin alone or in combination with surfactin against the three Fusarium species.
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Bioactive Marine Xanthones: A Review. Mar Drugs 2022; 20:md20010058. [PMID: 35049913 PMCID: PMC8778107 DOI: 10.3390/md20010058] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 12/27/2021] [Accepted: 12/29/2021] [Indexed: 02/08/2023] Open
Abstract
The marine environment is an important source of specialized metabolites with valuable biological activities. Xanthones are a relevant chemical class of specialized metabolites found in this environment due to their structural variety and their biological activities. In this work, a comprehensive literature review of marine xanthones reported up to now was performed. A large number of bioactive xanthone derivatives (169) were identified, and their structures, biological activities, and natural sources were described. To characterize the chemical space occupied by marine-derived xanthones, molecular descriptors were calculated. For the analysis of the molecular descriptors, the xanthone derivatives were grouped into five structural categories (simple, prenylated, O-heterocyclic, complex, and hydroxanthones) and six biological activities (antitumor, antibacterial, antidiabetic, antifungal, antiviral, and miscellaneous). Moreover, the natural product-likeness and the drug-likeness of marine xanthones were also assessed. Marine xanthone derivatives are rewarding bioactive compounds and constitute a promising starting point for the design of other novel bioactive molecules.
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Karuppiah V, Zhixiang L, Liu H, Murugappan V, Kumaran S, Perianaika Anahas AM, Chen J. Co-cultivation of T. asperellum GDFS1009 and B. amyloliquefaciens 1841: Strategy to regulate the production of ligno-cellulolytic enzymes for the lignocellulose biomass degradation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 301:113833. [PMID: 34592667 DOI: 10.1016/j.jenvman.2021.113833] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 08/21/2021] [Accepted: 09/22/2021] [Indexed: 06/13/2023]
Abstract
The influence of fossil fuels on the environment focused on the development of new technology on biofuels. In this situation, lignocellulolytic hydrolysis enzymes such as Cellobiohydrolase, β-Glucosidase, Endoglucanase, cellulase and xylanase have broad applications in the biofuel production. The Trichoderma have used for the production of cellulase and xylanase to hydrolyze the lignocellulose. Hence, in the present study, co-culture has been employed to induce the production of polysaccharide hydrolyzing enzymes under both induction and repression conditions. The enzyme activity and its gene expression were induced by the co-culture of T. asperellum and B. amyloliquefaciens compared to the monoculture. Further, the co-culture upregulated the transcription regulatory genes and downregulated the repressor genes under both repressor and inducer conditions, respectively. The crude enzyme produced by the co-culture and monocultures using the optimized medium containing molasses, cornmeal and rice bran were further used to hydrolyze the pretreated corn Stover, rice straw, and wheat straw. These results indicate that the co-culture of T. asperellum and B. amyloliquefaciens is a promising and inexpensive method to advance the innovation on the continuous production of cellulase and xylanase under different circumstances for the bioconversion of lignocellulosic biomass into glucose for the bio-fuels.
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Affiliation(s)
- Valliappan Karuppiah
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Lu Zhixiang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Hongyi Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Vallikkannu Murugappan
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, PR China
| | - Subramanian Kumaran
- Centre for Drug Discovery and Development, Sathyabama Institute of Science and Technology, Chennai, Tamilnadu, 600119, India
| | | | - Jie Chen
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, PR China; The State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
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Promotion of the Hypocrellin Yield by a Co-Culture of Shiraia bambusicola (GDMCC 60438) with Arthrinium sp. AF-5 Fungus. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7040316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Hypocrellin is a natural 3,10-xylene-4,9-anthracene derivative compound that originates from the stroma of Shiraia bambusicola (S. bambusicola) and Hypocrella bambusae with excellent photobiological activities. Submerged fermentation with the mycelia of S. bambusicola is generally regarded as an ideal technology for hypocrellin production. This study developed a co-cultivation strategy for an obvious promotion of the hypocrellin yield by incubating S. bambusicola (GDMCC 60438) with the endophyte fungus Arthrinium sp. AF-5 isolated from the bamboo tissue. The results indicated that the yield of hypocrellin A (HA) reached a 66.75 mg/g carbon source after an 84-h co-cultivation of the two strains, which was a four-time increase of that by the fermentation only with the S. bambusicola. The microscope observation found that the mycelia of the two strains were intertwined with each other to form the mycelium pellets during the co-cultivation. Moreover, the mycelium pellets of the co-culture showed a contracted and slightly damaged morphology. The addition of H2O2 in the fermentation media could further increase the HA production by 18.31%.
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Hao X, Li S, Ni J, Wang G, Li F, Li Q, Chen S, Shu J, Gan M. Acremopeptaibols A-F, 16-Residue Peptaibols from the Sponge-Derived Acremonium sp. IMB18-086 Cultivated with Heat-Killed Pseudomonas aeruginosa. JOURNAL OF NATURAL PRODUCTS 2021; 84:2990-3000. [PMID: 34781681 DOI: 10.1021/acs.jnatprod.1c00834] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Six new 16-residue peptaibols, acremopeptaibols A-F (1-6), along with five known compounds, were isolated from the cultures of the sponge-associated fungus Acremonium sp. IMB18-086 grown in the presence of the autoclaved bacterium Pseudomonas aeruginosa on solid rice medium. The peptaibol sequences were established based on comprehensive analysis of 1D and 2D NMR spectroscopic data in conjunction with HRESIMS/MS experiments. The configurations of the amino acid residues were determined by advanced Marfey's analysis. Compounds 1-6 feature the lack of the highly conserved Thr6 and Hyp10 residues in comparison with other members of the SF3 subfamily peptaibols. A plausible biosynthetic pathway of compounds 1-6 was proposed on the basis of genomic analysis. Compounds 1, 5, 7, and 10 exhibited significant antimicrobial activity against Staphylococcus aureus, methicillin-resistant S. aureus, Bacillus subtilis, and Candida albicans. Compounds 7-10 showed potent cytotoxicities against the A549 and/or HepG2 cancer cell lines.
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Affiliation(s)
- Xiaomeng Hao
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Shasha Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Jun Ni
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Guiyang Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Fang Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Qin Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
- Key Laboratory of Modern Preparation of Traditional Chinese Medicines, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, People's Republic of China
| | - Shuzhen Chen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
| | - Jicheng Shu
- Key Laboratory of Modern Preparation of Traditional Chinese Medicines, Ministry of Education, Jiangxi University of Traditional Chinese Medicine, Nanchang 330004, People's Republic of China
| | - Maoluo Gan
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People's Republic of China
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Lyu HN, Zhang J, Zhou S, Liu HW, Zhuang WY, Li SM, Yin WB. Heterologous expression of a single fungal HR-PKS leads to the formation of diverse 2-alkenyl-tetrahydropyrans in model fungi. Org Biomol Chem 2021; 19:8377-8383. [PMID: 34528986 DOI: 10.1039/d1ob01501j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
2-Alkenyl-tetrahydropyrans belong to a rare class of natural products that exhibit broad antifungal activities. Their structural instability and rareness in nature have restrained their discovery and drug development. In this study, the heterologous expression of a single highly reducing polyketide synthase (HR-PKS, App1) from Trichoderma applanatum in Aspergillus nidulans leads to the formation of seven 2-alkenyl-tetrahydropyran derivatives including one known compound virensol C (1) and six new compounds (2-7). However, introducing App1 into Saccharomyces cerevisiae resulted in the identification of additional two 2-alkenyl-tetrahydropyrans lacking the hydroxyl or methoxyl group at the C-2 position (8 and 9). The structures of the isolated compounds were elucidated by extensive spectroscopic analysis using NMR and HR-ESI-MS.
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Affiliation(s)
- Hai-Ning Lyu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China. .,Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, People's Republic of China
| | - Jinyu Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China. .,Savaid Medical School, University of Chinese Academy of Sciences, Beijing100049, People's Republic of China
| | - Shuang Zhou
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.
| | - Hong-Wei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.
| | - Wen-Ying Zhuang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Marburg 35037, Germany
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China. .,Savaid Medical School, University of Chinese Academy of Sciences, Beijing100049, People's Republic of China
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Biological activities of a polysaccharide from the coculture of Ganoderma lucidum and Flammulina velutipes mycelia in submerged fermentation. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.06.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Gakuubi MM, Munusamy M, Liang ZX, Ng SB. Fungal Endophytes: A Promising Frontier for Discovery of Novel Bioactive Compounds. J Fungi (Basel) 2021; 7:786. [PMID: 34682208 PMCID: PMC8538612 DOI: 10.3390/jof7100786] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 12/13/2022] Open
Abstract
For years, fungi have served as repositories of bioactive secondary metabolites that form the backbone of many existing drugs. With the global rise in infections associated with antimicrobial resistance, in addition to the growing burden of non-communicable disease, such as cancer, diabetes and cardiovascular ailments, the demand for new drugs that can provide an improved therapeutic outcome has become the utmost priority. The exploration of microbes from understudied and specialized niches is one of the promising ways of discovering promising lead molecules for drug discovery. In recent years, a special class of plant-associated fungi, namely, fungal endophytes, have emerged as an important source of bioactive compounds with unique chemistry and interesting biological activities. The present review focuses on endophytic fungi and their classification, rationale for selection and prioritization of host plants for fungal isolation and examples of strategies that have been adopted to induce the activation of cryptic biosynthetic gene clusters to enhance the biosynthetic potential of fungal endophytes.
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Affiliation(s)
- Martin Muthee Gakuubi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore; (M.M.G.); (M.M.)
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore;
| | - Madhaiyan Munusamy
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore; (M.M.G.); (M.M.)
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore;
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore; (M.M.G.); (M.M.)
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