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Guo L, Xi B, Lu L. Strategies to enhance production of metabolites in microbial co-culture systems. BIORESOURCE TECHNOLOGY 2024; 406:131049. [PMID: 38942211 DOI: 10.1016/j.biortech.2024.131049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/06/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
Increasing evidence shows that microbial synthesis plays an important role in producing high value-added products. However, microbial monoculture generally hampers metabolites production and limits scalability due to the increased metabolic burden on the host strain. In contrast, co-culture is a more flexible approach to improve the environmental adaptability and reduce the overall metabolic burden. The well-defined co-culturing microbial consortia can tap their metabolic potential to obtain yet-to-be discovered and pre-existing metabolites. This review focuses on the use of a co-culture strategy and its underlying mechanisms to enhance the production of products. Notably, the significance of comprehending the microbial interactions, diverse communication modes, genetic information, and modular co-culture involved in co-culture systems were highlighted. Furthermore, it addresses the current challenges and outlines potential future directions for microbial co-culture. This review provides better understanding the diversity and complexity of the interesting interaction and communication to advance the development of co-culture techniques.
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Affiliation(s)
- Lichun Guo
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214122, PR China; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Bingwen Xi
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214122, PR China
| | - Liushen Lu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214122, PR China.
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2
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Zheng Y, Qin S, Xu L, Sang Z, Chen C, Tan J, Huang Y, Li M, Zou Z. Ochrolines A-C, three new indole diketopiperazines from cultures of endophytic fungi Bionectria ochroleuca SLJB-2. Fitoterapia 2024; 173:105809. [PMID: 38168565 DOI: 10.1016/j.fitote.2023.105809] [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: 12/17/2023] [Accepted: 12/29/2023] [Indexed: 01/05/2024]
Abstract
Three new indole diketopiperazines, ochrolines A-C (1-3), along with three known compounds (4-6), were isolated and identified from the EtOAc extract of the solid fermentation of Bionectria ochroleuca SLJB-2. Notably, compound 1 featured a natural rarely-occurring caged skeleton with a 6/5/6/7 heterotetracyclic bridged ring system. The structures including absolute configurations of 1-3 were fully accomplished by extensive spectroscopic analyses, DFT GIAO 13C NMR and electronic circular dichroism (ECD) calculations. The plausible biogenetic pathways of these new indole diketopiperazines were also proposed. Moreover, the cytotoxic activity screening revealed that compound 2 exhibited moderate inhibitory effect against A549 with inhibition rate of 57.44% at the concentration of 50 μM and compound 1 exhibited mild inhibitory activities against A549, Hela and MCF-7.
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Affiliation(s)
- Yuting Zheng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Siyu Qin
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Li Xu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Zihuan Sang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Chen Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Jianbing Tan
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China
| | - Yuantao Huang
- Affiliated Haikou Hospital of Xiangya School of Medicine, Central South University, Haikou 570100, China
| | - Meifang Li
- Affiliated Haikou Hospital of Xiangya School of Medicine, Central South University, Haikou 570100, China
| | - Zhenxing Zou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China; Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University, Changsha 410013, China.
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3
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Cowled MS, Kalaitzis JA, Crombie A, Chen R, Sbaraini N, Lacey E, Piggott AM. Fungal Duel between Penicillium brasilianum and Aspergillus nomius Results in Dual Induction of Miktospiromide A and Kitrinomycin A. JOURNAL OF NATURAL PRODUCTS 2023; 86:2398-2406. [PMID: 37737825 DOI: 10.1021/acs.jnatprod.3c00593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Cocultivation of the fungi Penicillium brasilianum MST-FP1927 and Aspergillus nomius MST-FP2004 resulted in the reciprocal induction of two new compounds, miktospiromide A (1) from A. nomius and kitrinomycin A (2) from P. brasilianum. A third new compound, kitrinomycin B (3), was also identified from an axenic culture of P. brasilianum, along with the previously reported compounds austalide K (4), 17S-dihydroaustalide K (5), verruculogen (6), and fumitremorgin B (7). The structures of 1-3 were elucidated by detailed spectroscopic analysis and DFT calculations, while 4-7 were identified by comparison to authentic standards. The genome of A. nomius MST-FP2004 was sequenced, and a putative biosynthetic gene cluster for 1 was identified. Compound 2 showed activity against murine melanoma NS-1 cells (LD99 7.8 μM) and the bovine parasite Tritrichomonas foetus (LD99 4.8 μM).
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Affiliation(s)
- Michael S Cowled
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - John A Kalaitzis
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Andrew Crombie
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - Rachel Chen
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - Nicolau Sbaraini
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Ernest Lacey
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - Andrew M Piggott
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
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4
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Li X, Xu H, Li Y, Liao S, Liu Y. Exploring Diverse Bioactive Secondary Metabolites from Marine Microorganisms Using Co-Culture Strategy. Molecules 2023; 28:6371. [PMID: 37687200 PMCID: PMC10489945 DOI: 10.3390/molecules28176371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/17/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
The isolation and identification of an increasing number of secondary metabolites featuring unique skeletons and possessing diverse bioactivities sourced from marine microorganisms have garnered the interest of numerous natural product chemists. There has been a growing emphasis on how to cultivate microorganisms to enhance the chemical diversity of metabolites and avoid the rediscovery of known ones. Given the significance of secondary metabolites as a means of communication among microorganisms, microbial co-culture has been introduced. By mimicking the growth patterns of microbial communities in their natural habitats, the co-culture strategy is anticipated to stimulate biosynthetic gene clusters that remain dormant under traditional laboratory culture conditions, thereby inducing the production of novel secondary metabolites. Different from previous reviews mainly focusing on fermentation conditions or metabolite diversities from marine-derived co-paired strains, this review covers the marine-derived co-culture microorganisms from 2012 to 2022, and turns to a particular discussion highlighting the selection of co-paired strains for marine-derived microorganisms, especially the fermentation methods for their co-cultural apparatus, and the screening approaches for the convenient and rapid detection of novel metabolites, as these are important in the co-culture. Finally, the structural and bioactivity diversities of molecules are also discussed. The challenges and prospects of co-culture are discussed on behave of the views of the authors.
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Affiliation(s)
- Xiaolin Li
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huayan Xu
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yuyue Li
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shengrong Liao
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yonghong Liu
- Research Center for Marine Microbes, CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China
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5
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Li W, Zhu Y, Li K, Wang L, Li D, Liu N, Huang S. Synergistic remediation of phenanthrene-cadmium co-contaminants by an immobilized acclimated bacterial-fungal consortium and its community response. CHEMOSPHERE 2023:139234. [PMID: 37327827 DOI: 10.1016/j.chemosphere.2023.139234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 04/20/2023] [Accepted: 06/13/2023] [Indexed: 06/18/2023]
Abstract
Bioremediation has tremendous potential to mitigate the serious threats posed by polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs). In the present study, nine bacterial-fungal consortia were progressively acclimated under different culture conditions. Among them, a microbial consortium 1, originating from activated sludge and copper mine sludge microorganisms, was developed through the acclimation of a multi-substrate intermediate (catechol)-target contaminant (Cd2+, phenanthrene (PHE)). Consortium 1 exhibited the best PHE degradation, with an efficiency of 95.6% after 7 d of inoculation, and its tolerance concentration for Cd2+ was up to 1800 mg/L within 48 h. Bacteria Pandoraea and Burkholderia-Caballeronia-Paraburkholderia, as well as fungi Ascomycota and Basidiomycota predominated in the consortium 1. Furthermore, a biochar-loaded consortium was constructed to better cope with the co-contamination behavior, which exhibited excellent adaptation to Cd2+ ranging of 50-200 mg/L. Immobilized consortium efficiently degraded 92.02-97.77% of 50 mg/L PHE within 7 d while removing 93.67-99.04% of Cd2+. In remediation of co-pollution, immobilization technology improved the bioavailability of PHE and dehydrogenase activity of the consortium to enhance PHE degradation, and the phthalic acid pathway was the main metabolic pathway. As for Cd2+ removal, oxygen-containing functional groups (-OH, C=O, and C-O) of biochar or microbial cell walls and EPS components, fulvic acid and aromatic proteins, participated through chemical complexation and precipitation. Furthermore, immobilization led to more active consortium metabolic activity during the reaction, and the community structure developed in a more favorable direction. The dominant species were Proteobacteria, Bacteroidota, and Fusarium, and the predictive expression of functional genes corresponding to key enzymes was elevated. This study provides a basis for combining biochar and acclimated bacterial-fungal consortia for co-contaminated site remediation.
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Affiliation(s)
- Wei Li
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221116, China
| | - Yanfeng Zhu
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221116, China
| | - Kang Li
- College of Environmental Science and Engineering, Peking University, Beijing, 100871, China
| | - Liping Wang
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221116, China.
| | - Dan Li
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221116, China
| | - Na Liu
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221116, China
| | - Shaomeng Huang
- School of Environment Science and Spatial Informatics, China University of Mining and Technology, Xuzhou, 221116, China
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Wang L, Jiang Q, Chen S, Wang S, Lu J, Gao X, Zhang D, Jin X. Natural epidithiodiketopiperazine alkaloids as potential anticancer agents: Recent mechanisms of action, structural modification, and synthetic strategies. Bioorg Chem 2023; 137:106642. [PMID: 37276722 DOI: 10.1016/j.bioorg.2023.106642] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/18/2023] [Accepted: 05/27/2023] [Indexed: 06/07/2023]
Abstract
Cancer has become a grave health crisis that threatens the lives of millions of people worldwide. Because of the drawbacks of the available anticancer drugs, the development of novel and efficient anticancer agents should be encouraged. Epidithiodiketopiperazine (ETP) alkaloids with a 2,5-diketopiperazine (DKP) ring equipped with transannular disulfide or polysulfide bridges or S-methyl moieties constitute a special subclass of fungal natural products. Owing to their privileged sulfur units and intriguing architectural structures, ETP alkaloids exhibit excellent anticancer activities by regulating multiple cancer proteins/signaling pathways, including HIF-1, NF-κB, NOTCH, Wnt, and PI3K/AKT/mTOR, or by inducing cell-cycle arrest, apoptosis, and autophagy. Furthermore, a series of ETP alkaloid derivatives obtained via structural modification showed more potent anticancer activity than natural ETP alkaloids. To solve supply difficulties from natural resources, the total synthetic routes for several ETP alkaloids have been designed. In this review, we summarized several ETP alkaloids with anticancer properties with particular emphasis on their underlying mechanisms of action, structural modifications, and synthetic strategies, which will offer guidance to design and innovate potential anticancer drugs.
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Affiliation(s)
- Lin Wang
- School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Qinghua Jiang
- Department of Pharmacy, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Siyu Chen
- China Medical University-Queen's University of Belfast Joint College, China Medical University, Shenyang 110122, China
| | - Siyi Wang
- The 1st Clinical Department, China Medical University, Shenyang 110122, China
| | - Jingyi Lu
- School of Pharmacy, China Medical University, Shenyang 110122, China
| | - Xun Gao
- Jiangsu Institute Marine Resources Development, Jiangsu Ocean University, Lianyungang 222005, China
| | - Dongfang Zhang
- School of Pharmacy, China Medical University, Shenyang 110122, China.
| | - Xin Jin
- School of Pharmacy, China Medical University, Shenyang 110122, China.
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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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Pacheco-Tapia R, Ortíz S, Jargeat P, Amasifuen C, Vansteelandt M, Haddad M. Exploration of the Production of Three Thiodiketopiperazines by an Endophytic Fungal Strain of Cophinforma mamane. Chem Biodivers 2023; 20:e202201087. [PMID: 36919620 DOI: 10.1002/cbdv.202201087] [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: 11/17/2022] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 03/16/2023]
Abstract
Endophytic fungi possess a versatile metabolism which is related to their ability to live in diverse ecological niches. While culturing under laboratory conditions, their metabolism is mainly influenced by the culture media, time of incubation and other physicochemical factors. In this study, we focused on the production of 3 thiodiketopiperazines (TDKPs) botryosulfuranols A-C produced by an endophytic strain of Cophinforma mamane isolated from the leaves of Bixa orellana L collected in the Peruvian Amazon. We studied the time-course production of botryosulfuranols A-C during 28 days and evaluated the variations in the production of secondary metabolites, including the TDKPs, produced by C. mamane in response to different culture media, light versus dark conditions and different incubation times. We observed a short time-frame production of botryosulfuranol C while its production was significantly affected by the light conditions and nutrients of the culture media. Botryosulfuranols A and B showed a similar production pattern and a similar response to culturing conditions. Molecular networking allowed us to detect three compounds related to TDKPs that will be the focus of future experiments.
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Affiliation(s)
- Romina Pacheco-Tapia
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, France
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Sergio Ortíz
- Therapeutic Innovation Laboratory UMR CNRS 7200, Faculty of Pharmacy, Université de Strasbourg, Strasbourg, France
| | - Patricia Jargeat
- Laboratoire Evolution et Diversité Biologique UMR 5174, Université de Toulouse, CNRS, IRD, France
| | - Carlos Amasifuen
- Instituto Nacional de Innovación Agraria, Dirección de Recursos Genéticos y Biotecnología, Avenida La Molina 1981, Lima, 15024, Perú
- Present address: Epigénomique Fonctionnelle et Physiologie Moléculaire Du Diabète et Maladies Associées UMR 1283/8199, Université de Lille, Lille, France
| | | | - Mohamed Haddad
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, France
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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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11
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Mittermeier F, Bäumler M, Arulrajah P, García Lima JDJ, Hauke S, Stock A, Weuster‐Botz D. Artificial microbial consortia for bioproduction processes. Eng Life Sci 2023; 23:e2100152. [PMID: 36619879 PMCID: PMC9815086 DOI: 10.1002/elsc.202100152] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/03/2022] [Accepted: 03/24/2022] [Indexed: 01/11/2023] Open
Abstract
The application of artificial microbial consortia for biotechnological production processes is an emerging field in research as it offers great potential for the improvement of established as well as the development of novel processes. In this review, we summarize recent highlights in the usage of various microbial consortia for the production of, for example, platform chemicals, biofuels, or pharmaceutical compounds. It aims to demonstrate the great potential of co-cultures by employing different organisms and interaction mechanisms and exploiting their respective advantages. Bacteria and yeasts often offer a broad spectrum of possible products, fungi enable the utilization of complex lignocellulosic substrates via enzyme secretion and hydrolysis, and microalgae can feature their abilities to fixate CO2 through photosynthesis for other organisms as well as to form lipids as potential fuelstocks. However, the complexity of interactions between microbes require methods for observing population dynamics within the process and modern approaches such as modeling or automation for process development. After shortly discussing these interaction mechanisms, we aim to present a broad variety of successfully established co-culture processes to display the potential of artificial microbial consortia for the production of biotechnological products.
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Affiliation(s)
- Fabian Mittermeier
- Department of Energy and Process EngineeringTUM School of Engineering and DesignChair of Biochemical EngineeringTechnical University of MunichGarchingGermany
| | - Miriam Bäumler
- Department of Energy and Process EngineeringTUM School of Engineering and DesignChair of Biochemical EngineeringTechnical University of MunichGarchingGermany
| | - Prasika Arulrajah
- TUM School of Engineering and DesignTechnical University of MunichGarchingGermany
| | | | - Sebastian Hauke
- TUM School of Engineering and DesignTechnical University of MunichGarchingGermany
| | - Anna Stock
- TUM School of Engineering and DesignTechnical University of MunichGarchingGermany
| | - Dirk Weuster‐Botz
- Department of Energy and Process EngineeringTUM School of Engineering and DesignChair of Biochemical EngineeringTechnical University of MunichGarchingGermany
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12
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Hocq R, Sauer M. An artificial coculture fermentation system for industrial propanol production. FEMS MICROBES 2022. [DOI: 10.1093/femsmc/xtac013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
Converting plant biomass into biofuels and biochemicals via microbial fermentation has received considerable attention in the quest for finding renewable energies and materials. Most approaches have so far relied on cultivating a single microbial strain, tailored for a specific purpose. However, this contrasts to how nature works, where microbial communities rather than single species perform all tasks. In artificial coculture systems, metabolic synergies are rationally designed by carefully selecting and simultaneously growing different microbes, taking advantage of the broader metabolic space offered by the use of multiple organisms.
1-propanol and 2-propanol, as biofuels and precursors for propylene, are interesting target molecules to valorize plant biomass. Some solventogenic Clostridia can naturally produce 2-propanol in the so-called Isopropanol-Butanol-Ethanol (IBE) fermentation, by coupling 2-propanol synthesis to acetate and butyrate reduction into ethanol and 1-butanol.
In this work, we hypothesized propanoate would be converted into 1-propanol by the IBE metabolism, while driving at the same time 2-propanol synthesis. We first verified this hypothesis and chose two propionic acid bacteria (PAB) strains as propanoate producers. While consecutive PAB and IBE fermentations only resulted in low propanol titers, coculturing Propionibacterium freudenreichii and Clostridium beijerinckii at various inoculation ratios yielded much higher solvent concentrations, with as much as 21 g/L of solvents (58% increase compared to C. beijerinckii monoculture) and 12 g/L of propanol (98% increase). Taken together, our results underline how artificial cocultures can be used to foster metabolic synergies, increasing fermentative performances and orienting the carbon flow towards a desired product.
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Affiliation(s)
- Rémi Hocq
- CD-Laboratory for Biotechnology of Glycerol, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
- Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Michael Sauer
- CD-Laboratory for Biotechnology of Glycerol, BOKU-University of Natural Resources and Life Sciences, Vienna, Austria
- Institute of Microbiology and Microbial Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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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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Pacheco-Tapia R, Vásquez-Ocmín P, Duthen S, Ortiz S, Jargeat P, Amasifuen C, Haddad M, Vansteelandt M. Chemical modulation of the metabolism of an endophytic fungal strain of Cophinforma mamane using epigenetic modifiers and amino-acids. Fungal Biol 2022; 126:385-394. [DOI: 10.1016/j.funbio.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/03/2022] [Accepted: 02/25/2022] [Indexed: 11/26/2022]
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15
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Cryptic Metabolites from Marine-Derived Microorganisms Using OSMAC and Epigenetic Approaches. Mar Drugs 2022; 20:md20020084. [PMID: 35200614 PMCID: PMC8879561 DOI: 10.3390/md20020084] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/12/2022] [Accepted: 01/16/2022] [Indexed: 02/04/2023] Open
Abstract
Marine microorganisms have proven to be a source of new natural products with a wide spectrum of biological activities relevant in different industrial sectors. The ever-increasing number of sequenced microbial genomes has highlighted a discrepancy between the number of gene clusters potentially encoding the production of natural products and the actual number of chemically characterized metabolites for a given microorganism. Homologous and heterologous expression of these biosynthetic genes, which are often silent under experimental laboratory culture conditions, may lead to the discovery of new cryptic natural products of medical and biotechnological interest. Several new genetic and cultivation-based strategies have been developed to meet this challenge. The OSMAC approach (one strain—many compounds), based on modification of growth conditions, has proven to be a powerful strategy for the discovery of new cryptic natural products. As a direct extension of this approach, the addition of chemical elicitors or epigenetic modifiers have also been used to activate silent genes. This review looks at the structures and biological activities of new cryptic metabolites from marine-derived microorganisms obtained using the OSMAC approach, the addition of chemical elicitors, and enzymatic inhibitors and epigenetic modifiers. It covers works published up to June 2021.
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Ścigaczewska A, Boruta T, Bizukojć M. Quantitative Morphological Analysis of Filamentous Microorganisms in Cocultures and Monocultures: Aspergillus terreus and Streptomyces rimosus Warfare in Bioreactors. Biomolecules 2021; 11:1740. [PMID: 34827738 PMCID: PMC8615777 DOI: 10.3390/biom11111740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 11/25/2022] Open
Abstract
The aim of this study was to quantitatively characterize the morphology of the filamentous microorganisms Aspergillus terreus ATCC 20542 and Streptomyces rimosus ATCC 10970, cocultivated in stirred tank bioreactors, and to characterize their mutual influence with the use of quantitative image analysis. Three distinct coculture initiation strategies were applied: preculture versus preculture, spores versus spores and preculture versus preculture with time delay for one of the species. Bioreactor cocultures were accompanied by parallel monoculture controls. The results recorded for the mono- and cocultures were compared in order to investigate the effect of cocultivation on the morphological evolution of A. terreus and S. rimosus. Morphology-related observations were also confronted with the analysis of secondary metabolism. The morphology of the two studied filamentous species strictly depended on the applied coculture initiation strategy. In the cocultures initiated by the simultaneous inoculation, S. rimosus gained domination or advance over A. terreus. The latter microorganism dominated only in these experiments in which S. rimosus was introduced with a delay.
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Affiliation(s)
- Anna Ścigaczewska
- Department of Bioprocess Engineering, Faculty of Process and Environmental Engineering, Lodz University of Technology, ul. Wolczanska 213, 90-924 Lodz, Poland; (T.B.); (M.B.)
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Deep learning strategies for active secondary metabolites biosynthesis from fungi: Harnessing artificial manipulation and application. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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18
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Espinosa-Ortiz EJ, Rene ER, Gerlach R. Potential use of fungal-bacterial co-cultures for the removal of organic pollutants. Crit Rev Biotechnol 2021; 42:361-383. [PMID: 34325585 DOI: 10.1080/07388551.2021.1940831] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fungi and bacteria coexist in a wide variety of natural and artificial environments which can lead to their association and interaction - ranging from antagonism to cooperation - that can affect the survival, colonization, spatial distribution and stress resistance of the interacting partners. The use of polymicrobial cultivation approaches has facilitated a more thorough understanding of microbial dynamics in mixed microbial communities, such as those composed of fungi and bacteria, and their influence on ecosystem functions. Mixed (multi-domain) microbial communities exhibit unique associations and interactions that could result in more efficient systems for the degradation and removal of organic pollutants. Several previous studies have reported enhanced biodegradation of certain pollutants when using combined fungal-bacterial treatments compared to pure cultures or communities of either fungi or bacteria (single domain systems). This article reviews: (i) the mechanisms of pollutant degradation that can occur in fungal-bacterial systems (e.g.: co-degradation, production of secondary metabolites, enhancement of degradative enzyme production, and transport of bacteria by fungal mycelia); (ii) case studies using fungal-bacterial co-cultures for the removal of various organic pollutants (synthetic dyes, polycyclic aromatic hydrocarbons, pesticides, and other trace or volatile organic compounds) in different environmental matrices (e.g. water, gas/vapors, soil); (iii) the key aspects of engineering artificial fungal-bacterial co-cultures, and (iv) the current challenges and future perspectives of using fungal-bacterial co-cultures for environmental remediation.
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Affiliation(s)
- Erika J Espinosa-Ortiz
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
| | - Eldon R Rene
- Department of Water Supply, Sanitary and Environmental Engineering, IHE Delft Institute for Water Education, 2601DA Delft, The Netherlands
| | - Robin Gerlach
- Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT, USA
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19
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Kim JH, Lee N, Hwang S, Kim W, Lee Y, Cho S, Palsson BO, Cho BK. Discovery of novel secondary metabolites encoded in actinomycete genomes through coculture. J Ind Microbiol Biotechnol 2021; 48:6119915. [PMID: 33825906 PMCID: PMC9113425 DOI: 10.1093/jimb/kuaa001] [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: 09/27/2020] [Accepted: 11/02/2020] [Indexed: 01/23/2023]
Abstract
Actinomycetes are a rich source of bioactive natural products important for novel drug leads. Recent genome mining approaches have revealed an enormous number of secondary metabolite biosynthetic gene clusters (smBGCs) in actinomycetes. However, under standard laboratory culture conditions, many smBGCs are silent or cryptic. To activate these dormant smBGCs, several approaches, including culture-based or genetic engineering-based strategies, have been developed. Above all, coculture is a promising approach to induce novel secondary metabolite production from actinomycetes by mimicking an ecological habitat where cryptic smBGCs may be activated. In this review, we introduce coculture studies that aim to expand the chemical diversity of actinomycetes, by categorizing the cases by the type of coculture partner. Furthermore, we discuss the current challenges that need to be overcome to support the elicitation of novel bioactive compounds from actinomycetes.
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Affiliation(s)
- Ji Hun Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Namil Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Woori Kim
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Yongjae Lee
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences and KI for the BioCentury, 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, 2800 Lyngby, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,Intelligent Synthetic Biology Center, Daejeon 34141, Republic of Korea
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20
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Mandal V, Adhikary R, Maiti PK, Mandal S, Mandal V. Morpho-biochemical and molecular characterization of two new strains of Aspergillus fumigatus nHF-01 and A. fumigatus PPR-01 producing broad-spectrum antimicrobial compounds. Braz J Microbiol 2021; 52:905-917. [PMID: 33715141 DOI: 10.1007/s42770-021-00439-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 02/02/2021] [Indexed: 11/30/2022] Open
Abstract
The main objective of the study is to characterize two new strains of Aspergillus fumigatus through morphometric, biochemical, molecular methods, and to evaluate their antimicrobial potentiality. The micro-morphotaxonomy, growth, and metabolic behavior of the strains, nHF-01 and PPR-01, were studied in different growth conditions and compared with standard strain. The molecular characterization was done by sequencing the ncrDNA ITS1-5.8S-ITS2 and D1-D2 domains of the nc 28S rDNA region and compared with a secondary structure-based phylogenetic tree. The secretory antimicrobials and pigments were characterized by TLC, UV-Vis, and FT-IR spectroscopy. Both the strains showed distinct growth patterns in different nutritional media and could assimilate a wide range of carbohydrates with distinctive biochemical properties. The molecular characterization revealed the strains, nHF-01 and PPR-01, as Aspergillus fumigatus (GenBank Accession No. MN190286 and MN190284, respectively). It was observed that the strain nHF-01 produces red to brownish pigments having mild antimicrobial activity while the strain PPR-01 does not represent such transformations. The extractable compounds had a significant antimicrobial potentiality against the human pathogenic bacteria. From this analysis, it can be concluded that the nHF-01 and PPR-01 strains are distinct from other A. fumigatus by their unique characters. Large-scale production and detailed molecular elucidation of the antimicrobial compounds may lead to the discovery of new antimicrobial compounds from these strains.
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Affiliation(s)
- Vivekananda Mandal
- Plant and Microbial Physiology and Biochemistry Laboratory, Department of Botany, University of Gour Banga, P.O. - Mokdumpur, Malda, WB, 732 103, India
| | - Rajsekhar Adhikary
- Plant and Microbial Physiology and Biochemistry Laboratory, Department of Botany, University of Gour Banga, P.O. - Mokdumpur, Malda, WB, 732 103, India
| | - Pulak Kumar Maiti
- Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700 019, India
| | - Sukhendu Mandal
- Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, West Bengal, 700 019, India
| | - Vivekananda Mandal
- Plant and Microbial Physiology and Biochemistry Laboratory, Department of Botany, University of Gour Banga, P.O. - Mokdumpur, Malda, WB, 732 103, India.
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21
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Biofuels from Micro-Organisms: Thermodynamic Considerations on the Role of Electrochemical Potential on Micro-Organisms Growth. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11062591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biofuels from micro-organisms represents a possible response to the carbon dioxide mitigation. One open problem is to improve their productivity, in terms of biofuels production. To do so, an improvement of the present model of growth and production is required. However, this implies an understanding of the growth spontaneous conditions of the bacteria. In this paper, a thermodynamic approach is developed in order to highlight the fundamental role of the electrochemical potential in bacteria proliferation. Temperature effect on the biosystem behaviour has been pointed out. The results link together the electrochemical potential, the membrane electric potential, the pH gradient through the membrane, and the temperature, with the result of improving the thermodynamic approaches, usually introduced in this topic of research.
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22
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Silva AD, Ambrozin ARP, de Camargo AFS, Cruz FDPN, Ferreira LLG, Krogh R, Silva TL, Camargo ILBDC, Andricopulo AD, Vieira PC. Liquid Fungal Cocultivation as a Strategy to Access Bioactive Metabolites. PLANTA MEDICA 2021; 87:187-195. [PMID: 32645738 DOI: 10.1055/a-1200-2046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Fungi are a rich source of bioactive compounds. Fungal cocultivation is a method of potentiating chemical interactions and, consequently, increasing bioactive molecule production. In this study, we evaluated the bactericidal, antiprotozoal, and cathepsin V inhibition activities of extracts from axenic cultures of 6 fungi (Fusarium guttiforme, Pestalotiopsis diospyri, Phoma caricae-papayae, Colletotrichum horii, Phytophthora palmivora, and C. gloeosporioides) that infest tropical fruits and 57 extracts obtained by their cocultivation. Our results reveal that fungal cocultivation enhances the biological activity of the samples, since all extracts that were active on Gram-positive bacteria, Gram-negative bacteria, Trypanosoma cruzi, and Leishmania infantum were obtained from cocultivation. Bacterial growth is either totally or partially inhibited by 46% of the extracts. Two extracts containing mainly fusaric and 9,10-dehydrofusaric acids were particularly active. The presence of the fungus F. guttiforme in co-cultures that give rise to extracts with the highest activities against L. infantum. An axenic culture gave rise to the most active extract for the inhibition of cathepsin V; however, other coculture extracts also exhibited activity toward this biological target. Therefore, the results of the biological activities indicate that fungal cocultivation increased the biological potential of samples, likely due to the hostile and competitive environment that pushes microorganisms to produce substances important for defense and allows access to metabolic routes then silenced in milder cultivation conditions.
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Affiliation(s)
- Airton Damasceno Silva
- Department of Chemistry, Federal University of São Carlos (UFSCar), São Carlos, SP, Brazil
| | | | | | | | | | - Renata Krogh
- São Carlos Institute of Physics, University of São Paulo (USP), São Carlos, SP, Brazil
| | - Taynara Lopes Silva
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | | | | | - Paulo Cezar Vieira
- Department of Chemistry, Federal University of São Carlos (UFSCar), São Carlos, SP, Brazil
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil
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Metabolic Profile of Scytalidium parasiticum- Ganoderma boninense Co-Cultures Revealed the Alkaloids, Flavonoids and Fatty Acids that Contribute to Anti-Ganoderma Activity. Molecules 2020; 25:molecules25245965. [PMID: 33339375 PMCID: PMC7767070 DOI: 10.3390/molecules25245965] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/03/2022] Open
Abstract
In solving the issue of basal stem rot diseases caused by Ganoderma, an investigation of Scytalidium parasiticum as a biological control agent that suppresses Ganoderma infection has gained our interest, as it is more environmentally friendly. Recently, the fungal co-cultivation has emerged as a promising method to discover novel antimicrobial metabolites. In this study, an established technique of co-culturing Scytalidium parasiticum and Ganoderma boninense was applied to produce and induce metabolites that have antifungal activity against G. boninense. The crude extract from the co-culture media was applied to a High Performance Liquid Chromatography (HPLC) preparative column to isolate the bioactive compounds, which were tested against G. boninense. The fractions that showed inhibition against G. boninense were sent for a Liquid Chromatography-Time of Flight-Mass Spectrometry (LC-TOF-MS) analysis to further identify the compounds that were responsible for the microbicidal activity. Interestingly, we found that eudistomin I, naringenin 7-O-beta-D-glucoside and penipanoid A, which were present in different abundances in all the active fractions, except in the control, could be the antimicrobial metabolites. In addition, the abundance of fatty acids, such as oleic acid and stearamide in the active fraction, also enhanced the antimicrobial activity. This comprehensive metabolomics study could be used as the basis for isolating biocontrol compounds to be applied in oil palm fields to combat a Ganoderma infection.
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Multifarious Elicitors: Invoking Biosynthesis of Various Bioactive Secondary Metabolite in Fungi. Appl Biochem Biotechnol 2020; 193:668-686. [PMID: 33135129 DOI: 10.1007/s12010-020-03423-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/11/2020] [Indexed: 10/23/2022]
Abstract
Natural products are considered to be the lifeline treatment for several diseases where their structural complexity makes them a source of potential lead molecules. As a producer of antibiotics, food colorants, enzymes, and nutritious food, fungi are beneficial to humans. Fungi, as a source of novel natural products, draw attention of scientists. However, redundant isolation of metabolite retards the rate of discovery. So, apart from the standard conditions for the production of secondary metabolites, certain induction strategies are used to trigger biosynthetic genes in fungi. Advancement in the computational tools helps in connecting gene clusters and their metabolite production. Therefore, modern analytical tools and the genomic era in hand leads to the identification of manifold of cryptic metabolites. The cryptic biosynthetic gene cluster (BGC) has become a treasure hunt for new metabolites representing biosynthetic pathways, regulatory mechanisms, and other factors. This review includes the use of chemical inducers/epigenetic modifiers and co-culture (species interaction) techniques to induce these BGCs. Furthermore, it cites a detailed representation of molecules isolated using these strategies. Since the induction occurs on the genomic molecular DNA and histones, this together brings a significant exploration of the biosynthetic pathways.Graphical Abstract.
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25
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de Amorim MR, Wijeratne EMK, Zhou S, Arnold AE, Batista ANL, Batista JM, Dos Santos LC, Gunatilaka AAL. An epigenetic modifier induces production of 3-(4-oxopyrano)-chromen-2-ones in Aspergillus sp. AST0006, an endophytic fungus of Astragalus lentiginosus. Tetrahedron 2020; 76:131525. [PMID: 33716326 PMCID: PMC7945046 DOI: 10.1016/j.tet.2020.131525] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Incorporation of the epigenetic modifier suberoylanilide hydroxamic acid (SAHA) into a potato dextrose broth culture of the endophytic fungus Aspergillus sp. AST0006 affected its polyketide biosynthetic pathway providing two new 3-(4-oxopyrano)-chromen-2-ones, aspyranochromenones A (1) and B (2), and the isocoumarin, (-)-6,7-dihydroxymellein (3). Eight additional metabolites (4-11) and two biotransformation products of SAHA (12-13) were also encountered. The planar structures and relative configurations of the new metabolites 1-2 were elucidated with the help of high-resolution mass, 1D and 2D NMR spectroscopic data and the absolute configurations of 1-3 were determined by comparison of experimental and calculated ECD data. Possible biosynthetic pathways to 1 and 2 are presented.
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Affiliation(s)
- Marcelo R de Amorim
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
- Institute of Chemistry, São Paulo State University, Araraquara, São Paulo 14800-900, Brazil
| | - E M Kithsiri Wijeratne
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Shengliang Zhou
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, 101 Shanghai Rd, Xuzhou 221116, P. R. China
| | - A Elizabeth Arnold
- School of Plant Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson, Arizona 85721, United States
| | - Andrea N L Batista
- Department of Organic Chemistry, Chemistry Institute, Fluminense Federal University, Niterói, RJ 24020-141, Brazil
| | - João M Batista
- Institute of Science and Technology, Federal University of São Paulo, São José dos Campos, São Paulo 12231-280, Brazil
| | - Lourdes C Dos Santos
- Institute of Chemistry, São Paulo State University, Araraquara, São Paulo 14800-900, Brazil
| | - A A Leslie Gunatilaka
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
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26
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Liang L, Wang G, Haltli B, Marchbank DH, Stryhn H, Correa H, Kerr RG. Metabolomic Comparison and Assessment of Co-cultivation and a Heat-Killed Inducer Strategy in Activation of Cryptic Biosynthetic Pathways. JOURNAL OF NATURAL PRODUCTS 2020; 83:2696-2705. [PMID: 32869646 DOI: 10.1021/acs.jnatprod.0c00621] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Co-cultivation has been used as a promising tool to turn on or up-regulate cryptic biosynthetic pathways for microbial natural product discovery. Recently, a modified culturing strategy similar to co-cultivation was investigated, where heat-killed inducer cultures were supplemented to the culture medium of producer fermentations to induce cryptic pathways. In the present study, the repeatability and effectiveness of both methods in turning on cryptic biosynthetic pathways were unbiasedly assessed using UHPLC-HRESIMS-based metabolomics analysis. Both induction methods had good repeatability, and they resulted in very different induced metabolites from the tested producers. Co-cultivation generated more induced mass features than the heat-killed inducer cultures, while both methods resulted in the induction of mass features not observed using the other induction method. As examples, pathways leading to two new natural products, N-carbamoyl-2-hydroxy-3-methoxybenzamide (1) and carbazoquinocin G (5), were induced and up-regulated through co-culturing a producer Streptomyces sp. RKND-216 with inducers Alteromonas sp. RKMC-009 and M. smegmatis ATCC 120515, respectively.
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Affiliation(s)
- Libang Liang
- Department of Chemistry, University of Prince Edward Island, Charlottetown C1A 4P3, Canada
| | - Guanqiao Wang
- Department of Chemistry, University of Prince Edward Island, Charlottetown C1A 4P3, Canada
| | - Bradley Haltli
- Nautilus Biosciences Croda, Charlottetown C1A 4P3, Canada
| | - Douglas H Marchbank
- Department of Chemistry, University of Prince Edward Island, Charlottetown C1A 4P3, Canada
- Nautilus Biosciences Croda, Charlottetown C1A 4P3, Canada
| | | | - Hebelin Correa
- Nautilus Biosciences Croda, Charlottetown C1A 4P3, Canada
| | - Russell G Kerr
- Department of Chemistry, University of Prince Edward Island, Charlottetown C1A 4P3, Canada
- Nautilus Biosciences Croda, Charlottetown C1A 4P3, Canada
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Lee LH, Goh BH, Chan KG. Editorial: Actinobacteria: Prolific Producers of Bioactive Metabolites. Front Microbiol 2020; 11:1612. [PMID: 32973689 PMCID: PMC7472881 DOI: 10.3389/fmicb.2020.01612] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/19/2020] [Indexed: 12/17/2022] Open
Affiliation(s)
- Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Subang Jaya, Malaysia
| | - Bey-Hing Goh
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- Biofunctional Molecule Exploratory Research Group (BMEX), School of Pharmacy, Monash University Malaysia, Bandar Sunway, Malaysia
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- International Genome Centre, Jiangsu University, Zhenjiang, China
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28
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Qian X, Chen L, Sui Y, Chen C, Zhang W, Zhou J, Dong W, Jiang M, Xin F, Ochsenreither K. Biotechnological potential and applications of microbial consortia. Biotechnol Adv 2020; 40:107500. [DOI: 10.1016/j.biotechadv.2019.107500] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 11/13/2019] [Accepted: 12/17/2019] [Indexed: 12/20/2022]
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29
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Bull AT, Goodfellow M. Dark, rare and inspirational microbial matter in the extremobiosphere: 16 000 m of bioprospecting campaigns. MICROBIOLOGY-SGM 2020; 165:1252-1264. [PMID: 31184575 DOI: 10.1099/mic.0.000822] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The rationale of our bioprospecting campaigns is that the extremobiosphere, particularly the deep sea and hyper-arid deserts, harbours undiscovered biodiversity that is likely to express novel chemistry and biocatalysts thereby providing opportunities for therapeutic drug and industrial process development. We have focused on actinobacteria because of their frequent role as keystone species in soil ecosystems and their unrivalled track record as a source of bioactive compounds. Population numbers and diversity of actinobacteria in the extremobiosphere are traditionally considered to be low, although they often comprise the dominant bacterial biota. Recent metagenomic evaluation of 'the uncultured microbial majority' has now revealed enormous taxonomic diversity among 'dark' and 'rare' actinobacteria in samples as diverse as sediments from the depths of the Mariana Trench and soils from the heights of the Central Andes. The application of innovative culture and screening options that emphasize rigorous dereplication at each stage of the analysis, and strain prioritization to identify 'gifted' organisms, have been deployed to detect and characterize bioactive hit compounds and sought-after catalysts from this hitherto untapped resource. The rewards include first-in-a-class chemical entities with novel modes of action, as well as a growing microbial seed bank that represents a potentially enormous source of biotechnological and therapeutic innovation.
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Affiliation(s)
- Alan T Bull
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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30
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Thissera B, Alhadrami HA, Hassan MHA, Hassan HM, Behery FA, Bawazeer M, Yaseen M, Belbahri L, Rateb ME. Induction of Cryptic Antifungal Pulicatin Derivatives from Pantoea agglomerans by Microbial Co-Culture. Biomolecules 2020; 10:E268. [PMID: 32050703 PMCID: PMC7072716 DOI: 10.3390/biom10020268] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 02/06/2023] Open
Abstract
Microbial co-culture or mixed fermentation proved to be an efficient strategy to expand chemical diversity by the induction of cryptic biosynthetic pathways, and in many cases led to the production of new antimicrobial agents. In the current study, we report a rare example of the induction of silent/cryptic bacterial biosynthetic pathway by the co-culture of Durum wheat plant roots-associated bacterium Pantoea aggolomerans and date palm leaves-derived fungus Penicillium citrinum. The initial co-culture indicated a clear fungal growth inhibition which was confirmed by the promising antifungal activity of the co-culture total extract against Pc. LC-HRMS chemical profiling demonstrated a huge suppression in the production of secondary metabolites (SMs) of axenic cultures of both species with the emergence of new metabolites which were dereplicated as a series of siderophores. Large-scale co-culture fermentation led to the isolation of two new pulicatin derivatives together with six known metabolites which were characterised using HRESIMS and NMR analyses. During the in vitro antimicrobial evaluation of the isolated compounds, pulicatin H (2) exhibited the strongest antifungal activity against Pc, followed by aeruginaldehyde (1) and pulicatin F (4), hence explaining the initial growth suppression of Pc in the co-culture environment.
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Affiliation(s)
- Bathini Thissera
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK; (B.T.); (M.B.); (M.Y.)
| | - Hani A. Alhadrami
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- King Fahd Medical Research Centre, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Marwa H. A. Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt; (M.H.A.H.); (H.M.H.)
| | - Hossam M. Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt; (M.H.A.H.); (H.M.H.)
| | - Fathy A. Behery
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt;
- Department of Pharmacy, College of Pharmacy, Riyadh Elm University, Riyadh 11681, Saudi Arabia
| | - Majed Bawazeer
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK; (B.T.); (M.B.); (M.Y.)
| | - Mohammed Yaseen
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK; (B.T.); (M.B.); (M.Y.)
| | - Lassaad Belbahri
- Laboratory of Soil Biology, University of Neuchatel, 2000 Neuchatel, Switzerland;
| | - Mostafa E. Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK; (B.T.); (M.B.); (M.Y.)
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt; (M.H.A.H.); (H.M.H.)
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31
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Arora D, Gupta P, Jaglan S, Roullier C, Grovel O, Bertrand S. Expanding the chemical diversity through microorganisms co-culture: Current status and outlook. Biotechnol Adv 2020; 40:107521. [PMID: 31953204 DOI: 10.1016/j.biotechadv.2020.107521] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 11/29/2019] [Accepted: 01/13/2020] [Indexed: 12/17/2022]
Abstract
Natural products (NPs) are considered as a cornerstone for the generation of bioactive leads in drug discovery programs. However, one of the major limitations of NP drug discovery program is "rediscovery" of known compounds, thereby hindering the rate of drug discovery efficiency. Therefore, in recent years, to overcome these limitations, a great deal of attention has been drawn towards understanding the role of microorganisms' co-culture in inducing novel chemical entities. Such induction could be related to activation of genes which might be silent or expressed at very low levels (below detection limit) in pure-strain cultures under normal laboratory conditions. In this review, chemical diversity of compounds isolated from microbial co-cultures, is discussed. For this purpose, chemodiversity has been represented as a chemical-structure network based on the "Tanimoto Structural Similarity Index". This highlights the huge structural diversity induced by microbial co-culture. In addition, the current trends in microbial co-culture research are highlighted. Finally, the current challenges (1 - induction monitoring, 2 - reproducibility, 3 - growth time effect and 4 - up-scaling for isolation purposes) are discussed. The information in this review will support researchers to design microbial co-culture strategies for future research efforts. In addition, guidelines for co-culture induction reporting are also provided to strengthen future reporting in this NP field.
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Affiliation(s)
- Divya Arora
- Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Jammu Campus, Jammu 180001, India; Groupe Mer, Molécules, Santé-EA 2160, Faculté des Sciences pharmaceutiques et biologiques, Université de Nantes, 9 rue Bias, BP 53508, F-44035 Nantes Cedex 01, France
| | - Prasoon Gupta
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Jammu Campus, Jammu 180001, India
| | - Sundeep Jaglan
- Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Jammu Campus, Jammu 180001, India
| | - Catherine Roullier
- Groupe Mer, Molécules, Santé-EA 2160, Faculté des Sciences pharmaceutiques et biologiques, Université de Nantes, 9 rue Bias, BP 53508, F-44035 Nantes Cedex 01, France
| | - Olivier Grovel
- Groupe Mer, Molécules, Santé-EA 2160, Faculté des Sciences pharmaceutiques et biologiques, Université de Nantes, 9 rue Bias, BP 53508, F-44035 Nantes Cedex 01, France
| | - Samuel Bertrand
- Groupe Mer, Molécules, Santé-EA 2160, Faculté des Sciences pharmaceutiques et biologiques, Université de Nantes, 9 rue Bias, BP 53508, F-44035 Nantes Cedex 01, France.
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32
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Critical Assessment of Streptomyces spp. Able to Control Toxigenic Fusaria in Cereals: A Literature and Patent Review. Int J Mol Sci 2019; 20:ijms20246119. [PMID: 31817248 PMCID: PMC6941072 DOI: 10.3390/ijms20246119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/18/2019] [Accepted: 12/01/2019] [Indexed: 12/18/2022] Open
Abstract
Mycotoxins produced by Fusarium species on cereals represent a major concern for food safety worldwide. Fusarium toxins that are currently under regulation for their content in food include trichothecenes, fumonisins, and zearalenone. Biological control of Fusarium spp. has been widely explored with the aim of limiting disease occurrence, but few efforts have focused so far on limiting toxin accumulation in grains. The bacterial genus Streptomyces is responsible for the production of numerous drug molecules and represents a huge resource for the discovery of new molecules. Streptomyces spp. are also efficient plant colonizers and able to employ different mechanisms of control against toxigenic fungi on cereals. This review describes the outcomes of research using Streptomyces strains and/or their derived molecules to limit toxin production and/or contamination of Fusarium species in cereals. Both the scientific and patent literature were analyzed, starting from the year 2000, and we highlight promising results as well as the current pitfalls and limitations of this approach.
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33
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Jia B, Ma YM, Liu B, Chen P, Hu Y, Zhang R. Synthesis, Antimicrobial Activity, Structure-Activity Relationship, and Molecular Docking Studies of Indole Diketopiperazine Alkaloids. Front Chem 2019; 7:837. [PMID: 31850323 PMCID: PMC6897290 DOI: 10.3389/fchem.2019.00837] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/18/2019] [Indexed: 12/16/2022] Open
Abstract
Strategies for the synthesis of indole diketopiperazine alkaloids (indole DKPs) have been described and involve three analogs of indole DKPs. The antimicrobial activity and structure-activity relationship (SAR) of 24 indole DKPs were explored. Compounds 3b and 3c were found to be the most active, with minimum inhibitory concentrations (MIC) values in the range of 0.94–3.87 μM (0.39–1.56 μg/mL) against the four tested bacteria (Staphylococcus aureus, Bacillus subtilis, Pseudomonas aeruginosa, and Escherichia coli). Furthermore, compounds 4a and 4b displayed broad-spectrum antimicrobial activity with MIC values of 1.10–36.9 μM (0.39–12.5 μg/mL) against all tested bacteria and plant pathogenic fungi (Colletotrichum gloeosporioides, Valsa mali, Alternaria alternata and Alternaria brassicae). According to the in silico study, compounds 3c showed significant binding affinity to the FabH protein from Escherichia coli, which has been identified as the key target enzyme of fatty acid synthesis (FAS) in bacteria. Therefore, these compounds are not only promising new antibacterial agents but also potential FabH inhibitors.
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Affiliation(s)
- Bin Jia
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Yang-Min Ma
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Bin Liu
- School of Pharmacy, Shaanxi Institute of International Trade and Commerce, Xi'an, China.,Collaborative Innovation Center of Green Manufacturing Technology for Traditional Chinese Medicine in Shaanxi Province, Xi'an, China
| | - Pu Chen
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Yan Hu
- Shaanxi Key Laboratory of Chemical Additives for Industry, College of Chemistry and Chemical Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Rui Zhang
- School of Arts and Sciences, Shaanxi University of Science and Technology, Xi'an, China
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34
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Advances in microbial culturing conditions to activate silent biosynthetic gene clusters for novel metabolite production. ACTA ACUST UNITED AC 2019; 46:1381-1400. [DOI: 10.1007/s10295-019-02198-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/24/2019] [Indexed: 02/08/2023]
Abstract
Abstract
Natural products (NPs) produced by bacteria and fungi are often used as therapeutic agents due to their complex structures and wide range of bioactivities. Enzymes that build NPs are encoded by co-localized biosynthetic gene clusters (BGCs), and genome sequencing has recently revealed that many BGCs are “silent” under standard laboratory conditions. There are numerous methods used to activate “silent” BGCs that rely either upon altering culture conditions or genetic modification. In this review, we discuss several recent microbial cultivation methods that have been used to expand the scope of NPs accessible in the laboratory. These approaches are divided into three categories: addition of a physical scaffold, addition of small molecule elicitors, and co-cultivation with another microbe.
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35
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Study of in vitro interaction between Fusarium verticillioides and Streptomyces sp. using metabolomics. Folia Microbiol (Praha) 2019; 65:303-314. [PMID: 31250362 DOI: 10.1007/s12223-019-00725-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 06/10/2019] [Indexed: 10/26/2022]
Abstract
The Streptomyces sp. strain AV05 isolated from an organic amendment was found to impact both growth and fumonisin production of Fusarium verticillioides during in vitro direct confrontation. In order to investigate the interactions between the Streptomyces sp. strain AV05 and F. verticillioides, a metabolomic approach was used. The study of the endometabolomes of the microorganisms was carried out in two different conditions: the microorganisms were cultivated alone or in confrontation. The aim of this study was to examine the modifications of the endometabolome of F. verticillioides in confrontation with the Streptomyces strain. The metabolites involved in these modifications were identified using 2D NMR. Many metabolites were found to be overproduced in confrontation assays with the Streptomyces strain, notably 16 proteinogenic amino acids, inosine, and uridine. This suggested that fungal metabolic pathways such as protein synthesis have been affected due to interaction. Thus, metabolomic studies, as well as proteomics or transcriptomics, are useful for deciphering the mechanisms of interactions between biological control agents and mycotoxigenic fungi. This comprehension is one of the key elements of the improvement of the selection and use of antagonistic agents.
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Acharya D, Miller I, Cui Y, Braun DR, Berres ME, Styles MJ, Li L, Kwan J, Rajski SR, Blackwell HE, Bugni TS. Omics Technologies to Understand Activation of a Biosynthetic Gene Cluster in Micromonospora sp. WMMB235: Deciphering Keyicin Biosynthesis. ACS Chem Biol 2019; 14:1260-1270. [PMID: 31120241 PMCID: PMC6591704 DOI: 10.1021/acschembio.9b00223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
DNA
sequencing of a large collection of bacterial genomes reveals
a wealth of orphan biosynthetic gene clusters (BGCs) with no identifiable
products. BGC silencing, for those orphan clusters that are truly
silent, rather than those whose products have simply evaded detection
and cluster correlation, is postulated to result from transcriptional
inactivation of these clusters under standard laboratory conditions.
Here, we employ a multi-omics approach to demonstrate how interspecies
interactions modulate the keyicin producing kyc cluster
at the transcriptome level in cocultures of kyc-bearing Micromonospora sp. and a Rhodococcus sp.
We further correlate coculture dependent changes in keyicin production
to changes in transcriptomic and proteomic profiles and show that
these changes are attributable to small molecule signaling consistent
with a quorum sensing pathway. In piecing together the various elements
underlying keyicin production in coculture, this study highlights
how omics technologies can expedite future efforts to understand and
exploit silent BGCs.
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Affiliation(s)
- Deepa Acharya
- Pharmaceutical Sciences Division, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Ian Miller
- Pharmaceutical Sciences Division, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Yusi Cui
- Pharmaceutical Sciences Division, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Doug R. Braun
- Pharmaceutical Sciences Division, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Mark E. Berres
- Bioinformatics Resource Center, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Matthew J. Styles
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Lingjun Li
- Pharmaceutical Sciences Division, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Jason Kwan
- Pharmaceutical Sciences Division, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Scott R. Rajski
- Pharmaceutical Sciences Division, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Helen E. Blackwell
- Department of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
| | - Tim S. Bugni
- Pharmaceutical Sciences Division, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
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Martín JF, Liras P. Harnessing microbiota interactions to produce bioactive metabolites: communication signals and receptor proteins. Curr Opin Pharmacol 2019; 48:8-16. [PMID: 30933876 DOI: 10.1016/j.coph.2019.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/23/2019] [Accepted: 02/27/2019] [Indexed: 11/30/2022]
Abstract
Numerous microbial communities live in soil, aquatic habitats, plants, and animal bodies. Microbial genome sequences have revealed that thousands of biosynthetic gene clusters (BGCs) are present in different bacteria and filamentous fungi. Many of these BGCs are not expressed in pure cultures in the laboratory. However, a large part of these silent clusters is expressed in nature when complex microbial populations are studied. The encoding specialized metabolites are frequently produced at very low concentrations but still they serve as communication signals that produce important biochemical and differentiation effects on other microorganisms of the consortium. Many specialized metabolites acting as communication signals have been identified, including autoinducers, intergeneric, and interkingdom cues. These signals trigger expression of silent BGCs in other microorganisms, thus providing new compounds with interesting biological and pharmacological activities. Examples of interactions between different bacteria or between bacteria and fungi are described here. Finally, the relevance of the human microbiota and the production in vivo of specialized metabolites of medical interest is discussed.
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Affiliation(s)
- Juan F Martín
- Department of Molecular Biology, Section Microbiology, University of León, 24071 León, Spain.
| | - Paloma Liras
- Department of Molecular Biology, Section Microbiology, University of León, 24071 León, Spain
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38
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Akone SH, Pham CD, Chen H, Ola ARB, Ntie-Kang F, Proksch P. Epigenetic modification, co-culture and genomic methods for natural product discovery. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2018-0118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Fungi and bacteria are encountered in many habitats where they live in complex communities interacting with one another mainly by producing secondary metabolites, which are organic compounds that are not directly involved in the normal growth, development, or reproduction of the organism. These organisms appear as a promising source for the discovery of novel bioactive natural products that may find their application in medicine. However, the production of secondary metabolites by those organisms when cultured axenically is limited as only a subset of biosynthetic genes is expressed under standard laboratory conditions leading to the search of new methods for the activation of the silent genes including epigenetic modification and co-cultivation. Biosynthetic gene clusters which produce secondary metabolites are known to be present in a heterochromatin state in which the transcription of constitutive genes is usually regulated by epigenetic modification including DNA methylation and histone deacetylation. Therefore, small-molecule epigenetic modifiers which promote changes in the structure of chromatin could control the expression of silent genes and may be rationally employed for the discovery of novel bioactive compounds. Co-cultivation, which is also known as mixed-fermentation, usually implies two or more microorganisms in the same medium in which the resulting competition is known to enhance the production of constitutively present compounds and/or to lead to the induction of cryptic metabolites that were not detected in axenic cultures of the considered axenic microorganism. Genomic strategies could help to identify biosynthetic gene clusters in fungal genomes and link them to their products by the means of novel algorithms as well as integrative pan-genomic approaches. Despite that all these techniques are still in their infancy, they appear as promising sources for the discovery of new bioactive compounds. This chapter presents recent ecological techniques for the discovery of new secondary metabolites that might find application in medicine.
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Palomo-Ligas L, Gutiérrez-Gutiérrez F, Ochoa-Maganda VY, Cortés-Zárate R, Charles-Niño CL, Castillo-Romero A. Identification of a novel potassium channel (GiK) as a potential drug target in Giardia lamblia: Computational descriptions of binding sites. PeerJ 2019; 7:e6430. [PMID: 30834181 PMCID: PMC6397635 DOI: 10.7717/peerj.6430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/10/2019] [Indexed: 12/12/2022] Open
Abstract
Background The protozoan Giardia lamblia is the causal agent of giardiasis, one of the main diarrheal infections worldwide. Drug resistance to common antigiardial agents and incidence of treatment failures have increased in recent years. Therefore, the search for new molecular targets for drugs against Giardia infection is essential. In protozoa, ionic channels have roles in their life cycle, growth, and stress response. Thus, they are promising targets for drug design. The strategy of ligand-protein docking has demonstrated a great potential in the discovery of new targets and structure-based drug design studies. Methods In this work, we identify and characterize a new potassium channel, GiK, in the genome of Giardia lamblia. Characterization was performed in silico. Because its crystallographic structure remains unresolved, homology modeling was used to construct the three-dimensional model for the pore domain of GiK. The docking virtual screening approach was employed to determine whether GiK is a good target for potassium channel blockers. Results The GiK sequence showed 24–50% identity and 50–90% positivity with 21 different types of potassium channels. The quality assessment and validation parameters indicated the reliability of the modeled structure of GiK. We identified 110 potassium channel blockers exhibiting high affinity toward GiK. A total of 39 of these drugs bind in three specific regions. Discussion The GiK pore signature sequence is related to the small conductance calcium-activated potassium channels (SKCa). The predicted binding of 110 potassium blockers to GiK makes this protein an attractive target for biological testing to evaluate its role in the life cycle of Giardia lamblia and potential candidate for the design of novel antigiardial drugs.
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Affiliation(s)
- Lissethe Palomo-Ligas
- Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Filiberto Gutiérrez-Gutiérrez
- Departamento de Química, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Verónica Yadira Ochoa-Maganda
- Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Rafael Cortés-Zárate
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Claudia Lisette Charles-Niño
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Araceli Castillo-Romero
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
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40
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Pan R, Bai X, Chen J, Zhang H, Wang H. Exploring Structural Diversity of Microbe Secondary Metabolites Using OSMAC Strategy: A Literature Review. Front Microbiol 2019; 10:294. [PMID: 30863377 PMCID: PMC6399155 DOI: 10.3389/fmicb.2019.00294] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 02/04/2019] [Indexed: 12/27/2022] Open
Abstract
Microbial secondary metabolites (MSMs) have played and continue to play a highly significant role in the drug discovery and development process. Genetically, MSM chemical structures are biologically synthesized by microbial gene clusters. Recently, however, the speed of new bioactive MSM discovery has been slowing down due to consistent employment of conventional cultivation and isolation procedure. In order to alleviate this challenge, a number of new approaches have been developed. The strategy of one strain many compounds (OSMAC) has been shown as a simple and powerful tool that can activate many silent biogenetic gene clusters in microorganisms to make more natural products. This review highlights important and successful examples using OSMAC approaches, which covers changing medium composition and cultivation status, co-cultivation with other strain(s), adding enzyme inhibitor(s) and MSM biosynthetic precursor(s). Available evidences had shown that variation of cultivation condition is the most effective way to produce more MSMs and facilitate the discovery of new therapeutic agents.
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Affiliation(s)
- Rui Pan
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Xuelian Bai
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Jianwei Chen
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Hong Wang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
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Liang L, Sproule A, Haltli B, Marchbank DH, Berrué F, Overy DP, McQuillan K, Lanteigne M, Duncan N, Correa H, Kerr RG. Discovery of a New Natural Product and a Deactivation of a Quorum Sensing System by Culturing a "Producer" Bacterium With a Heat-Killed "Inducer" Culture. Front Microbiol 2019; 9:3351. [PMID: 30705672 PMCID: PMC6344404 DOI: 10.3389/fmicb.2018.03351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 12/31/2018] [Indexed: 11/28/2022] Open
Abstract
Herein we describe a modified bacterial culture methodology as a tool to discover new natural products via supplementing actinomycete fermentation media with autoclaved cultures of “inducer” microbes. Using seven actinomycetes and four inducer microbes, we detected 28 metabolites that were induced in UHPLC-HRESIMS-based analysis of bacterial fermentations. Metabolomic analysis indicated that each inducer elicited a unique response from the actinomycetes and that some chemical responses were specific to each inducer-producer combination. Among these 28 metabolites, hydrazidomycin D, a new hydrazide-containing natural product was isolated from the pair Streptomyces sp. RKBH-B178 and Mycobacterium smegmatis. This result validated the effectiveness of the strategy in discovering new natural products. From the same set of induced metabolites, an in-depth investigation of a fermentation of Streptomyces sp. RKBH-B178 and autoclaved Pseudomonas aeruginosa led to the discovery of a glucuronidated analog of the pseudomonas quinolone signal (PQS). We demonstrated that RKBH-B178 is able to biotransform the P. aeruginosa quorum sensing molecules, 2-heptyl-4-quinolone (HHQ), and PQS to form PQS-GlcA. Further, PQS-GlcA was shown to have poor binding affinity to PqsR, the innate receptor of HHQ and PQS.
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Affiliation(s)
- Libang Liang
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Amanda Sproule
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Brad Haltli
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada.,Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada.,Nautilus Biosciences Croda, Charlottetown, PE, Canada
| | - Douglas H Marchbank
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada.,Nautilus Biosciences Croda, Charlottetown, PE, Canada
| | - Fabrice Berrué
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada
| | - David P Overy
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada.,Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada
| | | | - Martin Lanteigne
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Noelle Duncan
- Nautilus Biosciences Croda, Charlottetown, PE, Canada
| | | | - Russell G Kerr
- Department of Chemistry, University of Prince Edward Island, Charlottetown, PE, Canada.,Department of Biomedical Sciences, Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada.,Nautilus Biosciences Croda, Charlottetown, PE, Canada
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Oxidative enzymes activity and hydrogen peroxide production in white-rot fungi and soil-borne micromycetes co-cultures. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1413-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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43
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Mafezoli J, Xu YM, Hilário F, Freidhof B, Espinosa-Artiles P, dos Santos LC, de Oliveira MCF, Gunatilaka AAL. Modulation of polyketide biosynthetic pathway of the endophytic fungus, Anteaglonium sp. FL0768, by copper (II) and anacardic acid. PHYTOCHEMISTRY LETTERS 2018; 28:157-163. [PMID: 31354886 PMCID: PMC6660184 DOI: 10.1016/j.phytol.2018.10.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In an attempt to explore the biosynthetic potential of endosymbiotic fungi, the secondary metabolite profiles of the endophytic fungus, Anteaglonium sp. FL0768, cultured under a variety of conditions were investigated. In potato dextrose broth (PDB) medium, Anteaglonium sp. FL0768 produced the heptaketides, herbaridine A (1), herbarin (2), 1-hydroxydehydroherbarin (3), scorpinone (4), and the methylated hexaketide 9S,11R-(+)-ascosalitoxin (5). Incorporation of commonly used epigenetic modifiers, 5-azacytidine and suberoylanilide hydroxamic acid, into the PDB culture medium of this fungus had no effect on its secondary metabolite profile. However, the histone acetyl transferase inhibitor, anacardic acid, slightly affected the metabolite profile affording scorpinone (4) as the major metabolite together with 1-hydroxydehydroherbarin (3) and a different methylated hexaketide, ascochitine (6). Intriguingly, incorporaion of Cu2+ into the PDB medium enhanced production of metabolites and drastically affected the biosynthetic pathway resulting in the production of pentaketide dimers, palmarumycin CE4 (7), palmarumycin CP4 (8), and palmarumycin CP1 (9), in addition to ascochitine (6). The structure of the new metabolite 7 was established with the help of spectroscopic data and by MnO2 oxidation to the known pentaketide dimer, palmarumycin CP3 (10). Biosynthetic pathways to some metabolites in Anteaglonium sp. FL0768 are presented and possible effects of AA and Cu2+ on these pathways are discussed.
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Affiliation(s)
- Jair Mafezoli
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, USA
- Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Campus do Pici, Caixa Postal 6044, Fortaleza-CE, 60455-970, Brazil
| | - Ya-ming Xu
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, USA
| | - Felipe Hilário
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, USA
- Departamento de Química Orgânica, Instituto de Química, UNESP, Universidade Estadual Paulista, Araraquara, Sao Paulo, 14800-900, Brazil
| | - Brandon Freidhof
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, USA
| | - Patricia Espinosa-Artiles
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, USA
| | - Lourdes C. dos Santos
- Departamento de Química Orgânica, Instituto de Química, UNESP, Universidade Estadual Paulista, Araraquara, Sao Paulo, 14800-900, Brazil
| | - Maria C. F. de Oliveira
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, USA
- Departamento de Química Orgânica e Inorgânica, Universidade Federal do Ceará, Campus do Pici, Caixa Postal 6044, Fortaleza-CE, 60455-970, Brazil
| | - A. A. Leslie Gunatilaka
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, The University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, USA
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El-Hawary SS, Sayed AM, Mohammed R, Khanfar MA, Rateb ME, Mohammed TA, Hajjar D, Hassan HM, Gulder TAM, Abdelmohsen UR. New Pim-1 Kinase Inhibitor From the Co-culture of Two Sponge-Associated Actinomycetes. Front Chem 2018; 6:538. [PMID: 30525020 PMCID: PMC6262321 DOI: 10.3389/fchem.2018.00538] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/16/2018] [Indexed: 11/14/2022] Open
Abstract
Saccharomonospora sp. UR22 and Dietzia sp. UR66, two actinomycetes derived from the Red Sea sponge Callyspongia siphonella, were co-cultured and the induced metabolites were monitored by HPLC-DAD and TLC. Saccharomonosporine A (1), a novel brominated oxo-indole alkaloid, convolutamydine F (2) along with other three known induced metabolites (3-5) were isolated from the EtOAc extract of Saccharomonospora sp. UR22 and Dietzia sp. UR66 co-culture. Additionally, axenic culture of Saccharomonospora sp. UR22 led to isolation of six known microbial metabolites (6-11). A kinase inhibition assay results showed that compounds 1 and 3 were potent Pim-1 kinase inhibitors with an IC50 value of 0.3 ± 0.02 and 0.95 ± 0.01 μM, respectively. Docking studies revealed the binding mode of compounds 1 and 3 in the ATP pocket of Pim-1 kinase. Testing of compounds 1 and 3 displayed significant antiproliferative activity against the human colon adenocarcinoma HT-29, (IC50 3.6 and 3.7 μM, respectively) and the human promyelocytic leukemia HL-60, (IC50 2.8 and 4.2 μM, respectively). These results suggested that compounds 1 and 3 act as potential Pim-1 kinase inhibitors that mediate the tumor cell growth inhibitory effect. This study highlighted the co-cultivation approach as an effective strategy to increase the chemical diversity of the secondary metabolites hidden in the genomes of the marine actinomycetes.
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Affiliation(s)
- Seham S El-Hawary
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Ahmed M Sayed
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt.,Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - Rabab Mohammed
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt
| | - Mohammad A Khanfar
- Faculty of Pharmacy, The University of Jordan, Amman, Jordan.,College of Pharmacy, Alfaisal University, Riyadh, Saudi Arabia
| | - Mostafa E Rateb
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt.,School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley, United Kingdom.,Marine Biodiscovery Centre, University of Aberdeen, Aberdeen, United Kingdom
| | - Tarek A Mohammed
- Marine Invertebrates, National Institute of Oceanography and Fisheries, Red Sea Branch, Hurghada, Egypt
| | - Dina Hajjar
- Department of Biochemistry, Faculty of Science, Center for Science and Medical Research, University of Jeddah, Jeddah, Saudi Arabia
| | - Hossam M Hassan
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt.,Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - Tobias A M Gulder
- Department of Chemistry and Center for Integrated Protein Science Munich (CIPSM), Biosystems Chemistry, Technical University of Munich, Garching, Germany.,Chair of Technical Biochemistry, Technische Universität Dresden, Dresden, Germany
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Inter-Kingdom beach warfare: Microbial chemical communication activates natural chemical defences. ISME JOURNAL 2018; 13:147-158. [PMID: 30116041 DOI: 10.1038/s41396-018-0265-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 07/10/2018] [Accepted: 07/26/2018] [Indexed: 11/09/2022]
Abstract
An inter-kingdom beach warfare between a Streptomyces sp. and Aspergillus sp. co-isolated from shallow water beach sand, collected off Heron Island, Queensland, Australia, saw the bacteriostatic Aspergillus metabolite cyclo-(L-Phe-trans-4-hydroxy-L-Pro) (3) stimulate the Streptomyces to produce nitric oxide (NO), which in turn mediated transcriptional activation of a silent biosynthetic gene cluster (BGC) for fungistatic heronapyrrole B (1). Structure activity relationship studies, coupled with the use of NO synthase inhibitors, donors and scavangers, and both genomic and transcriptomic analyses, confirmed the extraordinary chemical cue specificity of 3, and its NO-mediated mechanism of transcriptional action. Our findings reveal the importance of inter-kingdom (fungal-bacterial) chemical communication in the regulation of silent BGCs coding for chemical defenses. We propose that the detection and characterisation of NO mediated transcriptional activation (NOMETA) of silent chemical defences in the environment, may inspire broader application in the field of microbial biodiscovery.
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46
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Copmans D, Rateb M, Tabudravu JN, Pérez-Bonilla M, Dirkx N, Vallorani R, Diaz C, Pérez del Palacio J, Smith AJ, Ebel R, Reyes F, Jaspars M, de Witte PAM. Zebrafish-Based Discovery of Antiseizure Compounds from the Red Sea: Pseurotin A 2 and Azaspirofuran A. ACS Chem Neurosci 2018; 9:1652-1662. [PMID: 29672015 DOI: 10.1021/acschemneuro.8b00060] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In search for novel antiseizure drugs (ASDs), the European FP7-funded PharmaSea project used zebrafish embryos and larvae as a drug discovery platform to screen marine natural products to identify promising antiseizure hits in vivo for further development. Within the framework of this project, seven known heterospirocyclic γ-lactams, namely, pseurotin A, pseurotin A2, pseurotin F1, 11- O-methylpseurotin A, pseurotin D, azaspirofuran A, and azaspirofuran B, were isolated from the bioactive marine fungus Aspergillus fumigatus, and their antiseizure activity was evaluated in the larval zebrafish pentylenetetrazole (PTZ) seizure model. Pseurotin A2 and azaspirofuran A were identified as antiseizure hits, while their close chemical analogues were inactive. Besides, electrophysiological analysis from the zebrafish midbrain demonstrated that pseurotin A2 and azaspirofuran A also ameliorate PTZ-induced epileptiform discharges. Next, to determine whether these findings translate to mammalians, both compounds were analyzed in the mouse 6 Hz (44 mA) psychomotor seizure model. They lowered the seizure duration dose-dependently, thereby confirming their antiseizure properties and suggesting activity against drug-resistant seizures. Finally, in a thorough ADMET assessment, pseurotin A2 and azaspirofuran A were found to be drug-like. Based on the prominent antiseizure activity in both species and the drug-likeness, we propose pseurotin A2 and azaspirofuran A as lead compounds that are worth further investigation for the treatment of epileptic seizures. This study not only provides the first evidence of antiseizure activity of pseurotins and azaspirofurans, but also demonstrates the value of the zebrafish model in (marine) natural product drug discovery in general, and for ASD discovery in particular.
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Affiliation(s)
- Daniëlle Copmans
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven - University of Leuven, 3000 Leuven, Belgium
| | - Mostafa Rateb
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, United Kingdom
- Faculty of Pharmacy, Pharmacognosy Department, Beni-Suef University, Beni-Suef 62513, Egypt
| | - Jioji N. Tabudravu
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, United Kingdom
| | - Mercedes Pérez-Bonilla
- Fundación
MEDINA, Centro de Excelencia en Investigación de Medicamentos
Innovadores en Andalucía, Parque Tecnológico de Ciencias
de la Salud, E-18016 Granada, Spain
| | - Nina Dirkx
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven - University of Leuven, 3000 Leuven, Belgium
| | - Riccardo Vallorani
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven - University of Leuven, 3000 Leuven, Belgium
| | - Caridad Diaz
- Fundación
MEDINA, Centro de Excelencia en Investigación de Medicamentos
Innovadores en Andalucía, Parque Tecnológico de Ciencias
de la Salud, E-18016 Granada, Spain
| | - José Pérez del Palacio
- Fundación
MEDINA, Centro de Excelencia en Investigación de Medicamentos
Innovadores en Andalucía, Parque Tecnológico de Ciencias
de la Salud, E-18016 Granada, Spain
| | - Alan J. Smith
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, United Kingdom
| | - Rainer Ebel
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, United Kingdom
| | - Fernando Reyes
- Fundación
MEDINA, Centro de Excelencia en Investigación de Medicamentos
Innovadores en Andalucía, Parque Tecnológico de Ciencias
de la Salud, E-18016 Granada, Spain
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, United Kingdom
| | - Peter A. M. de Witte
- Laboratory for Molecular Biodiscovery, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven - University of Leuven, 3000 Leuven, Belgium
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Nai C, Meyer V. From Axenic to Mixed Cultures: Technological Advances Accelerating a Paradigm Shift in Microbiology. Trends Microbiol 2018; 26:538-554. [DOI: 10.1016/j.tim.2017.11.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/25/2017] [Accepted: 11/08/2017] [Indexed: 02/07/2023]
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Bhatia SK, Bhatia RK, Choi YK, Kan E, Kim YG, Yang YH. Biotechnological potential of microbial consortia and future perspectives. Crit Rev Biotechnol 2018; 38:1209-1229. [PMID: 29764204 DOI: 10.1080/07388551.2018.1471445] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Design of a microbial consortium is a newly emerging field that enables researchers to extend the frontiers of biotechnology from a pure culture to mixed cultures. A microbial consortium enables microbes to use a broad range of carbon sources. It provides microbes with robustness in response to environmental stress factors. Microbes in a consortium can perform complex functions that are impossible for a single organism. With advancement of technology, it is now possible to understand microbial interaction mechanism and construct consortia. Microbial consortia can be classified in terms of their construction, modes of interaction, and functions. Here we discuss different trends in the study of microbial functions and interactions, including single-cell genomics (SCG), microfluidics, fluorescent imaging, and membrane separation. Community profile studies using polymerase chain-reaction denaturing gradient gel electrophoresis (PCR-DGGE), amplified ribosomal DNA restriction analysis (ARDRA), and terminal restriction fragment-length polymorphism (T-RFLP) are also reviewed. We also provide a few examples of their possible applications in areas of biopolymers, bioenergy, biochemicals, and bioremediation.
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Affiliation(s)
- Shashi Kant Bhatia
- a Department of Biological Engineering, College of Engineering , Konkuk University , Seoul , South Korea.,b Institute for Ubiquitous Information Technology and Application , Konkuk University , Seoul , South Korea
| | - Ravi Kant Bhatia
- c Department of Biotechnology , Himachal Pradesh University , Shimla , India
| | - Yong-Keun Choi
- a Department of Biological Engineering, College of Engineering , Konkuk University , Seoul , South Korea.,d Texas A&M AGRILIFE Research & Extension Center , Texas A&M University , Stephenville , TX , USA
| | - Eunsung Kan
- d Texas A&M AGRILIFE Research & Extension Center , Texas A&M University , Stephenville , TX , USA
| | - Yun-Gon Kim
- e Department of Chemical Engineering , Soongsil University , Seoul , South Korea
| | - Yung-Hun Yang
- a Department of Biological Engineering, College of Engineering , Konkuk University , Seoul , South Korea.,b Institute for Ubiquitous Information Technology and Application , Konkuk University , Seoul , South Korea
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Rare taxa and dark microbial matter: novel bioactive actinobacteria abound in Atacama Desert soils. Antonie van Leeuwenhoek 2018; 111:1315-1332. [PMID: 29721711 DOI: 10.1007/s10482-018-1088-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/20/2018] [Indexed: 12/19/2022]
Abstract
An "in house" taxonomic approach to drug discovery led to the isolation of diverse actinobacteria from hyper-arid, extreme hyper-arid and very high altitude Atacama Desert soils. A high proportion of the isolates were assigned to novel taxa, with many showing activity in standard antimicrobial plug assays. The application of more advanced taxonomic and screening strategies showed that strains classified as novel species of Lentzea and Streptomyces synthesised new specialised metabolites thereby underpinning the premise that the extreme abiotic conditions in the Atacama Desert favour the development of a unique actinobacterial diversity which is the basis of novel chemistry. Complementary metagenomic analyses showed that the soils encompassed an astonishing degree of actinobacterial 'dark matter', while rank-abundance analyses showed them to be highly diverse habitats mainly composed of rare taxa that have not been recovered using culture-dependent methods. The implications of these pioneering studies on future bioprospecting campaigns are discussed.
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50
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Natural product diversity of actinobacteria in the Atacama Desert. Antonie van Leeuwenhoek 2018; 111:1467-1477. [DOI: 10.1007/s10482-018-1030-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/25/2018] [Indexed: 11/26/2022]
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