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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] [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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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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Wang L, Ge S, Liang W, Liao W, Li W, Jiao G, Wei X, Shao G, Xie L, Sheng Z, Hu S, Tang S, Hu P. Genome-Wide Characterization Reveals Variation Potentially Involved in Pathogenicity and Mycotoxins Biosynthesis of Fusarium proliferatum Causing Spikelet Rot Disease in Rice. Toxins (Basel) 2022; 14:toxins14080568. [PMID: 36006230 PMCID: PMC9414198 DOI: 10.3390/toxins14080568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/04/2022] [Accepted: 08/17/2022] [Indexed: 12/12/2022] Open
Abstract
Fusarium proliferatum is the primary cause of spikelet rot disease in rice (Oryza sativa L.) in China. The pathogen not only infects a wide range of cereals, causing severe yield losses but also contaminates grains by producing various mycotoxins that are hazardous to humans and animals. Here, we firstly reported the whole-genome sequence of F. proliferatum strain Fp9 isolated from the rice spikelet. The genome was approximately 43.9 Mb with an average GC content of 48.28%, and it was assembled into 12 scaffolds with an N50 length of 4,402,342 bp. There is a close phylogenetic relationship between F. proliferatum and Fusarium fujikuroi, the causal agent of the bakanae disease of rice. The expansion of genes encoding cell wall-degrading enzymes and major facilitator superfamily (MFS) transporters was observed in F. proliferatum relative to other fungi with different nutritional lifestyles. Species-specific genes responsible for mycotoxins biosynthesis were identified among F. proliferatum and other Fusarium species. The expanded and unique genes were supposed to promote F. proliferatum adaptation and the rapid response to the host's infection. The high-quality genome of F. proliferatum strain Fp9 provides a valuable resource for deciphering the mechanisms of pathogenicity and secondary metabolism, and therefore shed light on development of the disease management strategies and detoxification of mycotoxins contamination for spikelet rot disease in rice.
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Knowles SL, Raja HA, Roberts CD, Oberlies NH. Fungal-fungal co-culture: a primer for generating chemical diversity. Nat Prod Rep 2022; 39:1557-1573. [PMID: 35137758 PMCID: PMC9384855 DOI: 10.1039/d1np00070e] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Indexed: 01/25/2023]
Abstract
Covering: 2002 to 2020In their natural environment, fungi must compete for resources. It has been hypothesized that this competition likely induces the biosynthesis of secondary metabolites for defence. In a quest to discover new chemical diversity from fungal cultures, a growing trend has been to recapitulate this competitive environment in the laboratory, essentially growing fungi in co-culture. This review covers fungal-fungal co-culture studies beginning with the first literature report in 2002. Since then, there has been a growing number of new secondary metabolites reported as a result of fungal co-culture studies. Specifically, this review discusses and provides insights into (1) rationale for pairing fungal strains, (2) ways to grow fungi for co-culture, (3) different approaches to screening fungal co-cultures for chemical diversity, (4) determining the secondary metabolite-producing strain, and (5) final thoughts regarding the fungal-fungal co-culture approach. Our goal is to provide a set of practical strategies for fungal co-culture studies to generate unique chemical diversity that the natural products research community can utilize.
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Affiliation(s)
- Sonja L Knowles
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Huzefa A Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Christopher D Roberts
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
| | - Nicholas H Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC, USA.
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Montoya-Martínez AC, O'Donnell K, Busman M, Vaughan MM, McCormick SP, Santillán-Mendoza R, Pineda-Vaca D, Clapes-Garduño L, Fernández-Pavía SP, Ploetz RC, Benítez-Malvido J, Montero-Castro JC, Rodríguez-Alvarado G. Weeds Harbor Fusarium Species that Cause Malformation Disease of Economically Important Trees in Western Mexico. PLANT DISEASE 2022; 106:612-622. [PMID: 34569826 DOI: 10.1094/pdis-06-21-1339-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Mango malformation disease (MMD) caused by Fusarium spp. is an important limiting factor in most production areas worldwide. Fusarium mexicanum and F. pseudocircinatum have been reported as causing MMD in Mexico. These two pathogens also cause a similar disease in Swietenia macrophylla (big-leaf mahogany malformation disease) in central western Mexico, and F. pseudocircinatum was recently reported as causing malformation disease in Tabebuia rosea (rosy trumpet) in the same region. These studies suggest that additional plant species, including weeds, might be hosts of these pathogens. The role that weed hosts might have in the disease cycle is unknown. The objectives of this work were to recover Fusarium isolates from understory vegetation in mango orchards with MMD, identify the Fusarium isolates through DNA sequence data, and determine whether F. mexicanum is capable of inducing disease in the weedy legume Senna uniflora (oneleaf senna). Additional objectives in this work were to compare Fusarium isolates recovered from weeds and mango trees in the same orchards by characterizing their phylogenetic relationships, assessing in vitro production of mycotoxins, and identifying their mating type idiomorph. A total of 59 Fusarium isolates from five species complexes were recovered from apical and lateral buds from four weed species. Two of the species within the F. fujikuroi species complex are known to cause MMD in Mexico. Trichothecene production was detected in five isolates, including F. sulawense and F. irregulare in the F. incarnatum-equiseti species complex and F. boothii in the F. sambucinum species complex. Both mating types were present among mango and weed isolates. This is the first report of herbaceous hosts harboring Fusarium species that cause mango malformation in Mexico. The information provided should prove valuable for further study of the epidemiological role of weeds in MMD and help manage the disease.
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Affiliation(s)
- Amelia C Montoya-Martínez
- Laboratorio de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
| | - Kerry O'Donnell
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, National Center for Agricultural Utilization Research, Peoria, IL 61604, U.S.A
| | - Mark Busman
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, National Center for Agricultural Utilization Research, Peoria, IL 61604, U.S.A
| | - Martha M Vaughan
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, National Center for Agricultural Utilization Research, Peoria, IL 61604, U.S.A
| | - Susan P McCormick
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, National Center for Agricultural Utilization Research, Peoria, IL 61604, U.S.A
| | - Ricardo Santillán-Mendoza
- Laboratorio de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
- Campo Experimental Ixtacuaco, CIRGOC, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Tlapacoyan, Veracruz, México
| | - Daniela Pineda-Vaca
- Laboratorio de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
| | - Lyana Clapes-Garduño
- Laboratorio de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
| | - Sylvia P Fernández-Pavía
- Laboratorio de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
| | - Randy C Ploetz
- Department of Plant Pathology, Tropical Research and Education Center, University of Florida, Homestead, FL 33031-3314, U.S.A
| | - Julieta Benítez-Malvido
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, Michoacán 58190, México
| | | | - Gerardo Rodríguez-Alvarado
- Laboratorio de Patología Vegetal, IIAF, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
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6
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Alfattani A, Marcourt L, Hofstetter V, Queiroz EF, Leoni S, Allard PM, Gindro K, Stien D, Perron K, Wolfender JL. Combination of Pseudo-LC-NMR and HRMS/MS-Based Molecular Networking for the Rapid Identification of Antimicrobial Metabolites From Fusarium petroliphilum. Front Mol Biosci 2021; 8:725691. [PMID: 34746230 PMCID: PMC8569130 DOI: 10.3389/fmolb.2021.725691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/06/2021] [Indexed: 01/31/2023] Open
Abstract
An endophytic fungal strain isolated from a seagrass endemic to the Mediterranean Sea (Posidonia oceanica) was studied in order to identify its antimicrobial constituents and further characterize the composition of its metabolome. It was identified as Fusarium petroliphilum by in-depth phylogenetic analyses. The ethyl acetate extract of that strain exhibited antimicrobial activities and an ability to inhibit quorum sensing of Staphylococcus aureus. To perform this study with a few tens of mg of extract, an innovative one-step generic strategy was devised. On one side, the extract was analyzed by UHPLC-HRMS/MS molecular networking for dereplication. On the other side, semi-preparative HPLC using a similar gradient profile was used for a single-step high-resolution fractionation. All fractions were systematically profiled by 1H-NMR. The data were assembled into a 2D contour map, which we call “pseudo-LC-NMR,” and combined with those of UHPLC-HRMS/MS. This further highlighted the connection within structurally related compounds, facilitated data interpretation, and provided an unbiased quantitative profiling of the main extract constituents. This innovative strategy led to an unambiguous characterization of all major specialized metabolites of that extract and to the localization of its bioactive compounds. Altogether, this approach identified 22 compounds, 13 of them being new natural products and six being inhibitors of the quorum sensing mechanism of S. aureus and Pseudomonas aeruginosa. Minor analogues were also identified by annotation propagation through the corresponding HRMS/MS molecular network, which enabled a consistent annotation of 27 additional metabolites. This approach was designed to be generic and applicable to natural extracts of the same polarity range.
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Affiliation(s)
- Abdulelah Alfattani
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, ISPSO, University of Geneva, Geneva, Switzerland
| | - Laurence Marcourt
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, ISPSO, University of Geneva, Geneva, Switzerland
| | - Valérie Hofstetter
- Institute for Plant Production Sciences IPS, Agroscope, Nyon, Switzerland
| | - Emerson Ferreira Queiroz
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, ISPSO, University of Geneva, Geneva, Switzerland
| | - Sara Leoni
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, ISPSO, University of Geneva, Geneva, Switzerland
| | - Katia Gindro
- Institute for Plant Production Sciences IPS, Agroscope, Nyon, Switzerland
| | - Didier Stien
- Laboratoire de Biodiversité et Biotechnologie Microbienne, USR3579, CNRS, Sorbonne Université, Banyuls-sur-mer, France
| | - Karl Perron
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, ISPSO, University of Geneva, Geneva, Switzerland
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7
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Rangel LI, Hamilton O, de Jonge R, Bolton MD. Fungal social influencers: secondary metabolites as a platform for shaping the plant-associated community. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:632-645. [PMID: 34510609 DOI: 10.1111/tpj.15490] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
Fungal secondary metabolites (FSMs) are capable of manipulating plant community dynamics by inhibiting or facilitating the establishment of co-habitating organisms. Although production of FSMs is not crucial for survival of the producer, their absence can indirectly impair growth and/or niche competition of these fungi on the plant. The presence of FSMs with no obvious consequence on the fitness of the producer leaves questions regarding ecological impact. This review investigates how fungi employ FSMs as a platform to mediate fungal-fungal, fungal-bacterial and fungal-animal interactions associated with the plant community. We discuss how the biological function of FSMs may indirectly benefit the producer by altering the dynamics of surrounding organisms. We introduce several instances where FSMs influence antagonistic- or alliance-driven interactions. Part of our aim is to decipher the meaning of the FSM 'language' as it is widely noted to impact the surrounding community. Here, we highlight the contribution of FSMs to plant-associated interaction networks that affect the host either broadly or in ways that may have previously been unclear.
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Affiliation(s)
- Lorena I Rangel
- Northern Crop Science Laboratory, US Dept. Agriculture, Fargo, ND, USA
| | - Olivia Hamilton
- Northern Crop Science Laboratory, US Dept. Agriculture, Fargo, ND, USA
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
| | - Ronnie de Jonge
- Department of Plant-Microbe Interactions, Utrecht University, Utrecht, The Netherlands
| | - Melvin D Bolton
- Northern Crop Science Laboratory, US Dept. Agriculture, Fargo, ND, USA
- Department of Plant Pathology, North Dakota State University, Fargo, ND, USA
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8
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Kapoore RV, Padmaperuma G, Maneein S, Vaidyanathan S. Co-culturing microbial consortia: approaches for applications in biomanufacturing and bioprocessing. Crit Rev Biotechnol 2021; 42:46-72. [PMID: 33980092 DOI: 10.1080/07388551.2021.1921691] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The application of microbial co-cultures is now recognized in the fields of biotechnology, ecology, and medicine. Understanding the biological interactions that govern the association of microorganisms would shape the way in which artificial/synthetic co-cultures or consortia are developed. The ability to accurately predict and control cell-to-cell interactions fully would be a significant enabler in synthetic biology. Co-culturing method development holds the key to strategically engineer environments in which the co-cultured microorganism can be monitored. Various approaches have been employed which aim to emulate the natural environment and gain access to the untapped natural resources emerging from cross-talk between partners. Amongst these methods are the use of a communal liquid medium for growth, use of a solid-liquid interface, membrane separation, spatial separation, and use of microfluidics systems. Maximizing the information content of interactions monitored is one of the major challenges that needs to be addressed by these designs. This review critically evaluates the significance and drawbacks of the co-culturing approaches used to this day in biotechnological applications, relevant to biomanufacturing. It is recommended that experimental results for a co-cultured species should be validated with different co-culture approaches due to variations in interactions that could exist as a result of the culturing method selected.
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Affiliation(s)
- Rahul Vijay Kapoore
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK.,Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | - Gloria Padmaperuma
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK
| | - Supattra Maneein
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, UK.,Department of Pharmaceutical, Chemical & Environmental Sciences, The University of Greenwich, Kent, UK
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Fumero MV, Sulyok M, Ramirez ML, Leslie JF, Chulze SN. Effects of water activity and temperature on fusaric and fusarinolic acid production by Fusarium temperatum. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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10
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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: 55] [Impact Index Per Article: 13.8] [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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11
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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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12
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Liu S, Wu B, Lv S, Shen Z, Li R, Yi G, Li C, Guo X. Genetic Diversity in FUB Genes of Fusarium oxysporum f. sp. cubense Suggests Horizontal Gene Transfer. FRONTIERS IN PLANT SCIENCE 2019; 10:1069. [PMID: 31552071 PMCID: PMC6738028 DOI: 10.3389/fpls.2019.01069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 08/07/2019] [Indexed: 05/02/2023]
Abstract
Fusaric acid (FA) is an important secondary metabolite of many Fusarium species and involved in the wilt symptoms caused in banana by Fusarium oxysporum f. sp. cubense (Foc). To investigate the evolution characteristics of the 12 Foc FA biosynthetic genes (FUB), coding sequences of the 12 FUB genes and three housekeeping genes, EF-1α/RPB1/RPB2 (translation elongation factor-1α/RNA polymerase II subunit I/RNA polymerase II subunit II), were subjected to genetic diversity analysis, phylogenetic analysis, recombination detection, and selective pressure analysis. The results of selective pressure analysis showed that the 15 genes were mainly subjected to negative selection. However, a significantly higher number of silent mutations, which could not be simply explained by selective pressure difference, were observed in the 12 FUB genes in Foc than in the three housekeeping genes. Infraspecies phylogeny and recombination detection analysis showed that significantly more horizontal gene transfer (HGT) events (normalized) had occurred in the FUB genes than in the three housekeeping genes. In addition, many of these events involved outgroup isolates and significantly increased the genetic diversity of FUB genes in Foc. The infraspecies phylogenetic analysis suggested that the polyphyletic phylogeny proposed for Foc requires further discussion, and the divergence of race 1, race 4, and the common ancestor of several F. oxysporum (Fo) isolates pathogenic to nonbanana plants should have diverged over a short period. Finally, our results suggest that the FUB genes in Fo should have benefited from HGT to gain a relatively high genetic diversity to respond to different host plants and environments despite mainly being subject to negative selection.
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Affiliation(s)
- Siwen Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Bo Wu
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shuxia Lv
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Zongzhuan Shen
- Jiangsu Key Lab for Solid Organic Waste Utilization, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Rong Li
- Jiangsu Key Lab for Solid Organic Waste Utilization, Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ganjun Yi
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chunyu Li
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Key Laboratory of Tropical and Subtropical Fruit Tree Research of Guangdong Province, Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- *Correspondence: Chunyu Li, ; Xiuwu Guo,
| | - Xiuwu Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- *Correspondence: Chunyu Li, ; Xiuwu Guo,
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Azzollini A, Boggia L, Boccard J, Sgorbini B, Lecoultre N, Allard PM, Rubiolo P, Rudaz S, Gindro K, Bicchi C, Wolfender JL. Dynamics of Metabolite Induction in Fungal Co-cultures by Metabolomics at Both Volatile and Non-volatile Levels. Front Microbiol 2018; 9:72. [PMID: 29459851 PMCID: PMC5807337 DOI: 10.3389/fmicb.2018.00072] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/11/2018] [Indexed: 11/24/2022] Open
Abstract
Fungal co-cultivation has emerged as a promising way for activating cryptic biosynthetic pathways and discovering novel antimicrobial metabolites. For the success of such studies, a key element remains the development of standardized co-cultivation methods compatible with high-throughput analytical procedures. To efficiently highlight induction processes, it is crucial to acquire a holistic view of intermicrobial communication at the molecular level. To tackle this issue, a strategy was developed based on the miniaturization of fungal cultures that allows for a concomitant survey of induction phenomena in volatile and non-volatile metabolomes. Fungi were directly grown in vials, and each sample was profiled by head space solid phase microextraction gas chromatography mass spectrometry (HS-SPME-GC-MS), while the corresponding solid culture medium was analyzed by liquid chromatography high resolution mass spectrometry (LC-HRMS) after solvent extraction. This strategy was implemented for the screening of volatile and non-volatile metabolite inductions in an ecologically relevant fungal co-culture of Eutypa lata (Pers.) Tul. & C. Tul. (Diatrypaceae) and Botryosphaeria obtusa (Schwein.) Shoemaker (Botryosphaeriaceae), two wood-decaying fungi interacting in the context of esca disease of grapevine. For a comprehensive evaluation of the results, a multivariate data analysis combining Analysis of Variance and Partial Least Squares approaches, namely AMOPLS, was used to explore the complex LC-HRMS and GC-MS datasets and highlight dynamically induced compounds. A time-series study was carried out over 9 days, showing characteristic metabolite induction patterns in both volatile and non-volatile dimensions. Relevant links between the dynamics of expression of specific metabolite production were observed. In addition, the antifungal activity of 2-nonanone, a metabolite incrementally produced over time in the volatile fraction, was assessed against Eutypa lata and Botryosphaeria obtusa in an adapted bioassay set for volatile compounds. This compound has shown antifungal activity on both fungi and was found to be co-expressed with a known antifungal compound, O-methylmellein, induced in solid media. This strategy could help elucidate microbial inter- and intra-species cross-talk at various levels. Moreover, it supports the study of concerted defense/communication mechanisms for efficiently identifying original antimicrobials.
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Affiliation(s)
- Antonio Azzollini
- School of Pharmaceutical Sciences (EPGL), University of Geneva, University of Lausanne, Centre Médical Universitaire (CMU), Geneva, Switzerland
| | - Lorenzo Boggia
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Julien Boccard
- School of Pharmaceutical Sciences (EPGL), University of Geneva, University of Lausanne, Centre Médical Universitaire (CMU), Geneva, Switzerland
| | - Barbara Sgorbini
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Nicole Lecoultre
- Plant Protection, Mycology and Biotechnology, Agroscope, Nyon, Switzerland
| | - Pierre-Marie Allard
- School of Pharmaceutical Sciences (EPGL), University of Geneva, University of Lausanne, Centre Médical Universitaire (CMU), Geneva, Switzerland
| | - Patrizia Rubiolo
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Serge Rudaz
- School of Pharmaceutical Sciences (EPGL), University of Geneva, University of Lausanne, Centre Médical Universitaire (CMU), Geneva, Switzerland
| | - Katia Gindro
- Plant Protection, Mycology and Biotechnology, Agroscope, Nyon, Switzerland
| | - Carlo Bicchi
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences (EPGL), University of Geneva, University of Lausanne, Centre Médical Universitaire (CMU), Geneva, Switzerland
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