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Elhalis H, See XY, Osen R, Chin XH, Chow Y. The potentials and challenges of using fermentation to improve the sensory quality of plant-based meat analogs. Front Microbiol 2023; 14:1267227. [PMID: 37860141 PMCID: PMC10582269 DOI: 10.3389/fmicb.2023.1267227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/19/2023] [Indexed: 10/21/2023] Open
Abstract
Despite the advancements made in improving the quality of plant-based meat substitutes, more work needs to be done to match the texture, appearance, and flavor of real meat. This review aims to cover the sensory quality constraints of plant-based meat analogs and provides fermentation as a sustainable approach to push these boundaries. Plant-based meat analogs have been observed to have weak and soft textural quality, poor mouth feel, an unstable color, and unpleasant and beany flavors in some cases, necessitating the search for efficient novel technologies. A wide range of microorganisms, including bacteria such as Lactobacillus acidophilus and Lactiplantibacillus plantarum, as well as fungi like Fusarium venenatum and Neurospora intermedia, have improved the product texture to mimic fibrous meat structures. Additionally, the chewiness and hardness of the resulting meat analogs have been further improved through the use of Bacillus subtilis. However, excessive fermentation may result in a decrease in the final product's firmness and produce a slimy texture. Similarly, several microbial metabolites can mimic the color and flavor of meat, with some concerns. It appears that fermentation is a promising approach to modulating the sensory profiles of plant-derived meat ingredients without adverse consequences. In addition, the technology of starter cultures can be optimized and introduced as a new strategy to enhance the organoleptic properties of plant-based meat while still meeting the needs of an expanding and sustainable economy.
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Affiliation(s)
- Hosam Elhalis
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Food Science and Technology, School of Chemical Engineering, The University of New South Wales, Sydney, NSW, Australia
| | - Xin Yi See
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Raffael Osen
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Xin Hui Chin
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yvonne Chow
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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Hashem AH, Attia MS, Kandil EK, Fawzi MM, Abdelrahman AS, Khader MS, Khodaira MA, Emam AE, Goma MA, Abdelaziz AM. Bioactive compounds and biomedical applications of endophytic fungi: a recent review. Microb Cell Fact 2023; 22:107. [PMID: 37280587 DOI: 10.1186/s12934-023-02118-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/22/2023] [Indexed: 06/08/2023] Open
Abstract
Human life has been significantly impacted by the creation and spread of novel species of antibiotic-resistant bacteria and virus strains that are difficult to manage. Scientists and researchers have recently been motivated to seek out alternatives and other sources of safe and ecologically friendly active chemicals that have a powerful and effective effect against a wide variety of pathogenic bacteria as a result of all these hazards and problems. In this review, endophytic fungi and their bioactive compounds and biomedical applications were discussed. Endophytes, a new category of microbial source that can produce a variety of biological components, have major values for study and broad prospects for development. Recently, endophytic fungi have received much attention as a source for new bioactive compounds. In addition, the variety of natural active compounds generated by endophytes is due to the close biological relationship between endophytes and their host plants. The bioactive compounds separated from endophytes are usually classified as steroids, xanthones, terpenoids, isocoumarins, phenols, tetralones, benzopyranones and enniatines. Moreover, this review discusses enhancement methods of secondary metabolites production by fungal endophytes which include optimization methods, co-culture method, chemical epigenetic modification and molecular-based approaches. Furthermore, this review deals with different medical applications of bioactive compounds such as antimicrobial, antiviral, antioxidant and anticancer activities in the last 3 years.
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Affiliation(s)
- Amr H Hashem
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt.
| | - Mohamed S Attia
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt.
| | - Esalm K Kandil
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Mahmoud M Fawzi
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Ahmed S Abdelrahman
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Mohamed S Khader
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Mohamed A Khodaira
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Abdallah E Emam
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Mohamed A Goma
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Amer M Abdelaziz
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt.
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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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Gakuubi MM, Munusamy M, Liang ZX, Ng SB. Fungal Endophytes: A Promising Frontier for Discovery of Novel Bioactive Compounds. J Fungi (Basel) 2021; 7:786. [PMID: 34682208 PMCID: PMC8538612 DOI: 10.3390/jof7100786] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 12/13/2022] Open
Abstract
For years, fungi have served as repositories of bioactive secondary metabolites that form the backbone of many existing drugs. With the global rise in infections associated with antimicrobial resistance, in addition to the growing burden of non-communicable disease, such as cancer, diabetes and cardiovascular ailments, the demand for new drugs that can provide an improved therapeutic outcome has become the utmost priority. The exploration of microbes from understudied and specialized niches is one of the promising ways of discovering promising lead molecules for drug discovery. In recent years, a special class of plant-associated fungi, namely, fungal endophytes, have emerged as an important source of bioactive compounds with unique chemistry and interesting biological activities. The present review focuses on endophytic fungi and their classification, rationale for selection and prioritization of host plants for fungal isolation and examples of strategies that have been adopted to induce the activation of cryptic biosynthetic gene clusters to enhance the biosynthetic potential of fungal endophytes.
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Affiliation(s)
- Martin Muthee Gakuubi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore; (M.M.G.); (M.M.)
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore;
| | - Madhaiyan Munusamy
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore; (M.M.G.); (M.M.)
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore;
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #01-02 Nanos, Singapore 138669, Singapore; (M.M.G.); (M.M.)
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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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Bhattarai K, Bastola R, Baral B. Antibiotic drug discovery: Challenges and perspectives in the light of emerging antibiotic resistance. ADVANCES IN GENETICS 2020; 105:229-292. [PMID: 32560788 DOI: 10.1016/bs.adgen.2019.12.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Amid a rising threat of antimicrobial resistance in a global scenario, our huge investments and high-throughput technologies injected for rejuvenating the key therapeutic scaffolds to suppress these rising superbugs has been diminishing severely. This has grasped world-wide attention, with increased consideration being given to the discovery of new chemical entities. Research has now proven that the relatively tiny and simpler microbes possess enhanced capability of generating novel and diverse chemical constituents with huge therapeutic leads. The usage of these beneficial organisms could help in producing new chemical scaffolds that govern the power to suppress the spread of obnoxious superbugs. Here in this review, we have explicitly focused on several appealing strategies employed for the generation of new chemical scaffolds. Also, efforts on providing novel insights on some of the unresolved questions in the production of metabolites, metabolic profiling and also the serendipity of getting "hit molecules" have been rigorously discussed. However, we are highly aware that biosynthetic pathway of different classes of secondary metabolites and their biosynthetic route is a vast topic, thus we have avoided discussion on this topic.
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Affiliation(s)
- Keshab Bhattarai
- University of Tübingen, Tübingen, Germany; Center for Natural and Applied Sciences (CENAS), Kathmandu, Nepal
| | - Rina Bastola
- Spinal Cord Injury Association-Nepal (SCIAN), Pokhara, Nepal
| | - Bikash Baral
- Spinal Cord Injury Association-Nepal (SCIAN), Pokhara, Nepal.
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S. Hifnawy M, Hassan HM, Mohammed R, M. Fouda M, Sayed AM, A. Hamed A, F. AbouZid S, Rateb ME, Alhadrami HA, Abdelmohsen UR. Induction of Antibacterial Metabolites by Co-Cultivation of Two Red-Sea-Sponge-Associated Actinomycetes Micromonospora sp. UR56 and Actinokinespora sp. EG49. Mar Drugs 2020; 18:md18050243. [PMID: 32380771 PMCID: PMC7281614 DOI: 10.3390/md18050243] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/23/2020] [Accepted: 04/30/2020] [Indexed: 02/07/2023] Open
Abstract
Liquid chromatography coupled with high resolution mass spectrometry (LC-HRESMS)-assisted metabolomic profiling of two sponge-associated actinomycetes, Micromonospora sp. UR56 and Actinokineospora sp. EG49, revealed that the co-culture of these two actinomycetes induced the accumulation of metabolites that were not traced in their axenic cultures. Dereplication suggested that phenazine-derived compounds were the main induced metabolites. Hence, following large-scale co-fermentation, the major induced metabolites were isolated and structurally characterized as the already known dimethyl phenazine-1,6-dicarboxylate (1), phenazine-1,6-dicarboxylic acid mono methyl ester (phencomycin; 2), phenazine-1-carboxylic acid (tubermycin; 3), N-(2-hydroxyphenyl)-acetamide (9), and p-anisamide (10). Subsequently, the antibacterial, antibiofilm, and cytotoxic properties of these metabolites (1–3, 9, and 10) were determined in vitro. All the tested compounds except 9 showed high to moderate antibacterial and antibiofilm activities, whereas their cytotoxic effects were modest. Testing against Staphylococcus DNA gyrase-B and pyruvate kinase as possible molecular targets together with binding mode studies showed that compounds 1–3 could exert their bacterial inhibitory activities through the inhibition of both enzymes. Moreover, their structural differences, particularly the substitution at C-1 and C-6, played a crucial role in the determination of their inhibitory spectra and potency. In conclusion, the present study highlighted that microbial co-cultivation is an efficient tool for the discovery of new antimicrobial candidates and indicated phenazines as potential lead compounds for further development as antibiotic scaffold.
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Affiliation(s)
- Mohamed S. Hifnawy
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, 11787 Cairo, Egypt;
| | - Hossam M. Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, 62514 Beni-Suef, Egypt; (H.M.H.); (R.M.); (S.F.A.)
| | - Rabab Mohammed
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, 62514 Beni-Suef, Egypt; (H.M.H.); (R.M.); (S.F.A.)
| | - Mohamed M. Fouda
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, 62513 Beni-Suef, Egypt; (M.M.F.); (A.M.S.)
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, 62513 Beni-Suef, Egypt; (M.M.F.); (A.M.S.)
| | - Ahmed A. Hamed
- Microbial Chemistry Department, National Research Center, 33 El-Buhouth Street, 12622 Giza, Egypt;
| | - Sameh F. AbouZid
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, 62514 Beni-Suef, Egypt; (H.M.H.); (R.M.); (S.F.A.)
| | - Mostafa E. Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK;
| | - Hani A. Alhadrami
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Special Infectious Agent Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence: (H.A.A.); (U.R.A.)
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, 61519 Minia, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Universities Zone, P.O. Box 61111 New Minia City, Egypt
- Correspondence: (H.A.A.); (U.R.A.)
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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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Oppong-Danquah E, Budnicka P, Blümel M, Tasdemir D. Design of Fungal Co-Cultivation Based on Comparative Metabolomics and Bioactivity for Discovery of Marine Fungal Agrochemicals. Mar Drugs 2020; 18:md18020073. [PMID: 31979232 PMCID: PMC7073616 DOI: 10.3390/md18020073] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/05/2020] [Accepted: 01/21/2020] [Indexed: 01/03/2023] Open
Abstract
Microbial co-cultivation is employed for awakening silent biosynthetic gene clusters (BGCs) to enhance chemical diversity. However, the selection of appropriate partners for co-cultivation remains a challenge. Furthermore, competitive interactions involving the suppression of BGCs or upregulation of known, functional metabolite(s) during co-cultivation efforts is also common. Herein, we performed an alternative approach for targeted selection of the best co-cultivation pair. Eight marine sediment-derived fungi were classified as strong or weak, based on their anti-phytopathogenic potency. The fungi were co-cultured systematically and analyzed for their chemical profiles and anti-phytopathogenic activity. Based on enhanced bioactivity and a significantly different metabolite profile including the appearance of a co-culture specific cluster, the co-culture of Plenodomus influorescens (strong) and Pyrenochaeta nobilis (weak) was prioritized for chemical investigation. Large-scale co-cultivation resulted in isolation of five polyketide type compounds: two 12-membered macrolides, dendrodolide E (1) and its new analog dendrodolide N (2), as well as two rare azaphilones spiciferinone (3) and its new analog 8a-hydroxy-spiciferinone (4). A well-known bis-naphtho-γ-pyrone type mycotoxin, cephalochromin (5), whose production was specifically enhanced in the co-culture, was also isolated. Chemical structures of compounds 1-5 were elucidated by NMR, HRMS and [] analyses. Compound 5 showed the strongest anti-phytopathogenic activity against Xanthomonas campestris and Phytophthora infestans with IC50 values of 0.9 and 1.7 µg/mL, respectively.
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Affiliation(s)
- Ernest Oppong-Danquah
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (E.O.-D.); (P.B.); (M.B.)
| | - Paulina Budnicka
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (E.O.-D.); (P.B.); (M.B.)
| | - Martina Blümel
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (E.O.-D.); (P.B.); (M.B.)
| | - Deniz Tasdemir
- GEOMAR Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Products Chemistry, GEOMAR Helmholtz Centre for Ocean Research Kiel, Am Kiel-Kanal 44, 24106 Kiel, Germany; (E.O.-D.); (P.B.); (M.B.)
- Faculty of Mathematics and Natural Science, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
- Correspondence: ; Tel.: +49-431-6004430
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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: 61] [Impact Index Per Article: 15.3] [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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Hautbergue T, Jamin EL, Debrauwer L, Puel O, Oswald IP. From genomics to metabolomics, moving toward an integrated strategy for the discovery of fungal secondary metabolites. Nat Prod Rep 2019; 35:147-173. [PMID: 29384544 DOI: 10.1039/c7np00032d] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fungal secondary metabolites are defined by bioactive properties that ensure adaptation of the fungus to its environment. Although some of these natural products are promising sources of new lead compounds especially for the pharmaceutical industry, others pose risks to human and animal health. The identification of secondary metabolites is critical to assessing both the utility and risks of these compounds. Since fungi present biological specificities different from other microorganisms, this review covers the different strategies specifically used in fungal studies to perform this critical identification. Strategies focused on the direct detection of the secondary metabolites are firstly reported. Particularly, advances in high-throughput untargeted metabolomics have led to the generation of large datasets whose exploitation and interpretation generally require bioinformatics tools. Then, the genome-based methods used to study the entire fungal metabolic potential are reported. Transcriptomic and proteomic tools used in the discovery of fungal secondary metabolites are presented as links between genomic methods and metabolomic experiments. Finally, the influence of the culture environment on the synthesis of secondary metabolites by fungi is highlighted as a major factor to consider in research on fungal secondary metabolites. Through this review, we seek to emphasize that the discovery of natural products should integrate all of these valuable tools. Attention is also drawn to emerging technologies that will certainly revolutionize fungal research and to the use of computational tools that are necessary but whose results should be interpreted carefully.
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Affiliation(s)
- T Hautbergue
- Toxalim (Research Centre in Food Toxicology) Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, F-31027 Toulouse, France.
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12
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Li HT, Zhou H, Duan RT, Li HY, Tang LH, Yang XQ, Yang YB, Ding ZT. Inducing Secondary Metabolite Production by Co-culture of the Endophytic Fungus Phoma sp. and the Symbiotic Fungus Armillaria sp. JOURNAL OF NATURAL PRODUCTS 2019; 82:1009-1013. [PMID: 30785282 DOI: 10.1021/acs.jnatprod.8b00685] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Co-culturing the endophytic fungus Phoma sp. YUD17001 from Gastrodia elata with Armillaria sp. in liquid nutrient medium resulted in the production of five new secondary metabolites, including two phenolic compounds, phexandiols A and B (1 and 2), three aliphatic ester derivatives, phomesters A-C (3-5), and a known fatty acid (6). The structures and absolute configurations of these compounds were elucidated by the interpretation of data from detailed spectroscopic analysis, Mosher's method, and electronic circular dichroism spectra, together with consideration of the biogenetic origins. None of the five new compounds were detected in single-strain cultures under identical fermentation conditions. The results of this work indicated that the production of 1-5 involved a complicated interaction process. None of the new compounds possessed significant cytotoxicity or antimicrobial activities.
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Affiliation(s)
- Hong-Tao Li
- Key Laboratory of Functional Molecules Analysis and Biotransformation, Yunnan Provincial Department of Education, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , People's Republic of China
| | - Hao Zhou
- Key Laboratory of Functional Molecules Analysis and Biotransformation, Yunnan Provincial Department of Education, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , People's Republic of China
| | - Rong-Ting Duan
- Key Laboratory of Functional Molecules Analysis and Biotransformation, Yunnan Provincial Department of Education, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , People's Republic of China
| | - Hong-Yu Li
- Key Laboratory of Functional Molecules Analysis and Biotransformation, Yunnan Provincial Department of Education, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , People's Republic of China
| | - Lin-Huan Tang
- Key Laboratory of Functional Molecules Analysis and Biotransformation, Yunnan Provincial Department of Education, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , People's Republic of China
| | - Xue-Qiong Yang
- Key Laboratory of Functional Molecules Analysis and Biotransformation, Yunnan Provincial Department of Education, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , People's Republic of China
| | - Ya-Bin Yang
- Key Laboratory of Functional Molecules Analysis and Biotransformation, Yunnan Provincial Department of Education, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , People's Republic of China
| | - Zhong-Tao Ding
- Key Laboratory of Functional Molecules Analysis and Biotransformation, Yunnan Provincial Department of Education, School of Chemical Science and Technology , Yunnan University , Kunming 650091 , People's Republic of China
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13
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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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14
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Venkatesh N, Keller NP. Mycotoxins in Conversation With Bacteria and Fungi. Front Microbiol 2019; 10:403. [PMID: 30941105 PMCID: PMC6433837 DOI: 10.3389/fmicb.2019.00403] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/15/2019] [Indexed: 12/22/2022] Open
Abstract
An important goal of the mycotoxin research community is to develop comprehensive strategies for mycotoxin control and detoxification. Although significant progress has been made in devising such strategies, yet, there are barriers to overcome and gaps to fill in order to design effective mycotoxin management techniques. This is in part due to a lack of understanding of why fungi produce these toxic metabolites. Here we present cumulative evidence from the literature that indicates an important ecological role for mycotoxins, with particular focus on Fusarium mycotoxins. Further, we suggest that understanding how mycotoxin levels are regulated by microbial encounters can offer novel insights for mycotoxin control in food and feed. Microbial degradation of mycotoxins provides a wealth of chemical information that can be harnessed for large-scale mycotoxin detoxification efforts.
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Affiliation(s)
- Nandhitha Venkatesh
- Department of Plant Pathology, University of Wisconsin—Madison, Madison, WI, United States
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI, United States
- Department of Bacteriology, University of Wisconsin—Madison, Madison, WI, United States
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15
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Nepomuceno VM, Kim H, Ding Y, Liu H, Sadek M, Ferreira D, Omarsdottir S, Murphy BT. Deconvolution of E/Z tetrahydroisoquinoline amide rotamers and conformers from a marine-derived Streptomyces strain. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.11.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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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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17
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Bao J, Wang J, Zhang XY, Nong XH, Qi SH. New Furanone Derivatives and Alkaloids from the Co-Culture of Marine-Derived Fungi Aspergillus sclerotiorum and Penicillium citrinum. Chem Biodivers 2017; 14. [PMID: 27936301 DOI: 10.1002/cbdv.201600327] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 11/29/2016] [Indexed: 02/05/2023]
Abstract
Six new compounds including two furanone derivatives sclerotiorumins A and B (1 and 2), one novel oxadiazin derivative sclerotiorumin C (3), one pyrrole derivative 1-(4-benzyl-1H-pyrrol-3-yl)ethanone (4), and two complexes of neoaspergillic acid aluminiumneohydroxyaspergillin (5) and ferrineohydroxyaspergillin (6) were isolated from the co-culture of marine-derived fungi Aspergillus sclerotiorum and Penicillium citrinum. Compound 3 was the first natural 1,2,4-oxadiazin-6-one. Compound 5 showed significant and selective cytotoxicity against human histiocytic lymphoma U937 cell line (IC50 = 4.2 μm) and strong toxicity towards brine shrimp (LC50 = 6.1 μm), and oppositely increased the growth and biofilm formation of Staphylococcus aureus.
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Affiliation(s)
- Jie Bao
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Material Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, P. R. China
| | - Jie Wang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Material Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, P. R. China
| | - Xiao-Yong Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Material Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, P. R. China
| | - Xu-Hua Nong
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Material Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, P. R. China
| | - Shu-Hua Qi
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Material Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, P. R. China
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18
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Huang H, Li H, Qiu Y, Hou L, Ju J, Li W. A New Dioic Acid from a wbl Gene Mutant of Deepsea-Derived Streptomyces somaliensis SCSIO ZH66. Mar Drugs 2016; 14:md14100184. [PMID: 27763499 PMCID: PMC5082332 DOI: 10.3390/md14100184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/01/2016] [Accepted: 10/08/2016] [Indexed: 01/08/2023] Open
Abstract
The wblAso gene functions as a global regulatory gene in a negative manner in deepsea-derived Streptomyces somaliensis SCSIO ZH66. A new dioic acid (1) as well as two known butenolides (2 and 3) were isolated from the ΔwblAso mutant strain of S. somaliensis SCSIO ZH66. The structure of 1 was elucidated by a combination of spectroscopic analyses, including MS and NMR techniques. In the cell growth inhibitory evaluation, compound 3 exhibited moderate activity against the human hepatic carcinoma cell line (Huh7.5) with an IC50 value of 19.4 μg/mL, while compounds 1 and 2 showed null activity up to 100 μg/mL.
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Affiliation(s)
- Huiming Huang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
| | - Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
| | - Yanhong Qiu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
| | - Lukuan Hou
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
| | - Jianhua Ju
- CAS Key Laboratory of Marine Bio-resources Sustainable Utilization, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China.
| | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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19
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Venugopalan A, Srivastava S. Endophytes as in vitro production platforms of high value plant secondary metabolites. Biotechnol Adv 2015. [PMID: 26225453 DOI: 10.1016/j.biotechadv.2015.07.004] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Many reports have been published on bioprospecting of endophytic fungi capable of producing high value bioactive molecules like, paclitaxel, vincristine, vinblastine, camptothecin and podophyllotoxin. However, commercial exploitation of endophytes for high value-low volume plant secondary metabolites remains elusive due to widely reported genomic instability of endophytes in the axenic culture. While most of the endophyte research focuses on screening endophytes for novel or existing high value biomolecules, very few reports seek to explore the possible mechanisms of production of host-plant associated or novel secondary metabolites in these organisms. With an overview of host-endophyte relationship and its possible impact on the secondary metabolite production potential of endophytes, the review highlights the evidence reported for and against the presence of host-independent biosynthetic machinery in endophytes. The review aims to address the question, why should and how can endophytes be exploited for large scale in vitro production of high value phytochemicals? In this regard, various bioprocess optimization strategies that have been applied to sustain and enhance the product yield from the endophytes have also been described in detail. Further, techniques like mixed fermentation/co-cultivation and use of epigenetic modifiers have also been discussed as potential strategies to activate cryptic gene clusters in endophytes, thereby aiding in novel metabolite discovery and overcoming the limitations associated with axenic culture of endophytes.
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Affiliation(s)
- Aarthi Venugopalan
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, India
| | - Smita Srivastava
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600 036, India.
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20
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Induced production of BE-31405 by co-culturing of Talaromyces siamensis FKA-61 with a variety of fungal strains. J Antibiot (Tokyo) 2015; 68:573-8. [DOI: 10.1038/ja.2015.28] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 02/21/2015] [Accepted: 02/24/2015] [Indexed: 01/25/2023]
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21
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Chagas FO, Caraballo-Rodriguez AM, Pupo MT. Endophytic Fungi as a Source of Novel Metabolites. Fungal Biol 2015. [DOI: 10.1007/978-1-4939-2531-5_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Bills G, Li Y, Chen L, Yue Q, Niu XM, An Z. New insights into the echinocandins and other fungal non-ribosomal peptides and peptaibiotics. Nat Prod Rep 2014; 31:1348-75. [PMID: 25156669 DOI: 10.1039/c4np00046c] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Non-ribosomal peptide synthetases (NRPSs) are a primary modality for fungal peptidic natural product assembly and are responsible for some of the best known, most useful, and most destructive fungal metabolites. Through genome sequencing and computer-assisted recognition of modular motifs of catalytic domains, one can now confidently identify most NRPS biosynthetic genes of a fungal strain. The biosynthetic gene clusters responsible for two of the most important classes of NRP fungal derived drugs, cyclosporine and the echinocandins, have been recently characterized by genomic sequencing and annotation. Complete biosynthetic gene clusters for the pneumocandins and echinocandins have been mapped at the genetic level and functionally characterized to some extent. Genomic sequencing of representative strains of most of the variants in the echinocandin family, including the wild-type of the three fungal strains employed for industrial-scale production of caspofungin, micafungin and anidulofungin, has enabled characterization of the basic architecture of the echinocandin NRPS pathways. A comparative analysis of how pathway genes cause variations in lipoinitiation, biosynthesis of the non-proteinogenic amino acids, amino acid substitutions, and hydroxylations and sulfonations of the core peptide and contribute to the molecular diversity of the family is presented. We also review new information on the natural functions of NRPs, the differences between fungal and bacterial NRPSs, and functional characterization of selected NRPS gene clusters. Continuing discovery of the new fungal nonribosomal peptides has contributed new structural diversity and potential insights into their biological functions among other natural peptides and peptaibiotics. We therefore provide an update on new peptides, depsipeptides and peptaibols discovered in the Fungi since 2009.
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Affiliation(s)
- Gerald Bills
- Texas Therapeutics Institute, The Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Centre at Houston, Houston, Texas 77054, USA.
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23
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Dashti Y, Grkovic T, Abdelmohsen UR, Hentschel U, Quinn RJ. Production of induced secondary metabolites by a co-culture of sponge-associated actinomycetes, Actinokineospora sp. EG49 and Nocardiopsis sp. RV163. Mar Drugs 2014; 12:3046-59. [PMID: 24857962 PMCID: PMC4052330 DOI: 10.3390/md12053046] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 03/04/2014] [Accepted: 04/10/2014] [Indexed: 01/15/2023] Open
Abstract
Two sponge-derived actinomycetes, Actinokineospora sp. EG49 and Nocardiopsis sp. RV163, were grown in co-culture and the presence of induced metabolites monitored by 1H NMR. Ten known compounds, including angucycline, diketopiperazine and β-carboline derivatives 1–10, were isolated from the EtOAc extracts of Actinokineospora sp. EG49 and Nocardiopsis sp. RV163. Co-cultivation of Actinokineospora sp. EG49 and Nocardiopsis sp. RV163 induced the biosynthesis of three natural products that were not detected in the single culture of either microorganism, namely N-(2-hydroxyphenyl)-acetamide (11), 1,6-dihydroxyphenazine (12) and 5a,6,11a,12-tetrahydro-5a,11a-dimethyl[1,4]benzoxazino[3,2-b][1,4]benzoxazine (13a). When tested for biological activity against a range of bacteria and parasites, only the phenazine 12 was active against Bacillus sp. P25, Trypanosoma brucei and interestingly, against Actinokineospora sp. EG49. These findings highlight the co-cultivation approach as an effective strategy to access the bioactive secondary metabolites hidden in the genomes of marine actinomycetes.
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Affiliation(s)
- Yousef Dashti
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
| | - Tanja Grkovic
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
| | - Usama Ramadan Abdelmohsen
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, D-97082 Würzburg, Germany.
| | - Ute Hentschel
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, D-97082 Würzburg, Germany.
| | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
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Bertrand S, Bohni N, Schnee S, Schumpp O, Gindro K, Wolfender JL. Metabolite induction via microorganism co-culture: a potential way to enhance chemical diversity for drug discovery. Biotechnol Adv 2014; 32:1180-204. [PMID: 24651031 DOI: 10.1016/j.biotechadv.2014.03.001] [Citation(s) in RCA: 297] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/28/2014] [Accepted: 03/03/2014] [Indexed: 02/08/2023]
Abstract
Microorganisms have a long track record as important sources of novel bioactive natural products, particularly in the field of drug discovery. While microbes have been shown to biosynthesize a wide array of molecules, recent advances in genome sequencing have revealed that such organisms have the potential to yield even more structurally diverse secondary metabolites. Thus, many microbial gene clusters may be silent under standard laboratory growth conditions. In the last ten years, several methods have been developed to aid in the activation of these cryptic biosynthetic pathways. In addition to the techniques that demand prior knowledge of the genome sequences of the studied microorganisms, several genome sequence-independent tools have been developed. One of these approaches is microorganism co-culture, involving the cultivation of two or more microorganisms in the same confined environment. Microorganism co-culture is inspired by the natural microbe communities that are omnipresent in nature. Within these communities, microbes interact through signaling or defense molecules. Such compounds, produced dynamically, are of potential interest as new leads for drug discovery. Microorganism co-culture can be achieved in either solid or liquid media and has recently been used increasingly extensively to study natural interactions and discover new bioactive metabolites. Because of the complexity of microbial extracts, advanced analytical methods (e.g., mass spectrometry methods and metabolomics) are key for the successful detection and identification of co-culture-induced metabolites. This review focuses on co-culture studies that aim to increase the diversity of metabolites obtained from microbes. The various strategies are summarized with a special emphasis on the multiple methods of performing co-culture experiments. The analytical approaches for studying these interaction phenomena are discussed, and the chemical diversity and biological activity observed among the induced metabolites are described.
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Affiliation(s)
- Samuel Bertrand
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland; 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
| | - Nadine Bohni
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland
| | - Sylvain Schnee
- Mycology and Biotechnology group, Institute for Plant Production Sciences IPS, Agroscope, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Olivier Schumpp
- Mycology and Biotechnology group, Institute for Plant Production Sciences IPS, Agroscope, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Katia Gindro
- Mycology and Biotechnology group, Institute for Plant Production Sciences IPS, Agroscope, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland.
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25
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Co-cultivation--a powerful emerging tool for enhancing the chemical diversity of microorganisms. Mar Drugs 2014; 12:1043-65. [PMID: 24549204 PMCID: PMC3944530 DOI: 10.3390/md12021043] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 01/23/2014] [Accepted: 02/06/2014] [Indexed: 02/03/2023] Open
Abstract
Marine-derived bacteria and fungi are promising sources of novel bioactive compounds that are important for drug discovery programs. However, as encountered in terrestrial microorganisms there is a high rate of redundancy that results in the frequent re-discovery of known compounds. Apparently only a part of the biosynthetic genes that are harbored by fungi and bacteria are transcribed under routine laboratory conditions which involve cultivation of axenic microbial strains. Many biosynthetic genes remain silent and are not expressed in vitro thereby seriously limiting the chemical diversity of microbial compounds that can be obtained through fermentation. In contrast to this, co-cultivation (also called mixed fermentation) of two or more different microorganisms tries to mimic the ecological situation where microorganisms always co-exist within complex microbial communities. The competition or antagonism experienced during co-cultivation is shown to lead to a significantly enhanced production of constitutively present compounds and/or to an accumulation of cryptic compounds that are not detected in axenic cultures of the producing strain. This review highlights the power of co-cultivation for increasing the chemical diversity of bacteria and fungi drawing on published studies from the marine and from the terrestrial habitat alike.
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26
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Whitt J, Shipley S, Newman DJ, Zuck KM. Tetramic acid analogues produced by coculture of Saccharopolyspora erythraea with Fusarium pallidoroseum. JOURNAL OF NATURAL PRODUCTS 2014; 77:173-7. [PMID: 24422636 PMCID: PMC3993930 DOI: 10.1021/np400761g] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Indexed: 05/18/2023]
Abstract
Coculture of the fungus Fusarium pallidoroseum with the bacterium Saccharopolyspora erythraea was found to produce three new decalin-type tetramic acid analogues related to equisetin. The structures were determined by spectroscopic methods. The absolute configurations were established by circular dichroism spectroscopy and comparing the data with those of equisetin.
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Affiliation(s)
- James Whitt
- SAIC-Frederick,
Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, Maryland 21702, United States
| | - Suzanne
M. Shipley
- SAIC-Frederick,
Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, Maryland 21702, United States
| | - David J. Newman
- Natural
Products Branch, Developmental Therapeutics Program, Frederick National
Laboratory for Cancer Research, National
Cancer Institute, P.O. Box B, Frederick, Maryland 21702, United States
| | - Karina M. Zuck
- SAIC-Frederick,
Inc., Frederick National Laboratory for Cancer Research, P.O. Box B, Frederick, Maryland 21702, United States
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27
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Ola ARB, Thomy D, Lai D, Brötz-Oesterhelt H, Proksch P. Inducing secondary metabolite production by the endophytic fungus Fusarium tricinctum through coculture with Bacillus subtilis. JOURNAL OF NATURAL PRODUCTS 2013; 76:2094-9. [PMID: 24175613 DOI: 10.1021/np400589h] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Coculturing the fungal endophyte Fusarium tricinctum with the bacterium Bacillus subtilis 168 trpC2 on solid rice medium resulted in an up to 78-fold increase in the accumulation in constitutively present secondary metabolites that included lateropyrone (5), cyclic depsipeptides of the enniatin type (6-8), and the lipopeptide fusaristatin A (9). In addition, four compounds (1-4) including (-)-citreoisocoumarin (2) as well as three new natural products (1, 3, and 4) were not present in discrete fungal and bacterial controls and only detected in the cocultures. The new compounds were identified as macrocarpon C (1), 2-(carboxymethylamino)benzoic acid (3), and (-)-citreoisocoumarinol (4) by analysis of the 1D and 2D NMR and HRMS data. Enniatins B1 (7) and A1 (8), whose production was particularly enhanced, inhibited the growth of the cocultivated B. subtilis strain with minimal inhibitory concentrations (MICs) of 16 and 8 μg/mL, respectively, and were also active against Staphylococcus aureus, Streptococcus pneumoniae, and Enterococcus faecalis with MIC values in the range 2-8 μg/mL. In addition, lateropyrone (5), which was constitutively present in F. tricinctum, displayed good antibacterial activity against B. subtilis, S. aureus, S. pneumoniae, and E. faecalis, with MIC values ranging from 2 to 8 μg/mL. All active compounds were equally effective against a multiresistant clinical isolate of S. aureus and a susceptible reference strain of the same species.
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Affiliation(s)
- Antonius R B Ola
- Institut für Pharmazeutische Biologie und Biotechnologie, Heinrich-Heine-Universität Düsseldorf , Universitätsstrasse 1, Geb. 26.23, 40225 Düsseldorf, Germany
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