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Ngamcharungchit C, Chaimusik N, Panbangred W, Euanorasetr J, Intra B. Bioactive Metabolites from Terrestrial and Marine Actinomycetes. Molecules 2023; 28:5915. [PMID: 37570885 PMCID: PMC10421486 DOI: 10.3390/molecules28155915] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Actinomycetes inhabit both terrestrial and marine ecosystems and are highly proficient in producing a wide range of natural products with diverse biological functions, including antitumor, immunosuppressive, antimicrobial, and antiviral activities. In this review, we delve into the life cycle, ecology, taxonomy, and classification of actinomycetes, as well as their varied bioactive metabolites recently discovered between 2015 and 2023. Additionally, we explore promising strategies to unveil and investigate new bioactive metabolites, encompassing genome mining, activation of silent genes through signal molecules, and co-cultivation approaches. By presenting this comprehensive and up-to-date review, we hope to offer a potential solution to uncover novel bioactive compounds with essential activities.
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Affiliation(s)
- Chananan Ngamcharungchit
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Mahidol University and Osaka University Collaborative Research Center on Bioscience and Biotechnology, Bangkok 10400, Thailand
| | - Nutsuda Chaimusik
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Mahidol University and Osaka University Collaborative Research Center on Bioscience and Biotechnology, Bangkok 10400, Thailand
| | - Watanalai Panbangred
- Research, Innovation and Partnerships Office, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
| | - Jirayut Euanorasetr
- Department of Microbiology, Faculty of Science, King Mongkut’s University of Technology Thonburi, Bangkok 10140, Thailand
- Laboratory of Biotechnological Research for Energy and Bioactive Compounds, Department of Microbiology, Faculty of Science, King Mongkut’s University of Technology Thonburi, Khet Thung Khru, Bangkok 10140, Thailand
| | - Bungonsiri Intra
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Mahidol University and Osaka University Collaborative Research Center on Bioscience and Biotechnology, Bangkok 10400, Thailand
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Yao H, Liu S, Liu T, Ren D, Yang Q, Zhou Z, Mao J. Screening of marine sediment-derived microorganisms and their bioactive metabolites: a review. World J Microbiol Biotechnol 2023; 39:172. [PMID: 37115432 DOI: 10.1007/s11274-023-03621-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023]
Abstract
Marine sediments are one of the largest habitats on Earth, and their unique ecology, such as high salinity, high pressure, and hypoxia, may activate certain silent genes in marine microbes, resulting in microbes, enzymes, active products, and specific metabolic pathways that can adapt to these specific ecological environments. Marine sediment-derived microorganisms and their bioactive metabolites are of great significance and have potential commercial development prospects for food, pharmaceutical, chemical industries, agriculture, environmental protection and human nutrition and health. In recent years, although there have been numerous scientific reports surrounding marine sediment-derived microorganisms and their bioactive metabolites, a comprehensive review of their research progress is lacking. This paper presents the development and renewal of traditional culture-dependent and omics analysis techniques and their application to the screening of marine sediment-derived microorganisms producing bioactive substances. It also highlights recent research advances in the last five years surrounding the types, functional properties and potential applications of bioactive metabolites produced by marine sediment-derived microorganisms. These bioactive metabolites mainly include antibiotics, enzymes, enzyme inhibitors, sugars, proteins, peptides, and some other small molecule metabolites. In addition, the review ends with concluding remarks on the challenges and future directions for marine sediment-derived microorganisms and their bioactive metabolites. The review report not only helps to deepen the understanding of marine sediment-derived microorganisms and their bioactive metabolites, but also provides some useful information for the exploitation and utilization of marine microbial resources and the mining of new compounds with potential functional properties.
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Affiliation(s)
- Hongli Yao
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Department of Biology and Food Engineering, Bozhou University, Bozhou, 236800, Anhui, China
| | - Shuangping Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, Guangdong, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China
| | - Tiantian Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China
| | - Dongliang Ren
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Qilin Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Zhilei Zhou
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, Guangdong, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China
| | - Jian Mao
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, Guangdong, China.
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
- Jiangnan University (Shaoxing) Industrial Technology Research Institute, Shaoxing, 31200, Zhejiang, China.
- National Engineering Research Center of Huangjiu, Zhejiang Guyuelongshan Shaoxing Wine CO., LTD, Shaoxing, 646000, Zhejiang, China.
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3
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Natural Marine Products: Anti-Colorectal Cancer In Vitro and In Vivo. Mar Drugs 2022; 20:md20060349. [PMID: 35736152 PMCID: PMC9229715 DOI: 10.3390/md20060349] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer, a malignant tumor with high mortality, has a poor prognosis due to drug resistance and toxicity in clinical surgery and chemotherapy. Thus, finding safer and more efficient drugs for clinical trials is vital and urgent. Natural marine compounds, with rich resources and original chemical structures, are applied widely in anticancer treatments. We provide a systematic overview of recently reported marine compounds such as alkaloids, peptides, terpenoids, polysaccharides, and carotenoids from in vitro, in vivo, and clinical studies. The in vitro studies summarized the marine origins and pharmacological mechanisms, including anti-proliferation, anti-angiogenesis, anti-migration, anti-invasion, the acceleration of cycle arrest, and the promotion of tumor apoptosis, of various compounds. The in vivo studies outlined the antitumor effects of marine compounds on colorectal cancer model mice and evaluated their efficacy in terms of tumor inhibition, hepatotoxicity, and nephrotoxicity. The clinical studies summarized the major chemical classifications and targets of action of the clinical drugs that have entered clinical approval and completed approval for marine anticancer. In summary, we present the current situation regarding the application of natural anti-colorectal cancer marine compounds and prospects for their clinical application.
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Abstract
Covering: 2020This review covers the literature published in 2020 for marine natural products (MNPs), with 757 citations (747 for the period January to December 2020) referring to compounds isolated from marine microorganisms and phytoplankton, green, brown and red algae, sponges, cnidarians, bryozoans, molluscs, tunicates, echinoderms, mangroves and other intertidal plants and microorganisms. The emphasis is on new compounds (1407 in 420 papers for 2020), together with the relevant biological activities, source organisms and country of origin. Pertinent reviews, biosynthetic studies, first syntheses, and syntheses that led to the revision of structures or stereochemistries, have been included. A meta analysis of bioactivity data relating to new MNPs reported over the last five years is also presented.
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Affiliation(s)
- Anthony R Carroll
- School of Environment and Science, Griffith University, Gold Coast, Australia. .,Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Brent R Copp
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | - Rohan A Davis
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia.,School of Enivironment and Science, Griffith University, Brisbane, Australia
| | - Robert A Keyzers
- Centre for Biodiscovery, School of Chemical and Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
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Mbaoji FN, Nweze JA, Yang L, Huang Y, Huang S, Onwuka AM, Peter IE, Mbaoji CC, Jiang M, Zhang Y, Pan L, Yang D. Novel Marine Secondary Metabolites Worthy of Development as Anticancer Agents: A Review. Molecules 2021; 26:molecules26195769. [PMID: 34641312 PMCID: PMC8510081 DOI: 10.3390/molecules26195769] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/14/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Secondary metabolites from marine sources have a wide range of biological activity. Marine natural products are promising candidates for lead pharmacological compounds to treat diseases that plague humans, including cancer. Cancer is a life-threatening disorder that has been difficult to overcome. It is a long-term illness that affects both young and old people. In recent years, significant attempts have been made to identify new anticancer drugs, as the existing drugs have been useless due to resistance of the malignant cells. Natural products derived from marine sources have been tested for their anticancer activity using a variety of cancer cell lines derived from humans and other sources, some of which have already been approved for clinical use, while some others are still being tested. These compounds can assault cancer cells via a variety of mechanisms, but certain cancer cells are resistant to them. As a result, the goal of this review was to look into the anticancer potential of marine natural products or their derivatives that were isolated from January 2019 to March 2020, in cancer cell lines, with a focus on the class and type of isolated compounds, source and location of isolation, cancer cell line type, and potency (IC50 values) of the isolated compounds that could be a guide for drug development.
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Affiliation(s)
- Florence Nwakaego Mbaoji
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, China; (F.N.M.); (J.A.N.); (Y.H.); (S.H.)
- College of Life Science and Technology of Guangxi University, Nanning 530004, China
- Department of Pharmacology and Toxicology, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka 410001, Enugu State, Nigeria; (A.M.O.); (I.E.P.); (C.C.M.)
| | - Justus Amuche Nweze
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, China; (F.N.M.); (J.A.N.); (Y.H.); (S.H.)
- Department of Science Laboratory Technology, Faculty of Physical Sciences, University of Nigeria, Nsukka 410001, Enugu State, Nigeria
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia in Ceske Budejovice, 37005 Ceske Budejovice, Czech Republic
- Soil and Water Research Infrastructure, Biology Centre, Czech Academy of Sciences, 37005 Ceske Budejovice, Czech Republic
| | - Liyan Yang
- Guangxi Biomass Industrialization Engineering Institute, National Engineering Research Center of Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass, Guangxi Academy of Sciences, Nanning 530007, China;
| | - Yangbin Huang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, China; (F.N.M.); (J.A.N.); (Y.H.); (S.H.)
| | - Shushi Huang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, China; (F.N.M.); (J.A.N.); (Y.H.); (S.H.)
| | - Akachukwu Marytheresa Onwuka
- Department of Pharmacology and Toxicology, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka 410001, Enugu State, Nigeria; (A.M.O.); (I.E.P.); (C.C.M.)
| | - Ikechukwu Emmanuel Peter
- Department of Pharmacology and Toxicology, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka 410001, Enugu State, Nigeria; (A.M.O.); (I.E.P.); (C.C.M.)
| | - Cynthia Chioma Mbaoji
- Department of Pharmacology and Toxicology, Faculty of Pharmaceutical Sciences, University of Nigeria, Nsukka 410001, Enugu State, Nigeria; (A.M.O.); (I.E.P.); (C.C.M.)
| | - Mingguo Jiang
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning 530008, China;
| | - Yunkai Zhang
- College of Life Science and Technology of Guangxi University, Nanning 530004, China
- Correspondence: (Y.Z.); (L.P.); (D.Y.); Tel.: +86-771-2503980 (L.P.); +86-771-2536109 (D.Y.)
| | - Lixia Pan
- Guangxi Biomass Industrialization Engineering Institute, National Engineering Research Center of Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass, Guangxi Academy of Sciences, Nanning 530007, China;
- Correspondence: (Y.Z.); (L.P.); (D.Y.); Tel.: +86-771-2503980 (L.P.); +86-771-2536109 (D.Y.)
| | - Dengfeng Yang
- Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning 530007, China; (F.N.M.); (J.A.N.); (Y.H.); (S.H.)
- Correspondence: (Y.Z.); (L.P.); (D.Y.); Tel.: +86-771-2503980 (L.P.); +86-771-2536109 (D.Y.)
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Flores Clavo R, Ruiz Quiñones N, Hernández-Tasco ÁJ, José Salvador M, Tasca Gois Ruiz AL, de Oliveira Braga LE, Henrique Costa J, Pacheco Fill T, Arce Gil ZL, Serquen Lopez LM, Fantinatti Garboggini F. Evaluation of antimicrobial and antiproliferative activities of Actinobacteria isolated from the saline lagoons of northwestern Peru. PLoS One 2021; 16:e0240946. [PMID: 34495972 PMCID: PMC8425546 DOI: 10.1371/journal.pone.0240946] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 07/15/2021] [Indexed: 11/18/2022] Open
Abstract
Extreme environments Morrope and Bayovar Salt lagoons, several ecosystems and microhabitats remain unexplored, and little is known about the diversity of Actinobacteria. We suggest that the endemic bacteria present in this extreme environment is a source of active molecules with anticancer, antimicrobial, and antiparasitic properties. Using phenotypic and genotypic characterization techniques, including 16S rRNA sequencing, we identified these bacteria as members of the genera Streptomyces, Pseudonocardia, Staphylococcus, Bacillus, and Pseudomonas. Actinobacteria strains were found predominantly. Phylogenetic analysis revealed 13 Actinobacteria clusters of Streptomyces, the main genus. Three Streptomycetes, strains MW562814, MW562805, and MW562807 showed antiproliferative activities against three tumor cell lines: U251 glioma, MCF7 breast, and NCI-H460 lung (non-small cell type); and antibacterial activity against Staphylococcus aureus ATCC 6538, Escherichia coli ATCC 10536, and the multidrug resistant Acinetobacter baumannii AC-972. The antiproliferative activities (measured as total growth inhibition [TGI]) of Streptomyces sp. MW562807 were 0.57 μg/mL, for 0.61 μg/mL, and 0.80 μg/mL for glioma, lung non-small cell type, and breast cancer cell lines, respectively; the methanolic fraction of the crude extract showed a better antiproliferative activity and could inhibit the growth of (U251 (TGI = 38.3 μg/mL), OVCAR-03 (TGI = 62.1 μg/mL), and K562 (TGI = 81.5 μg/mL)) of nine tumor cells types and one nontumor cell type. Extreme enviroments, such as the Morrope and Bayovar Salt saloons are promising sources of new bacteria, whose compounds may be useful for treating various infectious diseases or even some types of cancer.
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Affiliation(s)
- Rene Flores Clavo
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), University of Campinas (UNICAMP), Campinas, Paulínia, São Paulo, Brazil
- Department of Biotechnology, Research Center and Innovation and Sciences Actives Multidisciplinary (CIICAM), Chiclayo, Lambayeque, Perú
| | - Nataly Ruiz Quiñones
- Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), University of Campinas (UNICAMP), Campinas, Paulínia, São Paulo, Brazil
- Department of Biotechnology, Research Center and Innovation and Sciences Actives Multidisciplinary (CIICAM), Chiclayo, Lambayeque, Perú
| | - Álvaro Jose Hernández-Tasco
- Department of Plant Biology Bioactive Products, Institute of Biology Campinas, University of Campinas, Campinas, São Paulo, Brazil
| | - Marcos José Salvador
- Department of Plant Biology Bioactive Products, Institute of Biology Campinas, University of Campinas, Campinas, São Paulo, Brazil
| | | | | | | | | | - Zhandra Lizeth Arce Gil
- Catholic University Santo Toribio of Mogrovejo, Facultity of Human Medicine, Chiclayo, Lambayeque, Perú
| | - Luis Miguel Serquen Lopez
- Department of Biotechnology, Research Center and Innovation and Sciences Actives Multidisciplinary (CIICAM), Chiclayo, Lambayeque, Perú
- Direction of Investigation Hospital Regional Lambayeque, Chiclayo, Lambayeque, Perú
| | - Fabiana Fantinatti Garboggini
- Chemical, Biological and Agricultural Pluridisciplinary Research Center (CPQBA), University of Campinas (UNICAMP), Campinas, Paulínia, São Paulo, Brazil
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Goel N, Fatima SW, Kumar S, Sinha R, Khare SK. Antimicrobial resistance in biofilms: Exploring marine actinobacteria as a potential source of antibiotics and biofilm inhibitors. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 30:e00613. [PMID: 33996521 PMCID: PMC8105627 DOI: 10.1016/j.btre.2021.e00613] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/19/2021] [Accepted: 03/21/2021] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance (AMR) is one of the serious global public health threats that require immediate action. With the emergence of new resistance mechanisms in infection-causing microorganisms such as bacteria, fungi, and viruses, AMR threatens the effective prevention and treatment of diseases caused by them. This has resulted in prolonged illness, disability, and death. It has been predicted that AMR will lead to over ten million deaths by 2050. The rapid spread of multidrug-resistant bacteria is also causing old antibiotics to become ineffective. Among the diverse factors contributing to AMR, intrinsic biofilm development has been highlighted as an essential contributing facet. Moreover, biofilm-derived antibiotic tolerance leads to serious recurrent chronic infections. Therefore, the discovery of novel bioactive molecules is a potential solution that can help combat AMR. To achieve this, sustained mining of novel antimicrobial leads from actinobacteria, particularly marine actinobacteria, can be a promising strategy. Given their vast diversity and different habitats, the extraordinary capacity of actinobacteria can be tapped to synthesize new antibiotics or bioactive molecules for biofilm inhibition. Advanced screening strategies and novel approaches in the field of modern biochemical and molecular biology can be used to detect such new compounds. In view of this, the present review focuses on understanding some of the recent strategies to inhibit biofilm formation and explores the potential role of marine actinobacteria as sources of novel antibiotics and biofilm inhibitor molecules.
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Affiliation(s)
- Nikky Goel
- Department of Chemistry, Indian Institute of Technology Delhi, India
| | | | - Sumit Kumar
- Department of Chemistry, Indian Institute of Technology Delhi, India
| | | | - Sunil K. Khare
- Department of Chemistry, Indian Institute of Technology Delhi, India
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Chanadech S, Ruen-Ngam D, Intaraudom C, Pittayakhajonwut P, Chongruchiroj S, Pratuangdejkul J, Thawai C. Isolation of manumycin-type derivatives and genome characterization of a marine Streptomyces sp. C1-2. Res Microbiol 2021; 172:103812. [PMID: 33497762 DOI: 10.1016/j.resmic.2021.103812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 01/04/2021] [Accepted: 01/15/2021] [Indexed: 11/18/2022]
Abstract
A marine actinomycete strain C1-2 was taxonomically characterized as the genus Streptomyces, based on whole-genome sequence analysis. The highest average nucleotide identity (ANI) value (98.96%) and digital DNA-DNA hybridization (DDH) value (90.4%) were observed between Streptomyces sp. C1-2 and Streptomyces griseoaurantiacus. Thus, Streptomyces sp. C1-2 could be identified as S. griseoaurantiacus. Genome analysis revealed that Streptomyces sp. C1-2 contained 22 biosynthetic gene clusters (BGCs) for secondary metabolites, where among them, 54% have low similarities with known BGCs. The chemical investigation led to the isolation of three new manumycin-type derivatives and two known analog antibiotics named SW-B and cornifronin B. All compounds showed antioxidant activity with the half-maximal inhibitory concentration (IC50) values in a range of 50.82 ± 0.8-112.04 ± 1.0 μg/mL with no cytotoxicity against Vero cells. This is the first report of the antioxidant property of manumycin-type derivatives. Moreover, two known compounds exhibited antifungal activity against Phytophthora capsici, Fusarium oxysporum f. sp. cucumerinum, and Magnaporthe grisea, with the minimum inhibitory concentration (MIC) values in a range of 125-500 μg/mL.
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Affiliation(s)
- Sakkarn Chanadech
- Department of Biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand
| | - Duangkamol Ruen-Ngam
- Rattanakosin College for Sustainable Energy and Environment (RCSEE), Rajamangala University of Technology Rattanakosin, Nakhon Pathom, 73170, Thailand
| | - Chakapong Intaraudom
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathum Thani, 12120, Thailand
| | - Pattama Pittayakhajonwut
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Thailand Science Park, Phaholyothin Road, Klong Luang, Pathum Thani, 12120, Thailand
| | - Sumet Chongruchiroj
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Phayathai, Bangkok 10400, Thailand
| | - Jaturong Pratuangdejkul
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, Phayathai, Bangkok 10400, Thailand
| | - Chitti Thawai
- Department of Biology, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand; Actinobacterial Research Unit, Faculty of Science, King Mongkut's Institute of Technology Ladkrabang, Bangkok 10520, Thailand.
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Kautsar SA, van der Hooft JJJ, de Ridder D, Medema MH. BiG-SLiCE: A highly scalable tool maps the diversity of 1.2 million biosynthetic gene clusters. Gigascience 2021; 10:giaa154. [PMID: 33438731 PMCID: PMC7804863 DOI: 10.1093/gigascience/giaa154] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/29/2020] [Accepted: 11/29/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Genome mining for biosynthetic gene clusters (BGCs) has become an integral part of natural product discovery. The >200,000 microbial genomes now publicly available hold information on abundant novel chemistry. One way to navigate this vast genomic diversity is through comparative analysis of homologous BGCs, which allows identification of cross-species patterns that can be matched to the presence of metabolites or biological activities. However, current tools are hindered by a bottleneck caused by the expensive network-based approach used to group these BGCs into gene cluster families (GCFs). RESULTS Here, we introduce BiG-SLiCE, a tool designed to cluster massive numbers of BGCs. By representing them in Euclidean space, BiG-SLiCE can group BGCs into GCFs in a non-pairwise, near-linear fashion. We used BiG-SLiCE to analyze 1,225,071 BGCs collected from 209,206 publicly available microbial genomes and metagenome-assembled genomes within 10 days on a typical 36-core CPU server. We demonstrate the utility of such analyses by reconstructing a global map of secondary metabolic diversity across taxonomy to identify uncharted biosynthetic potential. BiG-SLiCE also provides a "query mode" that can efficiently place newly sequenced BGCs into previously computed GCFs, plus a powerful output visualization engine that facilitates user-friendly data exploration. CONCLUSIONS BiG-SLiCE opens up new possibilities to accelerate natural product discovery and offers a first step towards constructing a global and searchable interconnected network of BGCs. As more genomes are sequenced from understudied taxa, more information can be mined to highlight their potentially novel chemistry. BiG-SLiCE is available via https://github.com/medema-group/bigslice.
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Affiliation(s)
- Satria A Kautsar
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Justin J J van der Hooft
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, sThe Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
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Marine Sediment-Derived Streptomyces Strain Produces Angucycline Antibiotics against Multidrug-Resistant Staphylococcus aureus Harboring SCCmec Type 1 Gene. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2020. [DOI: 10.3390/jmse8100734] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Philippine archipelago is geographically positioned in the tropics with rich areas of marine biodiversity. Its marine sediments harbor actinomycetes that exhibit antibacterial activity. Screening of actinomycetes isolated from marine sediments collected near the coast of Islas de Gigantes, Iloilo showed one isolate that exhibited high activity against the multidrug-resistant Staphylococcus aureus (MRSA) strain carrying the Staphylococcal Cassette Chromosome mec (SCCmec) type 1 gene, a biomarker for drug resistance. The isolate was identified as Streptomyces sp. strain DSD011 based on its 16s rRNA and protein-coding genes (atpD, recA, rpoB, and trpB) sequences, and was found to be a new species of salt-tolerant marine Streptomyces. Further, the strain harbors both non-ribosomal peptide synthetase (NRPS) and type II polyketide synthase (PKS) in its genome. The targeted chromatographic isolation and chemical investigations by Liquid Chromatography Mass Spectrometry-Time of Flight (LCMS-TOF), tandem mass spectrometry (MS/MS), and Global Natural Product Social molecular networking (GNPS) of the antibiotics produced by the strain afforded the two polycyclic aromatic polyketide angucycline glycosides, fridamycin A (1) and fridamycin D (2), which are products of type II PKS biosynthesis. Compounds 1 and 2 displayed antibacterial activity against MRSA with minimum inhibitory concentration (MIC) of 500 μg/mL and 62.5 μg/mL, respectively. These results suggest that the underexplored marine sediments near the coast of Islas de Gigantes, Iloilo offer access to undiscovered Streptomyces species that are invaluable sources of antibiotic leads.
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