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Gamaleldin NM, Bahr HS, Millán-Aguiñaga N, Danesh M, Othman EM, Dandekar T, Hassan HM, Abdelmohsen UR. Targeting antimalarial metabolites from the actinomycetes associated with the Red Sea sponge Callyspongia siphonella using a metabolomic method. BMC Microbiol 2023; 23:396. [PMID: 38087203 PMCID: PMC10714608 DOI: 10.1186/s12866-023-03094-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 10/27/2023] [Indexed: 12/18/2023] Open
Abstract
Malaria is a persistent illness that is still a public health issue. On the other hand, marine organisms are considered a rich source of anti‑infective drugs and other medically significant compounds. Herein, we reported the isolation of the actinomycete associated with the Red Sea sponge Callyspongia siphonella. Using "one strain many compounds" (OSMAC) approach, a suitable strain was identified and then sub-cultured in three different media (M1, ISP2 and OLIGO). The extracts were evaluated for their in-vitro antimalarial activity against Plasmodium falciparum strain and subsequently analyzed by Liquid chromatography coupled with high-resolution mass spectrometry (LC-HR-MS). In addition, MetaboAnalyst 5.0 was used to statistically analyze the LC-MS data. Finally, Molecular docking was carried out for the dereplicated metabolites against lysyl-tRNA synthetase (PfKRS1). The phylogenetic study of the 16S rRNA sequence of the actinomycete isolate revealed its affiliation to Streptomyces genus. Antimalarial screening revealed that ISP2 media is the most active against Plasmodium falciparum strain. Based on LC-HR-MS based metabolomics and multivariate analyses, the static cultures of the media, ISP2 (ISP2-S) and M1 (M1-S), are the optimal media for metabolites production. OPLS-DA suggested that quinone derivatives are abundant in the extracts with the highest antimalarial activity. Fifteen compounds were identified where eight of these metabolites were correlated to the observed antimalarial activity of the active extracts. According to molecular docking experiments, saframycin Y3 and juglomycin E showed the greatest binding energy scores (-6.2 and -5.13) to lysyl-tRNA synthetase (PfKRS1), respectively. Using metabolomics and molecular docking investigation, the quinones, saframycin Y3 (5) and juglomycin E (1) were identified as promising antimalarial therapeutic candidates. Our approach can be used as a first evaluation stage in natural product drug development, facilitating the separation of chosen metabolites, particularly biologically active ones.
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Affiliation(s)
- Noha M Gamaleldin
- Department of Microbiology, Faculty of Pharmacy, the British University in Egypt (BUE), Cairo, 11837, Egypt
| | - Hebatallah S Bahr
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt
| | - Natalie Millán-Aguiñaga
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Ensenada, 22860, Baja California, México
| | - Mahshid Danesh
- Department of Bioinformatics, University of Würzburg, Am Hubland, 97074, BiocenterWürzburg, Germany
| | - Eman M Othman
- Department of Bioinformatics, University of Würzburg, Am Hubland, 97074, BiocenterWürzburg, Germany
- Department of Biochemistry, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, Am Hubland, 97074, BiocenterWürzburg, Germany
| | - Hossam M Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef, Egypt.
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, Egypt.
| | - Usama Ramadan Abdelmohsen
- Department of pharmacognosy, faculty of Pharmacy, Minia University, Minia, Egypt.
- Department of pharmacognosy, faculty of Pharmacy, Deraya University, New Minia City, 61111, Minia, Egypt.
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Rathinam AJ, Santhaseelan H, Dahms HU, Dinakaran VT, Murugaiah SG. Bioprospecting of unexplored halophilic actinobacteria against human infectious pathogens. 3 Biotech 2023; 13:398. [PMID: 37974926 PMCID: PMC10645811 DOI: 10.1007/s13205-023-03812-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/08/2023] [Indexed: 11/19/2023] Open
Abstract
Human pathogenic diseases received much attention recently due to their uncontrolled spread of antimicrobial resistance (AMR) which causes several threads every year. Effective alternate antimicrobials are urgently required to combat those disease causing infectious microbes. Halophilic actinobacteria revealed huge potentials and unexplored cultivable/non-cultivable actinobacterial species producing enormous antimicrobials have been proved in several genomics approaches. Potential gene clusters, PKS and NRPKS from Nocardia, Salinospora, Rhodococcus, and Streptomyces have wide range coding genes of secondary metabolites. Biosynthetic pathways identification via various approaches like genome mining, In silico, OSMAC (one strain many compound) analysis provides better identification of knowing the active metabolites using several databases like AMP, APD and CRAMPR, etc. Genome constellations of actinobacteria particularly the prediction of BGCs (Biosynthetic Gene Clusters) to mine the bioactive molecules such as pigments, biosurfactants and few enzymes have been reported for antimicrobial activity. Saltpan, saltlake, lagoon and haloalkali environment exploring potential actinobacterial strains Micromonospora, Kocuria, Pseudonocardia, and Nocardiopsis revealed several acids and ester derivatives with antimicrobial potential. Marine sediments and marine macro organisms have been found as significant population holders of potential actinobacterial strains. Deadly infectious diseases (IDs) including tuberculosis, ventilator-associated pneumonia and Candidiasis, have been targeted by halo-actinobacterial metabolites with promising results. Methicillin resistant Staphylococus aureus and virus like Encephalitic alphaviruses were potentially targeted by halophilic actinobacterial metabolites by the compound Homoseongomycin from sponge associated antinobacterium. In this review, we discuss the potential antimicrobial properties of various biomolecules extracted from the unexplored halophilic actinobacterial strains specifically against human infectious pathogens along with prospective genomic constellations.
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Affiliation(s)
- Arthur James Rathinam
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Henciya Santhaseelan
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708 Taiwan
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Hesketh-Best PJ, January GG, Koch MJ, Warburton PJ, Howell KL, Upton M. Whole genomes of deep-sea sponge-associated bacteria exhibit high novel natural product potential. FEMS MICROBES 2023; 4:xtad005. [PMID: 37333438 PMCID: PMC10117722 DOI: 10.1093/femsmc/xtad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/18/2023] [Accepted: 02/03/2023] [Indexed: 08/20/2023] Open
Abstract
Global antimicrobial resistance is a health crisis that can change the face of modern medicine. Exploring diverse natural habitats for bacterially-derived novel antimicrobial compounds has historically been a successful strategy. The deep-sea presents an exciting opportunity for the cultivation of taxonomically novel organisms and exploring potentially chemically novel spaces. In this study, the draft genomes of 12 bacteria previously isolated from the deep-sea sponges Phenomena carpenteri and Hertwigia sp. are investigated for the diversity of specialized secondary metabolites. In addition, early data support the production of antibacterial inhibitory substances produced from a number of these strains, including activity against clinically relevant pathogens Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus. Draft whole-genomes are presented of 12 deep-sea isolates, which include four potentially novel strains: Psychrobacter sp. PP-21, Streptomyces sp. DK15, Dietzia sp. PP-33, and Micrococcus sp. M4NT. Across the 12 draft genomes, 138 biosynthetic gene clusters were detected, of which over half displayed less than 50% similarity to known BGCs, suggesting that these genomes present an exciting opportunity to elucidate novel secondary metabolites. Exploring bacterial isolates belonging to the phylum Actinomycetota, Pseudomonadota, and Bacillota from understudied deep-sea sponges provided opportunities to search for new chemical diversity of interest to those working in antibiotic discovery.
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Affiliation(s)
- Poppy J Hesketh-Best
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, United Kingdom
| | - Grant G January
- School of Biomedical Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, United Kingdom
| | - Matthew J Koch
- School of Biomedical Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, United Kingdom
| | - Philip J Warburton
- School of Biomedical Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, United Kingdom
| | - Kerry L Howell
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, United Kingdom
| | - Mathew Upton
- School of Biomedical Sciences, University of Plymouth, Drake Circus, Plymouth PL4 8AA, United Kingdom
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4
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Su R, Zhang S, Zhang X, Wang S, Zhang W. Neglected skin-associated microbial communities: a unique immune defense strategy of Bufo raddei under environmental heavy metal pollution. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:22330-22342. [PMID: 36284045 DOI: 10.1007/s11356-022-23803-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Amphibians defend against pathogens using skin microbial communities, in addition to innate and adaptive immunity. Despite skin microbial communities play a key role in the immune function of amphibians, few studies have focused on the changes in its composition and function. In the present study, we identified the variation in adaptive immunity, as well as the corresponding changes in skin microbiome of Bufo raddei living in a heavy metal polluted area. The adaptive immunity of B. raddei in heavy metal polluted area was significantly lower than that in relatively unpolluted area. Further, different skin bacterial communities were found in the two areas. In the heavy metal polluted area, Actinobacteria and Microbacterium were the dominant bacteria in the skin microbiome of B. raddei, which showed broad-spectrum antibacterial activity. Besides, the antibiotic synthesis was also increased in metabolic pathways. The present study suggested that the adaptive immunity of B. raddei was weakened under long-term heavy metal stress. However, the toads increased the abundance of bacteriostatic bacteria by regulating the composition of skin microbiome, which released a large number of bacteriostatic metabolites and enhanced the host resistance to external pathogens in turn.
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Affiliation(s)
- Rui Su
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Sheng Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Xueying Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Shengnan Wang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Wenya Zhang
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environmental Pollution, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.
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Ricci F, Leggat W, Page CE, Ainsworth TD. Coral growth anomalies, neoplasms, and tumors in the Anthropocene. Trends Microbiol 2022; 30:1160-1173. [PMID: 35718641 DOI: 10.1016/j.tim.2022.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 01/13/2023]
Abstract
One of the most widespread coral diseases linked to anthropogenic activities and recorded on reefs worldwide is characterized by anomalous growth formations in stony corals, referred to as coral growth anomalies (GAs). The biological functions of GA tissue include limited reproduction, reduced access to resources, and weakened ability to defend against predators. Transcriptomic analyses have revealed that, in some cases, disease progression can involve host genes related to oncogenesis, suggesting that the GA tissues may be malignant neoplasms such as those developed by vertebrates. The number of studies reporting the presence of GAs in common reef-forming species highlights the urgency of a thorough understanding of the pathology and causative factors of this disease and its parallels to higher organism malignant tissue growth. Here, we review the current state of knowledge on the etiology and holobiont features of GAs in reef-building corals.
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Affiliation(s)
- Francesco Ricci
- University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington 2033, NSW, Australia.
| | - William Leggat
- University of Newcastle, School of Environmental and Life Sciences, Callaghan 2309, NSW, Australia
| | - Charlotte E Page
- University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington 2033, NSW, Australia
| | - Tracy D Ainsworth
- University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington 2033, NSW, Australia
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6
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Gamaleldin NM, Bahr HS, Mostafa YA, McAllister BF, El Zawily A, Ngwa CJ, Pradel G, Hassan HM, Abdelmohsen UR, Alkhalifah DHM, Hozzein WN. Metabolomic Profiling, In Vitro Antimalarial Investigation and In Silico Modeling of the Marine Actinobacterium Strain Rhodococcus sp. UR111 Associated with the Soft Coral Nephthea sp. Antibiotics (Basel) 2022; 11:1631. [PMID: 36421275 PMCID: PMC9686727 DOI: 10.3390/antibiotics11111631] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/28/2022] [Accepted: 11/03/2022] [Indexed: 09/24/2023] Open
Abstract
Malaria is a persistent illness with a great public health concern. To combat this fatal disease, developing effective antimalarial medications has become a necessity. In the present study, we described the actinomycetes associated with the Red Sea soft coral Nephthea sp. and isolated a strain that was sub-cultured in three different media (M1, ISP2, and OLIGO). Actinomycete isolate's phylogenetic analysis of the 16S rRNA gene revealed that it belongs to the genus Rhodococcus. In vitro screening of the antimalarial activity for three extracts against Plasmodium falciparum was carried out. Non-targeted metabolomics for the chemical characterization of the isolated actinomycete species UA111 derived extracts were employed using high-resolution liquid chromatography-mass spectrometry (LC-HR-MS) for dereplication purposes. Additionally, statistical analysis of the vast LC-MS data was performed using MetaboAnalyst 5.0. Finally, an in silico analysis was conducted to investigate the potential chemical compounds that could be the source of the antimalarial potential. The results revealed that ISP2 media extract is the most effective against Plasmodium falciparum, according to antimalarial screening (IC50 8.5 µg/mL), in contrast, OLIGO media extract was inactive. LC-HRMS-based metabolomics identified a range of metabolites, mainly alkaloids, from the genus Rhodococcus. On the other hand, multivariate analysis showed chemical diversity between the analyzed samples, with ISP2 extract being optimal. The docking analysis was able to anticipate the various patterns of interaction of the annotated compounds with three malarial protein targets (P. falciparum kinase, P. falciparum cytochrome bc1 complex, and P. falciparum lysyl-tRNA synthetase). Among all of the test compounds, perlolyrine (11) and 3097-B2 (12) displayed the best docking profiles. In conclusion, this work demonstrated the value of the established method for the metabolic profiling of marine actinomycetes using the data from liquid chromatography-mass spectrometry (LC-MS), which helps to streamline the difficult isolation stages required for their chemical characterization. In addition, the antimalarial efficacy of this strain has intriguing implications for future pharmaceutical development.
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Affiliation(s)
- Noha M. Gamaleldin
- Department of Microbiology, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo 11837, Egypt
| | - Hebatallah S. Bahr
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, Beni-Suef 62764, Egypt
| | - Yaser A. Mostafa
- Pharmaceutical Organic Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | | | - Amr El Zawily
- Department of Biology, University of Iowa, Iowa City, IA 52242-1324, USA
- Department of Plant and Microbiology, Faculty of Science, Damanhour University, Damanhour 22511, Egypt
| | - Che J. Ngwa
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, 52074 Aachen, Germany
| | - Gabriele Pradel
- Division of Cellular and Applied Infection Biology, Institute of Zoology, RWTH Aachen University, 52074 Aachen, Germany
| | - Hossam M. Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia 61519, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, Minia 61111, Egypt
| | - Dalal Hussien M. Alkhalifah
- Department of Biology, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Wael N. Hozzein
- Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62511, Egypt
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Chen CJ, Guo G, Li M, Liang XY, Gu YY. Diversity of endophytic bacteria of mulberry (Morus L.) under cold conditions. Front Microbiol 2022; 13:923162. [PMID: 35928145 PMCID: PMC9344060 DOI: 10.3389/fmicb.2022.923162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/01/2022] [Indexed: 11/26/2022] Open
Abstract
Endophytic bacteria are known to impact the growth and fitness of agriculturally relevant plants. However, there are limited reports describing endophytic bacteria related to mulberry (Morus L.). The present study used Illumina-based 16S rRNA gene sequencing to investigate the endophytic bacterial communities of two mulberry cultivars with differing resistance to low temperature, under cold conditions. In most cases, the bacterial communities of endophytes in the root exhibited higher richness compared with those in the stem, and the communities in resistant cultivar X792 exhibited higher richness compared with those of the sensitive cultivar “Da Shi” (DS). The difference in the proportion of unique operational taxonomic units showed the same trend. The number of genera with significant differences in abundance was greater between organs than between months, and greater between months than between cultivars. Microbial diversity analysis showed that Proteobacteria and Actinobacteria were the dominant phyla in all samples, while Pseudomonas, Steroidobacter, and Rhodococcus were the dominant genera in different samples. There were significant differences between cultivars DS and X792 in the relative abundance of Pseudomonas, Acidibacter, Frigoribacterium, Gaiella, and Pseudokineococcus. PICRUSt predictions indicated that the relative abundances of endophytic bacteria in membrane transport and signal transduction were significantly higher in the stem of resistant cultivar X792 in January compared with that of sensitive cultivar DS. Analysis of β-Diversity also revealed distinct differences in endophytic bacterial communities of stem and root, and communities of the stem in January and February. The complex correlation of the endophytic communities was higher in sensitive mulberry cultivar DS compared with resistant cultivar X792, in the stem compared with the root, and in January compared with February. Overall, findings from this study suggested that the diversity and community structure of endophytic bacteria in mulberry were significantly influenced by organs and months, followed by the host cultivar. The study provides insight into the complex microbial diversity of mulberry under cold conditions.
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Feeney MA, Newitt JT, Addington E, Algora-Gallardo L, Allan C, Balis L, Birke AS, Castaño-Espriu L, Charkoudian LK, Devine R, Gayrard D, Hamilton J, Hennrich O, Hoskisson PA, Keith-Baker M, Klein JG, Kruasuwan W, Mark DR, Mast Y, McHugh RE, McLean TC, Mohit E, Munnoch JT, Murray J, Noble K, Otani H, Parra J, Pereira CF, Perry L, Pintor-Escobar L, Pritchard L, Prudence SMM, Russell AH, Schniete JK, Seipke RF, Sélem-Mojica N, Undabarrena A, Vind K, van Wezel GP, Wilkinson B, Worsley SF, Duncan KR, Fernández-Martínez LT, Hutchings MI. ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria. Microb Genom 2022; 8. [PMID: 35775972 PMCID: PMC9455695 DOI: 10.1099/mgen.0.000824] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Actinobacteria is an ancient phylum of Gram-positive bacteria with a characteristic high GC content to their DNA. The ActinoBase Wiki is focused on the filamentous actinobacteria, such as Streptomyces species, and the techniques and growth conditions used to study them. These organisms are studied because of their complex developmental life cycles and diverse specialised metabolism which produces many of the antibiotics currently used in the clinic. ActinoBase is a community effort that provides valuable and freely accessible resources, including protocols and practical information about filamentous actinobacteria. It is aimed at enabling knowledge exchange between members of the international research community working with these fascinating bacteria. ActinoBase is an anchor platform that underpins worldwide efforts to understand the ecology, biology and metabolic potential of these organisms. There are two key differences that set ActinoBase apart from other Wiki-based platforms: [1] ActinoBase is specifically aimed at researchers working on filamentous actinobacteria and is tailored to help users overcome challenges working with these bacteria and [2] it provides a freely accessible resource with global networking opportunities for researchers with a broad range of experience in this field.
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Affiliation(s)
- Morgan Anne Feeney
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Jake Terry Newitt
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Emily Addington
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Lis Algora-Gallardo
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Craig Allan
- Swansea University Institute of Life Science, College of Medicine, Swansea, Wales, UK
| | - Lucas Balis
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Anna S Birke
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Laia Castaño-Espriu
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | | | - Rebecca Devine
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Damien Gayrard
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Jacob Hamilton
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Oliver Hennrich
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Paul A Hoskisson
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Molly Keith-Baker
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | | | - Worarat Kruasuwan
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - David R Mark
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Yvonne Mast
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Rebecca E McHugh
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Thomas C McLean
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Elmira Mohit
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - John T Munnoch
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Jordan Murray
- Department of Physics, SUPA, University of Strathclyde, Glasgow, G4 0NG, UK
| | - Katie Noble
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Hiroshi Otani
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA 94720, USA
| | - Jonathan Parra
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Camila F Pereira
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany
| | - Louisa Perry
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | | | - Leighton Pritchard
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | - Samuel M M Prudence
- School of Biological and Behavioral Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | | | - Jana K Schniete
- Biology Department, Edge Hill University, St Helens Road, Ormskirk, L39 4QP, UK
| | - Ryan F Seipke
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Nelly Sélem-Mojica
- Universidad Nacional Autónoma de México, Centro de Ciencias Matemáticas, en Morelia, Michoacán, Mexico
| | - Agustina Undabarrena
- Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Valparaíso, 2340000, Chile
| | - Kristiina Vind
- Host-Microbe Interactomics Group, Wageningen University, 6708 WD Wageningen, The Netherlands
| | - Gilles P van Wezel
- Microbial Biotechnology, Institute of Biology, Leiden University, Rapenburg, The Netherlands
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Sarah F Worsley
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Katherine R Duncan
- University of Strathclyde, Strathclyde Institute of Pharmacy and Biomedical Sciences, Glasgow, G4 0RE, UK
| | | | - Matthew I Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
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Carpi S, Scoditti E, Polini B, Brogi S, Calderone V, Proksch P, Ebada SS, Nieri P. Pro-Apoptotic Activity of the Marine Sponge Dactylospongia elegans Metabolites Pelorol and 5-epi-Ilimaquinone on Human 501Mel Melanoma Cells. Mar Drugs 2022; 20:md20070427. [PMID: 35877720 PMCID: PMC9317990 DOI: 10.3390/md20070427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 12/24/2022] Open
Abstract
The natural environment represents an important source of drugs that originates from the terrestrial and, in minority, marine organisms. Indeed, the marine environment represents a largely untapped source in the process of drug discovery. Among all marine organisms, sponges with algae represent the richest source of compounds showing anticancer activity. In this study, the two secondary metabolites pelorol (PEL) and 5-epi-ilimaquinone (EPI), purified from Dactylospongia elegans were investigated for their anti-melanoma activity. PEL and EPI induced cell growth repression of 501Mel melanoma cells in a concentration- and time-dependent manner. A cell cycle block in the G1 phase by PEL and EPI was also observed. Furthermore, PEL and EPI induced significant accumulation of DNA histone fragments in the cytoplasmic fraction, indicating a pro-apoptotic effect of both compounds. At the molecular level, PEL and EPI induced apoptosis through the increase in pro-apoptotic BAX expression, confirmed by the decrease in its silencing miR-214-3p and the decrease in the anti-apoptotic BCL-2, MCL1, and BIRC-5 mRNA expression, attested by the increase in their silencing miRNAs, i.e., miR-193a-3p and miR-16-5p. In conclusion, our data indicate that PEL and EPI exert cytotoxicity activity against 501Mel melanoma cells promoting apoptotic signaling and inducing changes in miRNA expression and their downstream effectors. For these reasons could represent promising lead compounds in the anti-melanoma drug research.
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Affiliation(s)
- Sara Carpi
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, 56126 Pisa, Italy
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (B.P.); (S.B.); (V.C.); (P.N.)
- Correspondence:
| | - Egeria Scoditti
- National Research Council (CNR), Institute of Clinical Physiology (IFC), 73100 Lecce, Italy;
| | - Beatrice Polini
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (B.P.); (S.B.); (V.C.); (P.N.)
- Department of Pathology, University of Pisa, Via Savi 10, 56126 Pisa, Italy
| | - Simone Brogi
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (B.P.); (S.B.); (V.C.); (P.N.)
- Interdepartmental Center of Marine Pharmacology (MArinePHARMA), University of Pisa, 56126 Pisa, Italy
| | - Vincenzo Calderone
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (B.P.); (S.B.); (V.C.); (P.N.)
- Interdepartmental Center of Marine Pharmacology (MArinePHARMA), University of Pisa, 56126 Pisa, Italy
| | - Peter Proksch
- Institute of Pharmaceutical Biology and Biotechnology, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Universtätsstrasse 1, 40225 Düsseldorf, Germany;
| | - Sherif S. Ebada
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt;
| | - Paola Nieri
- Department of Pharmacy, University of Pisa, 56126 Pisa, Italy; (B.P.); (S.B.); (V.C.); (P.N.)
- Interdepartmental Center of Marine Pharmacology (MArinePHARMA), University of Pisa, 56126 Pisa, Italy
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10
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Mothana AA, Al-Shamahy HA, Mothana RA, Khaled JM, Al-Rehaily AJ, Al-Mahdi AY, Lindequist U. Streptomyces sp. 1S1 isolated from Southern coast of the Red Sea as a renewable natural resource of several bioactive compounds. Saudi Pharm J 2021; 30:162-171. [PMID: 35528853 PMCID: PMC9072693 DOI: 10.1016/j.jsps.2021.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
Red Sea represents one of the most remarkable marine ecosystems. However, it is also one of the world's least explored areas of marine biodiversity. The aims of this investigation were therefore, to isolate marine microorganisms from the seashore sediments and water in shallow region from west Yemen coast, to assess their antimicrobial potential, to identify the highly active isolate, and to purify and identify the bioactive compounds from it. In this regard, twenty-five bacterial strains have been isolated from twenty samples and tested for their antimicrobial ability against some pathogenic bacteria and yeast by using the agar disk diffusion and agar well diffusion assay. Out of the total 25 marine actinomycetes isolates only 13 exhibited interesting antimicrobial activity. The morphological, biochemical, and phylogenetic characteristics of the potential isolate 1S1 were compatible with their classification in the genus Streptomyces. The 16S rRNA gene sequences have shown that the isolate 1S1 clustered with Streptomyces longisporoflavus. The strain Streptomyces sp. 1S1 was cultivated and extracted with ethyl acetate. The GC–MS study of the extract indicated the presence of certain fatty acyl compounds e.g., tetradecanoic acid, 9-octadecenoic acid, hexadecanoic acid, and 9,12,15-octadecatrienoic acid. Using chromatographic techniques, three compounds were isolated and by spectroscopic methods e.g., IR, MS and NMR structurally elucidated. The three compounds were identified as a triacylglyceride, 9-octadecenoic acid, and hexadecanoic acid. The study reinforces the evidence of the potential of Streptomyces sp and the ability to produce several antimicrobial compounds.
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Affiliation(s)
- Azal A. Mothana
- Department of Biology, Faculty of Marine Sciences and Environment, Al-Hodeida University, Al-Hodeida, Yemen
| | - Hassan A. Al-Shamahy
- Department of Medicinal Microbiology, Faculty of Medicine and Health Sciences, Sana’a University, Sana'a, Yemen
| | - Ramzi A. Mothana
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
- Corresponding author.
| | - Jamal M. Khaled
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Adnan J. Al-Rehaily
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah Y. Al-Mahdi
- Department of Microbiology, Faculty of Medicine, Lincoln University College, Malaysia
| | - Ulrike Lindequist
- Department of Pharmaceutical Biology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
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11
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Solid State Fermentation of Shrimp Shell Waste Using Pseudonocardia carboxydivorans 18A13O1 to Produce Bioactive Metabolites. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7040247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Marine actinomycetes are prolific microorganisms; however, knowledge of their diversity, distribution, and secondary metabolites is limited. Marine actinomycetes represent an untapped source of novel bioactive compounds. In this study, we investigated shrimp shell as substrates for model production bioactive metabolites from actinomycetes under solid state fermentation (SSF) conditions. A total of fifteen actinomycetes were isolated from six sponges and one tunicate. The isolated actinomycetes were grown on solid shrimp shells. Cultures of actinomycetes were extracted with ethyl acetate (EtOAc) and extracts were bioassayed for activity against Staphylococcus aureus. One isolate 18A13O1 from the sponge, Rhabdastrella globostellata, exhibited antibacterial activity on primary screening compared to the other samples and was chosen for further study. Visualization using SEM showed aerial and substrate mycelia. Through phylogenetic analysis, it was confirmed that isolate 18A13O1 is a Pseudonocardia carboxydivorans. Purification of an EtOAc extract yielded A13B2, which showed a minimum inhibition concentration against S. aureus at 15.6 μg/mL. It can be concluded that this basic information is very important for further studies related to the development of the production of bioactive secondary metabolites through the solid state fermentation process.
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12
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Ruocco N, Esposito R, Zagami G, Bertolino M, De Matteo S, Sonnessa M, Andreani F, Crispi S, Zupo V, Costantini M. Microbial diversity in Mediterranean sponges as revealed by metataxonomic analysis. Sci Rep 2021; 11:21151. [PMID: 34707182 PMCID: PMC8551288 DOI: 10.1038/s41598-021-00713-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Although the Mediterranean Sea covers approximately a 0.7% of the world's ocean area, it represents a major reservoir of marine and coastal biodiversity. Among marine organisms, sponges (Porifera) are a key component of the deep-sea benthos, widely recognized as the dominant taxon in terms of species richness, spatial coverage, and biomass. Sponges are evolutionarily ancient, sessile filter-feeders that harbor a largely diverse microbial community within their internal mesohyl matrix. In the present work, we firstly aimed at exploring the biodiversity of marine sponges from four different areas of the Mediterranean: Faro Lake in Sicily and "Porto Paone", "Secca delle fumose", "Punta San Pancrazio" in the Gulf of Naples. Eight sponge species were collected from these sites and identified by morphological analysis and amplification of several conserved molecular markers (18S and 28S RNA ribosomal genes, mitochondrial cytochrome oxidase subunit 1 and internal transcribed spacer). In order to analyze the bacterial diversity of symbiotic communities among these different sampling sites, we also performed a metataxonomic analysis through an Illumina MiSeq platform, identifying more than 1500 bacterial taxa. Amplicon Sequence Variants (ASVs) analysis revealed a great variability of the host-specific microbial communities. Our data highlight the occurrence of dominant and locally enriched microbes in the Mediterranean, together with the biotechnological potential of these sponges and their associated bacteria as sources of bioactive natural compounds.
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Affiliation(s)
- Nadia Ruocco
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Roberta Esposito
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy ,grid.4691.a0000 0001 0790 385XDepartment of Biology, University of Naples Federico II, Complesso Universitario Di Monte Sant’Angelo, Via Cinthia 21, 80126 Naples, Italy
| | - Giacomo Zagami
- grid.10438.3e0000 0001 2178 8421Dipartimento Di Scienze Biologiche, Chimiche, Farmaceutiche Ed Ambientali, Università Di Messina, 98100 Messina, Italy
| | - Marco Bertolino
- grid.5606.50000 0001 2151 3065DISTAV, Università Degli Studi Di Genova, Corso Europa 26, 16132 Genoa, Italy
| | - Sergio De Matteo
- grid.10438.3e0000 0001 2178 8421Dipartimento Di Scienze Biologiche, Chimiche, Farmaceutiche Ed Ambientali, Università Di Messina, 98100 Messina, Italy
| | | | | | - Stefania Crispi
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy ,grid.5326.20000 0001 1940 4177Institute of Biosciences and BioResources Naples, National Research Council of Italy, Naples, Italy
| | - Valerio Zupo
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Maria Costantini
- grid.6401.30000 0004 1758 0806Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
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13
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Isolation, Phylogenetic and Gephyromycin Metabolites Characterization of New Exopolysaccharides-Bearing Antarctic Actinobacterium from Feces of Emperor Penguin. Mar Drugs 2021; 19:md19080458. [PMID: 34436297 PMCID: PMC8400323 DOI: 10.3390/md19080458] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/13/2021] [Accepted: 08/11/2021] [Indexed: 12/15/2022] Open
Abstract
A new versatile actinobacterium designated as strain NJES-13 was isolated from the feces of the Antarctic emperor penguin. This new isolate was found to produce two active gephyromycin analogues and bioflocculanting exopolysaccharides (EPS) metabolites. Phylogenetic analysis based on pairwise comparison of 16S rRNA gene sequences showed that strain NJES-13 was closely related to Mobilicoccus pelagius Aji5-31T with a gene similarity of 95.9%, which was lower than the threshold value (98.65%) for novel species delineation. Additional phylogenomic calculations of the average nucleotide identity (ANI, 75.9–79.1%), average amino acid identity (AAI, 52.4–66.9%) and digital DNA–DNA hybridization (dDDH, 18.6–21.9%), along with the constructed phylogenomic tree based on the up-to-date bacterial core gene (UBCG) set from the bacterial genomes, unequivocally separated strain NJES-13 from its close relatives within the family Dermatophilaceae. Hence, it clearly indicated that strain NJES-13 represented a putative new actinobacterial species isolated from the gut microbiota of mammals inhabiting the Antarctic. The obtained complete genome of strain NJES-13 consisted of a circular 3.45 Mb chromosome with a DNA G+C content of 67.0 mol%. Furthering genome mining of strain NJES-13 showed the presence of five biosynthetic gene clusters (BGCs) including one type III PKS responsible for the biosynthesis of the core of gephyromycins, and a series of genes encoding for bacterial EPS biosynthesis. Thus, based on the combined phylogenetic and active metabolites characterization presented in this study, we confidently conclude that strain NJES-13 is a novel, fresh actinobacterial candidate to produce active gephyromycins and microbial bioflocculanting EPS, with potential pharmaceutical, environmental and biotechnological implications.
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14
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Existence in cellulose shelters: industrial and pharmaceutical leads of symbiotic actinobacteria from ascidian Phallusia nigra, Andaman Islands. World J Microbiol Biotechnol 2021; 37:120. [PMID: 34132920 DOI: 10.1007/s11274-021-03090-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/07/2021] [Indexed: 10/21/2022]
Abstract
The diversity of actinobacteria associated with marine ascidian Phallusia nigra from Andaman Islands was investigated. A total of 10 actinobacteria were isolated and based on the biochemical and molecular characterization, the isolates were assigned to 7 different actinobacterial genera. Eight putatively novel species belonging to genera Rhodococcus, Kineococcus, Kocuria, Janibacter, Salinispora and Arthrobacter were identified based on 16S rDNA sequence similarity with the NCBI database. The organic extracts of ten isolates displayed considerable bioactivity against test pathogens, which were Gram-positive and Gram-negative in nature. PCR-based screening for type I and type II polyketide synthases (PKS-I, PKS-II) and nonribosomal peptide synthetases (NRPS) revealed that, 10 actinobacterial isolates encoded at least one type of polyketide synthases biosynthesis gene. Majority of the isolates found to produce industrially important enzymes; amylase, protease, gelatinase, lipase, DNase, cellulase, urease, phosphatase and L-asparaginase. The present study emphasized that, ascidians are a prolific resource for novel bioactive actinobacteria with potential for novel drug discovery. This result expands the scope to functionally characterize the novel ascidian associated marine actinobacteria and their metabolites could be a source for the novel molecules of commercial interest.
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15
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Glaeser SP, Rückert C, Abdelmohsen UR, Winkler A, Blom J, Goesmann A, Kalinowski J, Hentschel U, Busse HJ, Kämpfer P. Streptomyces dysideae sp. nov., isolated from a marine Mediterranean sponge Dysidea tupha. Int J Syst Evol Microbiol 2021; 71. [PMID: 33512313 DOI: 10.1099/ijsem.0.004672] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive bacterium, strain RV15T, forming an extensively branched substrate mycelium and aerial hyphae that differentiate into spiral chains of spores, was isolated from a marine sponge Dysidea tupha collected from Rovinj (Croatia). Comparison of 16S rRNA gene sequences showed that strain RV15T is a member of the genus Streptomyces with highest sequence similarity to the type strains of Streptomyces caeruleatus (98.8 %), Streptomyces cyaneochromogenes (98.6 %) and Streptomyces shaanxiensis (98.5 %). Sequence similarities to all other Streptomyces types strains were below 98.5 %. The multilocus sequence analysis-based evolutionary distance, the average nucleotide identity value and the genome-to-genome distance of strain RV15T and the type strain of S. caeruleatus were clearly below the species cut-off values. Strain RV15T exhibited a quinone system composed of the major menaquinones MK-9(H4), MK-9(H6) and MK-9(H2), typical for the genus Streptomyces. The polar lipid profile of strain RV15T consisted of the predominant compounds diphosphatidylglycerol and phosphatidylethanolamine, moderate amounts of phosphatidylinositol, phosphatidylinositol mannoside, an unidentified lipid and an unidentified phospholipid. Major polyamines were spermine and spermidine. The diagnostic diaminoacid of the peptidoglycan was meso-diaminopimelic acid. The major fatty acids were iso C16 : 0, anteiso C17 : 1 ω9c and anteiso C17 : 0. The results of physiological and biochemical tests allowed further phenotypic differentiation of strain RV15T from its most-related species and hence clearly merits species status. We propose the name Streptomyces dysideae sp. nov. with the type strain RV15T (=DSM 42110T=LMG 27702T).
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Affiliation(s)
| | - Christian Rückert
- Department of Biology, Massachusetts Institute of Technology, MA, USA.,Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Germany
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, 61111 new Minia, Egypt.,Department of Pharmacognosy, Faculty of Pharmacy, Minia University61519 Minia, Egypt
| | - Anika Winkler
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-Universität Giessen, Germany
| | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-Universität Giessen, Germany
| | - Jörn Kalinowski
- Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Germany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Symbioses, D-24105 Kiel, Germany
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität, A-1210 Wien, Austria
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Universität Giessen, Germany
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16
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Kanchanasin P, Yuki M, Kudo T, Ohkuma M, Phongsopitanun W, Tanasupawat S. Nocardia terrae sp. nov., an actinomycete isolated from soil in Thailand. Arch Microbiol 2020; 203:1071-1077. [PMID: 33146799 DOI: 10.1007/s00203-020-02107-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 11/27/2022]
Abstract
A novel actinomycete strain ET3-3T isolated from soil collected from Chachoengsao province, Thailand was taxonomic evaluated using a polyphasic approach. Chemotaxonomic analysis indicated that meso-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. Mycolic acids were present. Ribose, arabinose, and galactose were detected in its whole-cell hydrolysates. The strain comprised C16:0 and TBSA 10-methyl C18:0 as the main fatty acids and MK-8(H4ω-cycl) as the predominant menaquinone. Major polar lipids were phosphatidylinositol, phosphatidylinositol mannoside, phosphatidylethanolamine, and diphosphatidylglycerol. The results of 16S rRNA gene sequence analysis showed that strain ET3-3T was closely related to Nocardia seriolae JCM 30082T (99.2%), Nocardia yunnanensis JCM 30082T (98.4%), and Nocardia concava JCM 12351T (98.2%). The draft genome of ET3-3T was 9.31 Mb with 8826 coding sequences with an average G + C content of 68.0%. The comparison of the draft genome of strain ET3-3T and N. seriolae NBRC 15557T showed the ANIb, ANIm and the digital DNA-DNA hybridization values of 86.3%, 88.5% and 32.9%, respectively. The results of the taxonomic analysis suggested that strain ET3-3T represented a novel species of the genus Nocardia for which the name Nocardia terrae sp. nov. is proposed. The type strain is ET3-3T (= JCM 33776T = TISTR 2837T).
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Affiliation(s)
- Pawina Kanchanasin
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Masahiro Yuki
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Takuji Kudo
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074, Japan
| | - Wongsakorn Phongsopitanun
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand
| | - Somboon Tanasupawat
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok, 10330, Thailand.
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17
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Elmallah MIY, Cogo S, Constantinescu AA, Elifio-Esposito S, Abdelfattah MS, Micheau O. Marine Actinomycetes-Derived Secondary Metabolites Overcome TRAIL-Resistance via the Intrinsic Pathway through Downregulation of Survivin and XIAP. Cells 2020; 9:cells9081760. [PMID: 32708048 PMCID: PMC7464567 DOI: 10.3390/cells9081760] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/13/2020] [Accepted: 07/21/2020] [Indexed: 01/03/2023] Open
Abstract
Resistance of cancer cells to tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis represents the major hurdle to the clinical use of TRAIL or its derivatives. The discovery and development of lead compounds able to sensitize tumor cells to TRAIL-induced cell death is thus likely to overcome this limitation. We recently reported that marine actinomycetes’ crude extracts could restore TRAIL sensitivity of the MDA-MB-231 resistant triple negative breast cancer cell line. We demonstrate in this study, that purified secondary metabolites originating from distinct marine actinomycetes (sharkquinone (1), resistomycin (2), undecylprodigiosin (3), butylcyclopentylprodigiosin (4), elloxizanone A (5) and B (6), carboxyexfoliazone (7), and exfoliazone (8)), alone, and in a concentration-dependent manner, induce killing in both MDA-MB-231 and HCT116 cell lines. Combined with TRAIL, these compounds displayed additive to synergistic apoptotic activity in the Jurkat, HCT116 and MDA-MB-231 cell lines. Mechanistically, these secondary metabolites induced and enhanced procaspase-10, -8, -9 and -3 activation leading to an increase in PARP and lamin A/C cleavage. Apoptosis induced by these compounds was blocked by the pan-caspase inhibitor QvD, but not by a deficiency in caspase-8, FADD or TRAIL agonist receptors. Activation of the intrinsic pathway, on the other hand, is likely to explain both their ability to trigger cell death and to restore sensitivity to TRAIL, as it was evidenced that these compounds could induce the downregulation of XIAP and survivin. Our data further highlight that compounds derived from marine sources may lead to novel anti-cancer drug discovery.
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Affiliation(s)
- Mohammed I. Y. Elmallah
- LNC, INSERM, UMR1231, F-21079 Dijon, France; (S.C.); (A.A.C.)
- UFR Science de Santé, Université de Bourgogne Franche-Comté, F-21079 Dijon, France
- Chemistry Department, Faculty of Science, Helwan University, 11795 Ain Helwan, Cairo 11795, Egypt;
- Correspondence: (M.I.Y.E.); (O.M.)
| | - Sheron Cogo
- LNC, INSERM, UMR1231, F-21079 Dijon, France; (S.C.); (A.A.C.)
- UFR Science de Santé, Université de Bourgogne Franche-Comté, F-21079 Dijon, France
- Graduate Programme in Health Sciences, Pontifícia Universidade Catolica do Parana, Curitiba 80215–901, Parana, Brazil;
| | - Andrei A. Constantinescu
- LNC, INSERM, UMR1231, F-21079 Dijon, France; (S.C.); (A.A.C.)
- UFR Science de Santé, Université de Bourgogne Franche-Comté, F-21079 Dijon, France
| | - Selene Elifio-Esposito
- Graduate Programme in Health Sciences, Pontifícia Universidade Catolica do Parana, Curitiba 80215–901, Parana, Brazil;
| | - Mohammed S. Abdelfattah
- Chemistry Department, Faculty of Science, Helwan University, 11795 Ain Helwan, Cairo 11795, Egypt;
- Marine Natural Products Unit (MNPRU), Faculty of Science, Helwan University, 11795 Ain Helwan, Cairo 11795, Egypt
| | - Olivier Micheau
- LNC, INSERM, UMR1231, F-21079 Dijon, France; (S.C.); (A.A.C.)
- UFR Science de Santé, Université de Bourgogne Franche-Comté, F-21079 Dijon, France
- Correspondence: (M.I.Y.E.); (O.M.)
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18
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Chanana S, Thomas CS, Zhang F, Rajski SR, Bugni TS. hcapca: Automated Hierarchical Clustering and Principal Component Analysis of Large Metabolomic Datasets in R. Metabolites 2020; 10:E297. [PMID: 32708222 PMCID: PMC7407629 DOI: 10.3390/metabo10070297] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/13/2020] [Accepted: 07/18/2020] [Indexed: 11/16/2022] Open
Abstract
Microbial natural product discovery programs face two main challenges today: rapidly prioritizing strains for discovering new molecules and avoiding the rediscovery of already known molecules. Typically, these problems have been tackled using biological assays to identify promising strains and techniques that model variance in a dataset such as PCA to highlight novel chemistry. While these tools have shown successful outcomes in the past, datasets are becoming much larger and require a new approach. Since PCA models are dependent on the members of the group being modeled, large datasets with many members make it difficult to accurately model the variance in the data. Our tool, hcapca, first groups strains based on the similarity of their chemical composition, and then applies PCA to the smaller sub-groups yielding more robust PCA models. This allows for scalable chemical comparisons among hundreds of strains with thousands of molecular features. As a proof of concept, we applied our open-source tool to a dataset with 1046 LCMS profiles of marine invertebrate associated bacteria and discovered three new analogs of an established anticancer agent from one promising strain.
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Affiliation(s)
| | | | | | | | - Tim S. Bugni
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA; (S.C.); (C.S.T.); (F.Z.); (S.R.R.)
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Actinomycetes from the Red Sea Sponge Coscinoderma mathewsi: Isolation, Diversity, and Potential for Bioactive Compounds Discovery. Microorganisms 2020; 8:microorganisms8050783. [PMID: 32456212 PMCID: PMC7285244 DOI: 10.3390/microorganisms8050783] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/26/2022] Open
Abstract
The diversity of actinomycetes associated with the marine sponge Coscinoderma mathewsi collected from Hurghada (Egypt) was studied. Twenty-three actinomycetes were separated and identified based on the 16S rDNA gene sequence analysis. Out of them, three isolates were classified as novel species of the genera Micromonospora, Nocardia, and Gordonia. Genome sequencing of actinomycete strains has revealed many silent biosynthetic gene clusters and has shown their exceptional capacity for the production of secondary metabolites, not observed under classical cultivation conditions. Therefore, the effect of mycolic-acid-containing bacteria or mycolic acid on the biosynthesis of cryptic natural products was investigated. Sponge-derived actinomycete Micromonospora sp. UA17 was co-cultured using liquid fermentation with two mycolic acid-containing actinomycetes (Gordonia sp. UA19 and Nocardia sp. UA 23), or supplemented with pure mycolic acid. LC-HRESIMS data were analyzed to compare natural production across all crude extracts. Micromonospora sp. UA17 was rich with isotetracenone, indolocarbazole, and anthracycline analogs. Some co-culture extracts showed metabolites such as a chlorocardicin, neocopiamycin A, and chicamycin B that were not found in the respective monocultures, suggesting a mycolic acid effect on the induction of cryptic natural product biosynthetic pathways. The antibacterial, antifungal, and antiparasitic activities for the different cultures extracts were also tested.
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Rajasabapathy R, Ghadi SC, Manikandan B, Mohandass C, Surendran A, Dastager SG, Meena RM, James RA. Antimicrobial profiling of coral reef and sponge associated bacteria from southeast coast of India. Microb Pathog 2020; 141:103972. [PMID: 31923557 DOI: 10.1016/j.micpath.2020.103972] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 12/13/2019] [Accepted: 01/06/2020] [Indexed: 12/20/2022]
Abstract
Culturable bacteria associated with marine sponges and coral mucus (collected from Gulf of Mannar and Palk Bay) were screened for their prospective antimicrobial compounds against 9 bacterial pathogens (Bacillus megaterium, B. cereus, Salmonella typhimurium, Staphylococcus aureus, Proteus vulgaris, Klebsillla pneumoniae, Escherichia coli, Pseudomonas aeruginosa and Acinetobacter baumannii) and a fungal pathogen (Candida albicans). Of the 263 bacterial isolates obtained during this study, 52 isolates displayed antimicrobial activity against one or more pathogens. 16S rRNA gene sequencing revealed that these 52 strains affiliated to 14 genera from three phyla Proteobacteria, Firmicutes and Actinobacteria. Sponge associated bacterial strains F-04, I-23, I-33 and G-03 inhibited the growth of all the bacterial pathogens tested in this study and significantly the former 2 strains inhibited the growth of fungal pathogen also. Majority of the potential strains (88.4% out of 52 strains) inhibited the growth of Bacillus cereus. Interestingly, an actinomycete strain F-04 (isolated from sponge Orina sagittaria) inhibited the growth of methicillin resistant Staphylococcus aureus. In total, 10 volatile organic compounds were determined from the ethyl acetate and hexane extract of the strain F-04 using GC-MS. Overall, marine bacteria isolated during this study demonstrate the potential for the development of broad spectrum antibiotics.
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Affiliation(s)
- Raju Rajasabapathy
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620024, Tamilnadu, India; Department of Biotechnology, Goa University, Taleigao Plateau, 403 206, Goa, India.
| | - Sanjeev C Ghadi
- Department of Biotechnology, Goa University, Taleigao Plateau, 403 206, Goa, India
| | - Balakrishnan Manikandan
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, 403004, Goa, India
| | - Chellandi Mohandass
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, 403004, Goa, India; CSIR-National Institute of Oceanography, Regional Centre, Lokhandwala Road, Four Bungalows, Andheri (West), Mumbai, 400 053, India
| | - Akhila Surendran
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, 403004, Goa, India; Department of Marine Microbiology, Kerala University of Fisheries and Ocean Studies, Kerala, 682506, India
| | - Syed G Dastager
- NCIM Resource Center, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Ram M Meena
- Biological Oceanography Division, CSIR-National Institute of Oceanography, Dona Paula, 403004, Goa, India
| | - Rathinam Arthur James
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620024, Tamilnadu, India.
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Nabil-Adam A, Shreadah MA, Abd El Moneam NM, El-Assar SA. Pesudomance sp. Bacteria Associated with Marine Sponge as a Promising and Sustainable Source of Bioactive Molecules. Curr Pharm Biotechnol 2019; 20:964-984. [PMID: 31258072 DOI: 10.2174/1389201020666190619092502] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 01/04/2019] [Accepted: 05/13/2019] [Indexed: 12/21/2022]
Abstract
BACKGROUND The study was conducted to identify the bacterial strain associated with marine sponge Hyrtiosaff. erectus collected from the Red Sea coastal water and to assess the utilization of their secondary metabolites for human benefit as antioxidant, anti-Alzheimer, anti-viral, anticancer and anti-inflammatory agent. METHODS After biochemical identification of Pesudomance sp. bacterial strain, the total polyphenol contents, cytotoxic, antioxidant, anti-Alzheimer, anti-viral, anticancer and anti-inflammatory activity of the Pesudomance sp. ethyl acetate extract were investigated by applying different biochemical assays. Polyphenol contents were investigated using spectrophotometric techniques. Antioxidant activity was determined by 1,1-diphenyl-2-picrylhydrazyl radical (DPPH), and 2,2/-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) ABTS radical scavenging activity assays. The cytotoxic effects were investigated by using the human cancerous cell lines. RESULTS The anti-Alzheimer, anti-viral, anticancer and anti-inflammatory activities were determined using ELISA. Qualitative phytochemical analysis of the Pesudomance sp. extract demonstrated the presence of a large and diverse group of substances such as alkaloids, carbohydrates, flavonoids, phenols, terpenoids, saponins, and tannins. The strong antioxidant activity of the Pesudomance sp. extract was mainly attributed to the protective role of polyphenols against reactive oxygen. It was also observed that Pesudomance sp. extract possessed significant anti-Alzheimer activity with 94% at 1 mg. The extract showed also high antiviral activity (90%) using reverse transcriptase enzymes inhibition assay. The examination of the anticancer activity by applying two experimental models, i.e., PTK and SHKI cleared out high significant percentages of 76.19 and 83.09 %; respectively. CONCLUSION The anti-inflammatory profiling using TNF, COX1, COX2, IL6 also revealed high antiinflammatory activity with different metabolic pathway of 62.70, 75.444, 79.27 and 54.15 %; respectively. The present study concluded that ethyl acetate extract of Pesudomance sp. possessed strong antioxidant, anti-Alzheimer, and anti-viral, anticancer and anti-inflammatory activities. Further studies are required to purify the bioactive compounds.
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Affiliation(s)
- Asmaa Nabil-Adam
- Marine Biotechnology and Natural products Lab (MBNP), National Institute of Oceanography & Fisheries (NIOF), Alexandria, Egypt
| | - Mohamed A Shreadah
- Marine Biotechnology and Natural products Lab (MBNP), National Institute of Oceanography & Fisheries (NIOF), Alexandria, Egypt
| | - Nehad M Abd El Moneam
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Samy A El-Assar
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
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Molecular Identification of Selected Streptomyces Strains Isolated from Mexican Tropical Soils and their Anti- Candida Activity. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16111913. [PMID: 31151174 PMCID: PMC6603721 DOI: 10.3390/ijerph16111913] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 11/23/2022]
Abstract
The increasing incidence of Candida albicans infections and resistance to current antifungal therapies has led to the search for new and more effective antifungal compounds. Actinobacterial species from the Streptomyces genus are recognized as some of the major producers of antimicrobial compounds. Therefore, the aims of this study were: (1) the identification of Streptomyces strains isolated from Mexican tropical acidic soils, (2) the evaluation of their antifungal activity on C. albicans, and (3) the exploration of the presence of polyketide synthase genes in their genome and antifungal secondary metabolites in their extracts. Four actinobacterial strains, isolated from previously unexplored soils with antibacterial antecedents, were selected. These strains were identified as Streptomycesangustmyceticus S6A-03, Streptomyces manipurensis S3A-05 and S3A-09, and Streptomyces parvisporogenes S2A-04, according to their molecular analyses. The ethanol extract of the lyophilized supernatant of S. parvisporogenes displayed the most interesting antifungal activity against C. albicans, with a minimum inhibitory concentration (MIC) of 0.5 mg/mL. Type I polyketide synthase (PKS-I) and non-ribosomal peptide synthase (NRPS) genes were detected in all strains. In addition, type II PKS genes (PKS-II) were also found in S.manipurensis S3A-05 and S. parvisporogenes. LC-UV-HRMS analysis of the active organic extract of S. parvisporogenes indicated the presence of the known antifungal compound carbazomycin G as the major component.
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Wu S, Ou H, Liu T, Wang D, Zhao J. Structure and dynamics of microbiomes associated with the marine sponge Tedania sp. during its life cycle. FEMS Microbiol Ecol 2019; 94:4956761. [PMID: 29617990 DOI: 10.1093/femsec/fiy055] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 03/29/2018] [Indexed: 12/20/2022] Open
Abstract
Tedania sp. is a dominant sponge that is ubiquitous along the southeast coast of China. High-throughput sequencing and transmission electron microscopy were used to describe a detailed profile of sponge-associated microbiomes at seven life stages: adult, embryo-containing spawning adult, embryo, pre-competent larva at 2 h and 4 h, competent larva at 8 h and post-larva within 1-2h after settlement, as well as the surrounding seawater. Among a total of 15098 operational taxonomic units (OTUs), 13 were present exclusively in all stages of the sponge life cycle and could thus be identified as sponge-specific bacteria. Many OTUs were shared between the sponge and seawater, though abundance differed. The relative abundance of β-Proteobacteria associated with sponges was much higher than found in seawater. The microbiomes from each life stage also exhibited a characteristic distribution. Synechococcales dominated in adults, and Enterobacteriaceae was prominent in larvae. The competent larva was notable, with sharp increases in the total OTUs, diversity indices, richness estimates and unique OTUs. Some bacterial groups that were rare in other sponge stages and seawater, such as Clostridia (5.6%), were markedly more abundant in competent larvae. In conclusion, this work greatly advances our understanding of the dynamics and persistence of the sponge-microbe association.
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Affiliation(s)
- Shufei Wu
- College of Ocean and Earth Sciences of Xiamen University, Xiamen 361005, China
| | - Huilong Ou
- College of Ocean and Earth Sciences of Xiamen University, Xiamen 361005, China
| | - Tan Liu
- College of Ocean and Earth Sciences of Xiamen University, Xiamen 361005, China
| | - Dexiang Wang
- College of Ocean and Earth Sciences of Xiamen University, Xiamen 361005, China
| | - Jing Zhao
- College of Ocean and Earth Sciences of Xiamen University, Xiamen 361005, China
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Al-Dhabi NA, Mohammed Ghilan AK, Esmail GA, Valan Arasu M, Duraipandiyan V, Ponmurugan K. Bioactivity assessment of the Saudi Arabian Marine Streptomyces sp. Al-Dhabi-90, metabolic profiling and its in vitro inhibitory property against multidrug resistant and extended-spectrum beta-lactamase clinical bacterial pathogens. J Infect Public Health 2019; 12:549-556. [PMID: 30755364 DOI: 10.1016/j.jiph.2019.01.065] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/10/2019] [Accepted: 01/27/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Metabolites obtained from the marine microorganisms were known for their important role in microbial inhibition. Interestingly, bioprospecting of secondary metabolites from marine derived actinomycetes has huge demand especially in the treatment of multi drug resistant clinical pathogens. The present study subjected towards the identification of promising antimicrobial actinomycetes from the Arabian Gulf regions and metabolic profiling of the crude organic solvent extract by chromatographic techniques. METHODS The strains were characterized by 16S rRNA sequencing. Extracellular metabolites were profiled by performing GC-MS analysis. MIC values of the compounds were detected using broth dilution technique. RESULTS A Gram positive, spore forming filamentous Streptomyces sp. Al-Dhabi-90 possessed good antibacterial activities against the drug resistant pathogens were confirmed by 16S rRNA gene sequencing. Further, the gas chromatography coupled with mass spectrum analysis data revealed that the organic solvent extract of the fermented Streptomyces sp. Al-Dhabi-90 contained major components such as 3-methylpyridazine, n-hexadecanoic acid, indazol-4-one, octadecanoic acid and 3a-methyl-6-((4-methylphenyl) sul respectively. The Minimum Inhibitory Concentration (MIC) of the extract against Staphylococcus aureus and Klebsiella pneumoniae were 12.5 and 50μg/ml respectively. Against drug resistant ESBL pathogens such as Escherichia coli, Pseudomonsa aeroginosa and Proteus mirabilis were 12.5, and 25μg/ml respectively. Interestingly, the extract showed promising activity against the vancomycin resistant Enterococcus faecium at 50μg/ml. The increased level of cellular constituents after the extract treatment evidenced that the metabolites altered the membrane integrity of the pathogens. CONCLUSION Conclusively, the marine Streptomyces sp. Al-Dhabi-90 is an ideal source for the treatment of multi drug resistant clinical pathogens.
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Affiliation(s)
- Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
| | - Abdul-Kareem Mohammed Ghilan
- Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Galal Ali Esmail
- Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Mariadhas Valan Arasu
- Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Veeramuthu Duraipandiyan
- Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Karuppiah Ponmurugan
- Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
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Tawfike A, Attia EZ, Desoukey SY, Hajjar D, Makki AA, Schupp PJ, Edrada-Ebel R, Abdelmohsen UR. New bioactive metabolites from the elicited marine sponge-derived bacterium Actinokineospora spheciospongiae sp. nov. AMB Express 2019; 9:12. [PMID: 30680548 PMCID: PMC6345950 DOI: 10.1186/s13568-018-0730-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 12/31/2018] [Indexed: 12/15/2022] Open
Abstract
Several approaches have been dedicated to activate the cryptic gene clusters in the genomes of actinomycetes for the targeted discovery of new fascinating biomedical lead structures. In the current study, N-acetylglucosamine was used to maximize the chemical diversity of sponge-derived actinomycete Actinokineospora spheciospongiae sp. nov. HR-ESI-MS was employed for dereplication study and orthogonal partial least square-discriminant analysis was applied to evaluate the HR-ESI-MS data of the different fractions. As a result, two new fridamycins H (1) and I (2), along with three known compounds actinosporin C (3), D (4), and G (5) were isolated from the solid culture of sponge-associated actinomycete Actinokineospora spheciospongiae sp. nov., elicited with N-acetylglucosamine. Characterization of the isolated compounds was pursued using mass spectrometry and NMR spectral data. Fridamycin H (1) exhibited significant growth inhibitory activity towards Trypanosoma brucei strain TC221. These results highlight the potential of elicitation in sponge-associated actinomycetes as an effective strategy for the discovery of new anti-infective natural products.
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Wooster MK, Voigt O, Erpenbeck D, Wörheide G, Berumen ML. Sponges of the Red Sea. CORAL REEFS OF THE RED SEA 2019. [DOI: 10.1007/978-3-030-05802-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Peng C, Wang H, Jiang Y, Yang J, Lai H, Wei X. Exploring the Abundance and Diversity of Bacterial Communities and Quantifying Antibiotic-Related Genes Along an Elevational Gradient in Taibai Mountain, China. MICROBIAL ECOLOGY 2018; 76:1053-1062. [PMID: 29744532 DOI: 10.1007/s00248-018-1197-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/27/2018] [Indexed: 06/08/2023]
Abstract
Thus far, no studies have investigated the soil microbial diversity over an elevational gradient in Taibai Mountain, the central massif of the Qinling Mountain Range. Here, we used Illumina sequencing and quantitative PCR of the 16S rRNA gene to assess the diversity and abundance of bacterial communities along an elevational gradient in representative vegetation soils in Taibai Mountain. We identified the soil, climate, and vegetation factors driving the variations in soil bacterial community structure by Pearson correlation and redundancy analysis. We also evaluated the potential for antibiotic discovery by quantitative PCR of the PKS-I, PKS-II, and NRPS genes from Actinobacteria. The results showed that soil bacterial alpha diversity increased first and then decreased with an elevational rise in both the northern and southern slopes of Taibai Mountain. The bacterial abundance was significantly correlated with soil organic matter and nitrate nitrogen. The average relative abundance of Actinobacteria in Taibai Mountain was markedly higher than those in other mountain forest soils. The absolute abundance of PKS and NPRS gene was significantly higher in the tested soils compared with the gene copy numbers reported in tropical urban soils. Taibai Mountain is rich in actinomycete resources and has great potential for antibiotic excavation.
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Affiliation(s)
- Chu Peng
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - He Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Yingying Jiang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Jinhua Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Hangxian Lai
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China.
| | - Xiaomin Wei
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China.
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Balasubramanian S, Skaf J, Holzgrabe U, Bharti R, Förstner KU, Ziebuhr W, Humeida UH, Abdelmohsen UR, Oelschlaeger TA. A New Bioactive Compound From the Marine Sponge-Derived Streptomyces sp. SBT348 Inhibits Staphylococcal Growth and Biofilm Formation. Front Microbiol 2018; 9:1473. [PMID: 30050506 PMCID: PMC6050364 DOI: 10.3389/fmicb.2018.01473] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/13/2018] [Indexed: 01/09/2023] Open
Abstract
Staphylococcus epidermidis, the common inhabitant of human skin and mucosal surfaces has emerged as an important pathogen in patients carrying surgical implants and medical devices. Entering the body via surgical sites and colonizing the medical devices through formation of multi-layered biofilms leads to refractory and persistent device-related infections (DRIs). Staphylococci organized in biofilms are more tolerant to antibiotics and immune responses, and thus are difficult-to-treat. The consequent morbidity and mortality, and economic losses in health care systems has strongly necessitated the need for development of new anti-bacterial and anti-biofilm-based therapeutics. In this study, we describe the biological activity of a marine sponge-derived Streptomyces sp. SBT348 extract in restraining staphylococcal growth and biofilm formation on polystyrene, glass, medically relevant titan metal, and silicone surfaces. A bioassay-guided fractionation was performed to isolate the active compound (SKC3) from the crude SBT348 extract. Our results demonstrated that SKC3 effectively inhibits the growth (MIC: 31.25 μg/ml) and biofilm formation (sub-MIC range: 1.95–<31.25 μg/ml) of S. epidermidis RP62A in vitro. Chemical characterization of SKC3 by heat and enzyme treatments, and mass spectrometry (HRMS) revealed its heat-stable and non-proteinaceous nature, and high molecular weight (1258.3 Da). Cytotoxicity profiling of SKC3 in vitro on mouse fibroblast (NIH/3T3) and macrophage (J774.1) cell lines, and in vivo on the greater wax moth larvae Galleria mellonella revealed its non-toxic nature at the effective dose. Transcriptome analysis of SKC3 treated S. epidermidis RP62A has further unmasked its negative effect on central metabolism such as carbon flux as well as, amino acid, lipid, and energy metabolism. Taken together, these findings suggest a potential of SKC3 as a putative drug to prevent staphylococcal DRIs.
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Affiliation(s)
| | - Joseph Skaf
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Würzburg, Germany
| | - Ulrike Holzgrabe
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Würzburg, Germany
| | - Richa Bharti
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Konrad U Förstner
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Wilma Ziebuhr
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Ute H Humeida
- GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Microbiology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Usama R Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Tobias A Oelschlaeger
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
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Giordano D, Costantini M, Coppola D, Lauritano C, Núñez Pons L, Ruocco N, di Prisco G, Ianora A, Verde C. Biotechnological Applications of Bioactive Peptides From Marine Sources. Adv Microb Physiol 2018; 73:171-220. [PMID: 30262109 DOI: 10.1016/bs.ampbs.2018.05.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This review is an overview on marine bioactive peptides with promising activities for the development of alternative drugs to fight human pathologies. In particular, we focus on potentially prolific producers of peptides in microorganisms, including sponge-associated bacteria and marine photoautotrophs such as microalgae and cyanobacteria. Microorganisms are still poorly explored for drug discovery, even if they are highly metabolically plastic and potentially amenable to culturing. This offers the possibility of obtaining a continuous source of bioactive compounds to satisfy the challenging demands of pharmaceutical industries. This review targets peptides because of the variety of potent biological activities demonstrated by these molecules, including antiviral, antimicrobial, antifungal, antioxidant, anticoagulant, antihypertensive, anticancer, antidiabetic, antiobesity, and calcium-binding bioactivities. Several of these peptides have already gained recognition as effective drug agents in recent years. We also focus on cutting-edge omic approaches for the discovery of novel compounds for pharmacological applications. With rapid depletion of natural resources, omic technologies may be the solution to efficiently produce a vast variety of novel peptides with unique pharmacological potential.
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Affiliation(s)
- Daniela Giordano
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy; Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Maria Costantini
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy; Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Daniela Coppola
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy
| | - Chiara Lauritano
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Laura Núñez Pons
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Nadia Ruocco
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy; Department of Biology, University of Napoli Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cinthia, Napoli, Italy; Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Napoli, Italy
| | - Guido di Prisco
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy
| | - Adrianna Ianora
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Cinzia Verde
- Institute of Biosciences and BioResources (IBBR), CNR, Napoli, Italy; Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy; Dipartimento di Biologia, Università Roma 3, Roma, Italy.
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30
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Abdelfattah MS, Elmallah MIY, Faraag AHI, Hebishy AMS, Ali NH. Heliomycin and tetracinomycin D: anthraquinone derivatives with histone deacetylase inhibitory activity from marine sponge-associated Streptomyces sp. SP9. 3 Biotech 2018; 8:282. [PMID: 29881660 DOI: 10.1007/s13205-018-1304-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/24/2018] [Indexed: 01/04/2023] Open
Abstract
Several actinomycetes strains were isolated from different marine sponges collected from the Red Sea shore in Egypt. The efficiency of their crude extracts to inhibit histone deacetylase (HDAC) enzyme was investigated in the nuclear extract of Hela cell line. The crude extract corresponding to Streptomyces sp. SP9 isolated from the marine sponge Pseudoceratina arabica showed a promising HDAC inhibitory activity with 64 and 81% at 50 and 100 µg/ml, respectively. The strain was identified as Streptomyces sp. by phylogenetic analyses based on its 16S rRNA gene sequence. The major compounds of Streptomyces sp. SP9 were isolated and purified by different chromatographic methods. The chemical structure of the isolated compounds was identified on the basis of their spectroscopic data including mass, 1H and 13C NMR, and by comparison with those of authenticated samples. Structures of compounds 1 and 2 were established as heliomycin and tetracenomycin D, respectively. These compounds exhibited HDAC inhibitory activities with IC50 values of 29.8 ± 0.04 µg/ml for heliomycin (1) and 10.9 ± 0.02 µg/ml for tetracenomycin D (2). A computational docking study for compounds 1 and 2 against HDAC1, HDAC2, and HDAC3 was performed to formulate a hypothetical mechanism by which the tested compounds inhibit HDAC. Tetracenomycin D (2) showed a good binding interactions with HDAC2 (- 5.230 kcal/mol) and HDAC3 (- 6.361 kcal/mol).
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Affiliation(s)
- Mohamed Saleh Abdelfattah
- 1Marine Natural Products Unit (MNPRU), Faculty of Science, Helwan University, Ain Helwan, 11795 Cairo, Egypt
- 2Chemistry Department, Faculty of Science, Helwan University, Ain Helwan, 11795 Cairo, Egypt
| | - Mohammed Ismail Youssef Elmallah
- 1Marine Natural Products Unit (MNPRU), Faculty of Science, Helwan University, Ain Helwan, 11795 Cairo, Egypt
- 2Chemistry Department, Faculty of Science, Helwan University, Ain Helwan, 11795 Cairo, Egypt
| | - Ahmed Hassan Ibrahim Faraag
- 3Botany and Microbiology Department, Faculty of Science, Helwan University, Ain Helwan, 11795 Cairo, Egypt
- 4Faculty of Science, Bioinformatics Center, Helwan University, Ain Helwan, 11795 Cairo, Egypt
| | - Ali Mohamed Salah Hebishy
- 1Marine Natural Products Unit (MNPRU), Faculty of Science, Helwan University, Ain Helwan, 11795 Cairo, Egypt
- 2Chemistry Department, Faculty of Science, Helwan University, Ain Helwan, 11795 Cairo, Egypt
| | - Neama Hassan Ali
- 2Chemistry Department, Faculty of Science, Helwan University, Ain Helwan, 11795 Cairo, Egypt
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Guo ZK, Wang R, Chen SQ, Chen FX, Liu TM, Yang MQ. Anthocidins A⁻D, New 5-Hydroxyanthranilic Acid Related Metabolites from the Sea Urchin-Associated Actinobacterium, Streptomyces sp. HDa1. Molecules 2018; 23:molecules23051032. [PMID: 29702622 PMCID: PMC6102551 DOI: 10.3390/molecules23051032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 11/16/2022] Open
Abstract
Four new 5-hydroxyanthranilic acid related compounds, named anthocidins A⁻D (1⁻4), two known analogues n-lauryl 5-hydroxyanthranilate (5) and isolauryl 5-hydroxyanthranilate (6), together with benzamide (7), 3-hydroxy-4-methoxycinnamamide (8), and (3S-cis)-hexahydro-3-[(3,4-dihydroxyphenyl)methyl]pyrrolo[1,2-a]pyrazine-1,4-dione (9), were isolated from the fermentation broth of the marine-derived actinomycete, Streptomyces sp. HDa1, which was isolated from the gut of a sea urchin, Anthocidaris crassispina, collected from Hainan Island, China. The structures of these secondary metabolites were elucidated on the basis of their 1D and 2D-NMR and mass spectroscopic data, and anthocidin A was confirmed by single-crystal X-ray diffraction with Cu Kα radiation. Anthocidins A⁻D (1⁻4) feature an acetyl group substitution at the amino group and varying alkyl side chains at the carboxyl group of 5-hydroxyanthranilic acid, and compound 5 was isolated as a natural product for the first time. The cytotoxic and antibacterial activity of compounds 1⁻9 were evaluated.
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Affiliation(s)
- Zhi-Kai Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: ; Tel.: +86-898-6689-2946
| | - Rong Wang
- Hainan Academy of Ocean and Fisheries Sciences, Haikou 570203, China; helen1982--@163.com (R.W.); (S.-Q.C.); (F.-X.C.); (M.-Q.Y.)
| | - Shi-Quan Chen
- Hainan Academy of Ocean and Fisheries Sciences, Haikou 570203, China; helen1982--@163.com (R.W.); (S.-Q.C.); (F.-X.C.); (M.-Q.Y.)
| | - Fu-Xiao Chen
- Hainan Academy of Ocean and Fisheries Sciences, Haikou 570203, China; helen1982--@163.com (R.W.); (S.-Q.C.); (F.-X.C.); (M.-Q.Y.)
| | - Tian-Mi Liu
- Hainan Testing Center for the Quality and Safety of Aquatic Products, Haikou 570206, China;
| | - Ming-Qiu Yang
- Hainan Academy of Ocean and Fisheries Sciences, Haikou 570203, China; helen1982--@163.com (R.W.); (S.-Q.C.); (F.-X.C.); (M.-Q.Y.)
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Zhou M, Liu F, Yang X, Jin J, Dong X, Zeng KW, Liu D, Zhang Y, Ma M, Yang D. Bacillibactin and Bacillomycin Analogues with Cytotoxicities against Human Cancer Cell Lines from Marine Bacillus sp. PKU-MA00093 and PKU-MA00092. Mar Drugs 2018; 16:E22. [PMID: 29320403 PMCID: PMC5793070 DOI: 10.3390/md16010022] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/21/2017] [Accepted: 01/05/2018] [Indexed: 12/12/2022] Open
Abstract
Nonribosomal peptides from marine Bacillus strains have received considerable attention for their complex structures and potent bioactivities. In this study, we carried out PCR-based genome mining for potential nonribosomal peptides producers from our marine bacterial library. Twenty-one "positive" strains were screened out from 180 marine bacterial strains, and subsequent small-scale fermentation, HPLC and phylogenetic analysis afforded Bacillus sp. PKU-MA00092 and PKU-MA00093 as two candidates for large-scale fermentation and isolation. Ten nonribosomal peptides, including four bacillibactin analogues (1-4) and six bacillomycin D analogues (5-10) were discovered from Bacillus sp. PKU-MA00093 and PKU-MA00092, respectively. Compounds 1 and 2 are two new compounds and the ¹H NMR and 13C NMR data of compounds 7 and 9 is first provided. All compounds 1-10 were assayed for their cytotoxicities against human cancer cell lines HepG2 and MCF7, and the bacillomycin D analogues 7-10 showed moderate cytotoxicities with IC50 values from 2.9 ± 0.1 to 8.2 ± 0.2 µM. The discovery of 5-10 with different fatty acid moieties gave us the opportunity to reveal the structure-activity relationships of bacillomycin analogues against these human cancer cell lines. These results enrich the structural diversity and bioactivity properties of nonribosomal peptides from marine Bacillus strains.
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Affiliation(s)
- Mengjie Zhou
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Fawang Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Xiaoyan Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Jing Jin
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Xin Dong
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Ke-Wu Zeng
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Dong Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Yingtao Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Ming Ma
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Donghui Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Natural Medicines, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
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An Overview on Marine Sponge-Symbiotic Bacteria as Unexhausted Sources for Natural Product Discovery. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040040] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Microbial symbiotic communities of marine macro-organisms carry functional metabolic profiles different to the ones found terrestrially and within surrounding marine environments. These symbiotic bacteria have increasingly been a focus of microbiologists working in marine environments due to a wide array of reported bioactive compounds of therapeutic importance resulting in various patent registrations. Revelations of symbiont-directed host specific functions and the true nature of host-symbiont interactions, combined with metagenomic advances detecting functional gene clusters, will inevitably open new avenues for identification and discovery of novel bioactive compounds of biotechnological value from marine resources. This review article provides an overview on bioactive marine symbiotic organisms with specific emphasis placed on the sponge-associated ones and invites the international scientific community to contribute towards establishment of in-depth information of the environmental parameters defining selection and acquisition of true symbionts by the host organisms.
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Diversity and Bioactivity of Marine Bacteria Associated with the Sponges Candidaspongia flabellata and Rhopaloeides odorabile from the Great Barrier Reef in Australia. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9030039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Cumsille A, Undabarrena A, González V, Claverías F, Rojas C, Cámara B. Biodiversity of Actinobacteria from the South Pacific and the Assessment of Streptomyces Chemical Diversity with Metabolic Profiling. Mar Drugs 2017; 15:E286. [PMID: 28892017 PMCID: PMC5618425 DOI: 10.3390/md15090286] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/29/2017] [Accepted: 08/31/2017] [Indexed: 01/21/2023] Open
Abstract
Recently, bioprospecting in underexplored habitats has gained enhanced focus, since new taxa of marine actinobacteria can be found, and thus possible new metabolites. Actinobacteria are in the foreground due to their versatile production of secondary metabolites that present various biological activities, such as antibacterials, antitumorals and antifungals. Chilean marine ecosystems remain largely unexplored and may represent an important source for the discovery of bioactive compounds. Various culture conditions to enrich the growth of this phylum were used and 232 bacterial strains were isolated. Comparative analysis of the 16S rRNA gene sequences led to identifying genetic affiliations of 32 genera, belonging to 20 families. This study shows a remarkable culturable diversity of actinobacteria, associated to marine environments along Chile. Furthermore, 30 streptomycete strains were studied to establish their antibacterial activities against five model strains, Staphylococcus aureus, Listeria monocytogenes, Salmonella enterica, Escherichia coli and Pseudomonas aeruginosa, demonstrating abilities to inhibit bacterial growth of Gram-positive bacteria. To gain insight into their metabolic profiles, crude extracts were submitted to liquid chromatography-high resolution mass spectrometry (LC-HRMS) analysis to assess the selection of streptomycete strains with potentials of producing novel bioactive metabolites. The combined approach allowed for the identification of three streptomycete strains to pursue further investigations. Our Chilean marine actinobacterial culture collection represents an important resource for the bioprospection of novel marine actinomycetes and its metabolites, evidencing their potential as producers of natural bioproducts.
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Affiliation(s)
- Andrés Cumsille
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile.
| | - Agustina Undabarrena
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile.
| | - Valentina González
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile.
| | - Fernanda Claverías
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile.
| | - Claudia Rojas
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile.
| | - Beatriz Cámara
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química & Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso 2340000, Chile.
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36
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Jose PA, Jha B. Intertidal marine sediment harbours Actinobacteria with promising bioactive and biosynthetic potential. Sci Rep 2017; 7:10041. [PMID: 28855551 PMCID: PMC5577230 DOI: 10.1038/s41598-017-09672-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 07/28/2017] [Indexed: 11/29/2022] Open
Abstract
Actinobacteria are the major source of bioactive natural products that find their value in research and drug discovery programmes. Antimicrobial resistance and the resulting high demand for novel antibiotics underscore the need for exploring novel sources of these bacteria endowed with biosynthetic potential. Intertidal ecosystems endure regular periods of immersion and emersion, and represent an untapped source of Actinobacteria. In this study, we studied the diversity and biosynthetic potential of cultivable Actinobacteria from intertidal sediments of Diu Island in the Arabian Sea. A total of 148 Actinobacteria were selectively isolated using a stamping method with eight isolation media. Isolates were grouped into OTUs based on their 16S rRNA gene sequence, and categorized within actinobacterial families such as Glycomycetaceae, Micromonosporaceae, Nocardiaceae, Nocardiopsaceae, Pseudonocardiaceae, Streptomycetaceae, and Thermomonosporaceae. The biosynthetic potential of the Actinobacteria, necessary for secondary metabolite biosynthesis, was screened and confirmed by extensive fingerprinting approaches based on genes coding for polyketide synthases and nonribosomal peptide synthetases. The observed biosynthetic potential was correlated with the antibacterial activity exhibited by these isolates in laboratory conditions. Ultimately, the results demonstrate that intertidal sediment is a rich source of diverse cultivable Actinobacteria with high potential to synthesize novel bioactive compounds in their genomes.
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Affiliation(s)
- Polpass Arul Jose
- Marine Biotechnology and Ecology Division, CSIR- Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar - 364002, Gujarat, India.
| | - Bhavanath Jha
- Marine Biotechnology and Ecology Division, CSIR- Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar - 364002, Gujarat, India. .,Academy of Scientific and Innovative Research (AcSIR), Council of Scientific and Industrial Research (CSIR), New Delhi, India.
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37
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Chanana S, Thomas CS, Braun DR, Hou Y, Wyche TP, Bugni TS. Natural Product Discovery Using Planes of Principal Component Analysis in R (PoPCAR). Metabolites 2017; 7:metabo7030034. [PMID: 28703778 PMCID: PMC5618319 DOI: 10.3390/metabo7030034] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 06/20/2017] [Accepted: 07/11/2017] [Indexed: 01/11/2023] Open
Abstract
Rediscovery of known natural products hinders the discovery of new, unique scaffolds. Efforts have mostly focused on streamlining the determination of what compounds are known vs. unknown (dereplication), but an alternative strategy is to focus on what is different. Utilizing statistics and assuming that common actinobacterial metabolites are likely known, focus can be shifted away from dereplication and towards discovery. LC-MS-based principal component analysis (PCA) provides a perfect tool to distinguish unique vs. common metabolites, but the variability inherent within natural products leads to datasets that do not fit ideal standards. To simplify the analysis of PCA models, we developed a script that identifies only those masses or molecules that are unique to each strain within a group, thereby greatly reducing the number of data points to be inspected manually. Since the script is written in R, it facilitates integration with other metabolomics workflows and supports automated mass matching to databases such as Antibase.
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Affiliation(s)
- Shaurya Chanana
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA.
| | - Chris S Thomas
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA.
| | - Doug R Braun
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA.
| | - Yanpeng Hou
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA.
| | - Thomas P Wyche
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA.
- Exploratory Science Center, Merck & Co., 320 Bent St., Cambridge, MA 02141, USA.
| | - Tim S Bugni
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA.
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38
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Building a bio-based industry in the Middle East through harnessing the potential of the Red Sea biodiversity. Appl Microbiol Biotechnol 2017; 101:4837-4851. [PMID: 28528426 PMCID: PMC5486811 DOI: 10.1007/s00253-017-8310-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 01/03/2023]
Abstract
The incentive for developing microbial cell factories for production of fuels and chemicals comes from the ability of microbes to deliver these valuable compounds at a reduced cost and with a smaller environmental impact compared to the analogous chemical synthesis. Another crucial advantage of microbes is their great biological diversity, which offers a much larger "catalog" of molecules than the one obtainable by chemical synthesis. Adaptation to different environments is one of the important drives behind microbial diversity. We argue that the Red Sea, which is a rather unique marine niche, represents a remarkable source of biodiversity that can be geared towards economical and sustainable bioproduction processes in the local area and can be competitive in the international bio-based economy. Recent bioprospecting studies, conducted by the King Abdullah University of Science and Technology, have established important leads on the Red Sea biological potential, with newly isolated strains of Bacilli and Cyanobacteria. We argue that these two groups of local organisms are currently most promising in terms of developing cell factories, due to their ability to operate in saline conditions, thus reducing the cost of desalination and sterilization. The ability of Cyanobacteria to perform photosynthesis can be fully exploited in this particular environment with one of the highest levels of irradiation on the planet. We highlight the importance of new experimental and in silico methodologies needed to overcome the hurdles of developing efficient cell factories from the Red Sea isolates.
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Thawai C, Rungjindamai N, Klanbut K, Tanasupawat S. Nocardia xestospongiae sp. nov., isolated from a marine sponge in the Andaman Sea. Int J Syst Evol Microbiol 2017; 67:1451-1456. [DOI: 10.1099/ijsem.0.001736] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- 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
| | - Nattawut Rungjindamai
- 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
| | - Khanungkan Klanbut
- 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
| | - Somboon Tanasupawat
- Departments of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
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40
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New approaches to antibiotic discovery. Biotechnol Lett 2017; 39:805-817. [DOI: 10.1007/s10529-017-2311-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/24/2017] [Indexed: 10/20/2022]
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41
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Gaikwad S, Shouche YS, Gade WN. Microbial community structure of two freshwater sponges using Illumina MiSeq sequencing revealed high microbial diversity. AMB Express 2016; 6:40. [PMID: 27299740 PMCID: PMC4908081 DOI: 10.1186/s13568-016-0211-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 06/03/2016] [Indexed: 11/10/2022] Open
Abstract
Sponges are primitive metazoans that are known to harbour diverse and abundant microbes. All over the world attempts are being made to exploit these microbes for their biotechnological potential to produce, bioactive compounds and antimicrobial peptides. However, the majority of the studies are focussed on the marine sponges and studies on the freshwater sponges have been neglected so far. To increase our understanding of the microbial community structure of freshwater sponges, microbiota of two fresh water sponges namely, Eunapius carteri and Corvospongilla lapidosa is explored for the first time using Next Generation Sequencing (NGS) technology. Overall the microbial composition of these sponges comprises of 14 phyla and on an average, more than 2900 OTUs were obtained from C. lapidosa while E. carteri showed 980 OTUs which is higher than OTUs obtained in the marine sponges. Thus, our study showed that, fresh water sponges also posses highly diverse microbial community than previously thought and it is distinct from the marine sponge microbiota. The present study also revealed that microbial community structure of both the sponges is significantly different from each other and their respective water samples. In the present study, we have detected many bacterial lineages belonging to Firmicutes, Actinobacteria, Proteobacteria, Planctomycetes, etc. that are known to produce compounds of biotechnological importance. Overall, this study gives insight into the microbial composition of the freshwater sponges which is highly diverse and needs to be studied further to exploit their biotechnological capabilities.
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Synthesis of ent-BE-43547A1 reveals a potent hypoxia-selective anticancer agent and uncovers the biosynthetic origin of the APD-CLD natural products. Nat Chem 2016; 9:264-272. [DOI: 10.1038/nchem.2657] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/26/2016] [Indexed: 01/15/2023]
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43
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Marine Microbiological Enzymes: Studies with Multiple Strategies and Prospects. Mar Drugs 2016; 14:md14100171. [PMID: 27669268 PMCID: PMC5082319 DOI: 10.3390/md14100171] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/04/2016] [Accepted: 09/14/2016] [Indexed: 11/16/2022] Open
Abstract
Marine microorganisms produce a series of promising enzymes that have been widely used or are potentially valuable for our daily life. Both classic and newly developed biochemistry technologies have been broadly used to study marine and terrestrial microbiological enzymes. In this brief review, we provide a research update and prospects regarding regulatory mechanisms and related strategies of acyl-homoserine lactones (AHL) lactonase, which is an important but largely unexplored enzyme. We also detail the status and catalytic mechanism of the main types of polysaccharide-degrading enzymes that broadly exist among marine microorganisms but have been poorly explored. In order to facilitate understanding, the regulatory and synthetic biology strategies of terrestrial microorganisms are also mentioned in comparison. We anticipate that this review will provide an outline of multiple strategies for promising marine microbial enzymes and open new avenues for the exploration, engineering and application of various enzymes.
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Al-Amoudi S, Essack M, Simões MF, Bougouffa S, Soloviev I, Archer JAC, Lafi FF, Bajic VB. Bioprospecting Red Sea Coastal Ecosystems for Culturable Microorganisms and Their Antimicrobial Potential. Mar Drugs 2016; 14:md14090165. [PMID: 27626430 PMCID: PMC5039536 DOI: 10.3390/md14090165] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 08/10/2016] [Accepted: 08/10/2016] [Indexed: 01/19/2023] Open
Abstract
Microorganisms that inhabit unchartered unique soil such as in the highly saline and hot Red Sea lagoons on the Saudi Arabian coastline, represent untapped sources of potentially new bioactive compounds. In this study, a culture-dependent approach was applied to three types of sediments: mangrove mud (MN), microbial mat (MM), and barren soil (BS), collected from Rabigh harbor lagoon (RHL) and Al-Kharrar lagoon (AKL). The isolated bacteria were evaluated for their potential to produce bioactive compounds. The phylogenetic characterization of 251 bacterial isolates based on the 16S rRNA gene sequencing, supported their assignment to five different phyla: Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Planctomycetes. Fifteen putative novel species were identified based on a 16S rRNA gene sequence similarity to other strain sequences in the NCBI database, being ≤98%. We demonstrate that 49 of the 251 isolates exhibit the potential to produce antimicrobial compounds. Additionally, at least one type of biosynthetic gene sequence, responsible for the synthesis of secondary metabolites, was recovered from 25 of the 49 isolates. Moreover, 10 of the isolates had a growth inhibition effect towards Staphylococcus aureus, Salmonella typhimurium and Pseudomonas syringae. We report the previously unknown antimicrobial activity of B. borstelensis, P. dendritiformis and M. salipaludis against all three indicator pathogens. Our study demonstrates the evidence of diverse cultured microbes associated with the Red Sea harbor/lagoon environments and their potential to produce antimicrobial compounds.
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Affiliation(s)
- Soha Al-Amoudi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
| | - Magbubah Essack
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
| | - Marta F Simões
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
- Biology Department, Edge Hill University, St. Helens Road, Lancashire, Ormskirk L39 4QP, UK.
| | - Salim Bougouffa
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
| | - Irina Soloviev
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
| | - John A C Archer
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
| | - Feras F Lafi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
| | - Vladimir B Bajic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia.
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45
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Isolation and characterization of marine-derived actinomycetes with cytotoxic activity from the Red Sea coast. Asian Pac J Trop Biomed 2016. [DOI: 10.1016/j.apjtb.2016.06.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Gopikrishnan V, Radhakrishnan M, Shanmugasundaram T, Pazhanimurugan R, Balagurunathan R. Antibiofouling potential of quercetin compound from marine-derived actinobacterium, Streptomyces fradiae PE7 and its characterization. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:13832-13842. [PMID: 27032633 DOI: 10.1007/s11356-016-6532-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 03/21/2016] [Indexed: 06/05/2023]
Abstract
An attempt has been made to isolate, purify and characterize antifouling compound from Streptomyces fradiae PE7 isolated from Vellar estuarine sediment, Parangipettai, South India. The microbial identification was done at species level based on its phenotypic, cell wall and molecular characteristics. Strain PE7 produced high quantity of antifouling compounds in agar surface fermentation when compared to submerged fermentation. In fermentation optimization, wide range of sugars, amino acids, minerals, pH, temperature and NaCl concentration was found to influence the antifouling compound production from the strain PE7. Antifouling compound PE7-C was purified from the crude extract by preparative TLC, and its activity against biofouling bacteria was confirmed by bioautography. Based on the physico-chemical characteristics, the chemical structure of the antifouling compound PE7-C was identified as quercetin (C15H10O7), a flavonoid class of compound with the molecular weight 302.23 g/mol. The purified quercetin was active against 18 biofouling bacteria with MIC range between 1.6 and 25 μg/ml, algal spore germination and mollusc foot adherence found at 100 μg/ml and 306 ± 19.6 μg ml(-1) respectively. The present study, for the first time, reported quercetin from marine-derived Streptomyces sp. PE7 with antifouling activity. This also leads to the repurposing of quercetin for the development of antifouling agent.
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Affiliation(s)
- Venugopal Gopikrishnan
- Centre for Drug Discovery and Development, Sathyabama University, Jeppiar Nagar, Chennai, 600 119, Tamil Nadu, India
| | - Manikkam Radhakrishnan
- Centre for Drug Discovery and Development, Sathyabama University, Jeppiar Nagar, Chennai, 600 119, Tamil Nadu, India
| | - Thangavel Shanmugasundaram
- Actinobacterial Research Laboratory, Department of Microbiology, Periyar University, Periyar Palkalai Nagar, Salem, 636 011, Tamil Nadu, India
| | - Raasaiyah Pazhanimurugan
- Actinobacterial Research Laboratory, Department of Microbiology, Periyar University, Periyar Palkalai Nagar, Salem, 636 011, Tamil Nadu, India
| | - Ramasamy Balagurunathan
- Actinobacterial Research Laboratory, Department of Microbiology, Periyar University, Periyar Palkalai Nagar, Salem, 636 011, Tamil Nadu, India.
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Ziemert N, Alanjary M, Weber T. The evolution of genome mining in microbes - a review. Nat Prod Rep 2016; 33:988-1005. [PMID: 27272205 DOI: 10.1039/c6np00025h] [Citation(s) in RCA: 404] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering: 2006 to 2016The computational mining of genomes has become an important part in the discovery of novel natural products as drug leads. Thousands of bacterial genome sequences are publically available these days containing an even larger number and diversity of secondary metabolite gene clusters that await linkage to their encoded natural products. With the development of high-throughput sequencing methods and the wealth of DNA data available, a variety of genome mining methods and tools have been developed to guide discovery and characterisation of these compounds. This article reviews the development of these computational approaches during the last decade and shows how the revolution of next generation sequencing methods has led to an evolution of various genome mining approaches, techniques and tools. After a short introduction and brief overview of important milestones, this article will focus on the different approaches of mining genomes for secondary metabolites, from detecting biosynthetic genes to resistance based methods and "evo-mining" strategies including a short evaluation of the impact of the development of genome mining methods and tools on the field of natural products and microbial ecology.
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Affiliation(s)
- Nadine Ziemert
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology and Biotechnology, University of Tuebingen, Germany.
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Nazir M, Pandey R, Siddiqi TO, Ibrahim MM, Qureshi MI, Abraham G, Vengavasi K, Ahmad A. Nitrogen-Deficiency Stress Induces Protein Expression Differentially in Low-N Tolerant and Low-N Sensitive Maize Genotypes. FRONTIERS IN PLANT SCIENCE 2016; 7:298. [PMID: 27047497 PMCID: PMC4800187 DOI: 10.3389/fpls.2016.00298] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 02/25/2016] [Indexed: 05/04/2023]
Abstract
Nitrogen (N) is essential for proper plant growth and its application has proven to be critical for agricultural produce. However, for unavoidable economic and environmental problems associated with excessive use of N-fertilizers, it is an urgent demand to manage application of fertilizers. Improving the N-use efficiency (NUE) of crop plants to sustain productivity even at low N levels is the possible solution. In the present investigation, contrasting low-N sensitive (HM-4) and low-N tolerant (PEHM-2) genotypes were identified and used for comparative proteome-profiling of leaves under optimum and low N as well as restoration of low N on 3rd (NR3) and 5th (NR5) days after re-supplying N. The analysis of differential expression pattern of proteins was performed by 2-D gel electrophoresis. Significant variations in the expression of proteins were observed under low N, which were genotype specific. In the leaf proteome, 25 spots were influenced by N treatment and four spots were different between the two genotypes. Most of the proteins that were differentially accumulated in response to N level and were involved in photosynthesis and metabolism, affirming the relationship between N and carbon metabolism. In addition to this, greater intensity of some defense proteins in the low N tolerant genotype was found that may have a possible role in imparting it tolerance under N starvation conditions. The new insights generated on maize proteome in response to N-starvation and restoration would be useful toward improvement of NUE in maize.
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Affiliation(s)
- Muslima Nazir
- Department of Botany, Faculty of Science, Jamia HamdardNew Delhi, India
| | - Renu Pandey
- Division of Plant Physiology, Indian Council of Agricultural Research-Indian Agricultural Research InstituteNew Delhi, India
| | - Tariq O. Siddiqi
- Department of Botany, Faculty of Science, Jamia HamdardNew Delhi, India
| | - Mohamed M. Ibrahim
- Department of Botany and Microbiology, Science College, King Saud UniversityRiyadh, Saudi Arabia
- Department of Botany and Microbiology, Faculty of Science, Alexandria UniversityAlexandria, Egypt
| | - Mohammad I. Qureshi
- Department of Biotechnology, Faculty of Natural Sciences, Jamia Millia IslamiaNew Delhi, India
| | - Gerard Abraham
- Centre for Conservation and Utilization of Blue Green Algae, Indian Council of Agricultural Research-Indian Agricultural Research InstituteNew Delhi, India
| | - Krishnapriya Vengavasi
- Division of Plant Physiology, Indian Council of Agricultural Research-Indian Agricultural Research InstituteNew Delhi, India
| | - Altaf Ahmad
- Department of Botany, Faculty of Life Sciences, Aligarh Muslim UniversityAligarh, India
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Horn H, Cheng C, Edrada-Ebel R, Hentschel U, Abdelmohsen UR. Draft genome sequences of three chemically rich actinomycetes isolated from Mediterranean sponges. Mar Genomics 2015; 24 Pt 3:285-7. [PMID: 26490827 DOI: 10.1016/j.margen.2015.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/08/2015] [Accepted: 10/08/2015] [Indexed: 01/10/2023]
Abstract
Metabolomic analysis has shown the chemical richness of the sponge-associated actinomycetes Streptomyces sp. SBT349, Nonomureae sp. SBT364, and Nocardiopsis sp. SBT366. The genomes of these actinomycetes were sequenced and the genomic potential for secondary metabolism was evaluated. Their draft genomes have sizes of 8.0, 10, and 5.8 Mb having 687, 367, and 179 contigs with a GC content of 71.6, 70.7, and 72.7%, respectively. Moreover, antiSMASH 3.0 predicted 108, 149, and 75 secondary metabolite gene clusters, respectively which highlight the metabolic capacity of the three actinomycete species to produce diverse classes of natural products.
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Affiliation(s)
- Hannes Horn
- Department of Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Cheng Cheng
- Department of Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, The John Arbuthnott Building, Glasgow, UK
| | - Ute Hentschel
- Department of Marine Microbiology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
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Sun W, Zhang F, He L, Karthik L, Li Z. Actinomycetes from the South China Sea sponges: isolation, diversity, and potential for aromatic polyketides discovery. Front Microbiol 2015; 6:1048. [PMID: 26483773 PMCID: PMC4589764 DOI: 10.3389/fmicb.2015.01048] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/14/2015] [Indexed: 12/21/2022] Open
Abstract
Marine sponges often harbor dense and diverse microbial communities including actinobacteria. To date no comprehensive investigation has been performed on the culturable diversity of the actinomycetes associated with South China Sea sponges. Structurally novel aromatic polyketides were recently discovered from marine sponge-derived Streptomyces and Saccharopolyspora strains, suggesting that sponge-associated actinomycetes can serve as a new source of aromatic polyketides. In this study, a total of 77 actinomycete strains were isolated from 15 South China Sea sponge species. Phylogenetic characterization of the isolates based on 16S rRNA gene sequencing supported their assignment to 12 families and 20 genera, among which three rare genera (Marihabitans, Polymorphospora, and Streptomonospora) were isolated from marine sponges for the first time. Subsequently, β-ketoacyl synthase (KSα) gene was used as marker for evaluating the potential of the actinomycete strains to produce aromatic polyketides. As a result, KSα gene was detected in 35 isolates related to seven genera (Kocuria, Micromonospora, Nocardia, Nocardiopsis, Saccharopolyspora, Salinispora, and Streptomyces). Finally, 10 strains were selected for small-scale fermentation, and one angucycline compound was detected from the culture extract of Streptomyces anulatus strain S71. This study advanced our knowledge of the sponge-associated actinomycetes regarding their diversity and potential in producing aromatic polyketides.
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Affiliation(s)
- Wei Sun
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Fengli Zhang
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Liming He
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Loganathan Karthik
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
| | - Zhiyong Li
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University Shanghai, China
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