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Samak ME, Solyman SM, Hanora A, Zakeer S. Metagenomic mining of two Egyptian Red Sea sponges associated microbial community. BMC Microbiol 2024; 24:315. [PMID: 39192220 DOI: 10.1186/s12866-024-03299-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/09/2024] [Indexed: 08/29/2024] Open
Abstract
The Red Sea is a promising habitat for the discovery of new bioactive marine natural products. Sponges associated microorganisms represent a wealthy source of compounds with unique chemical structures and diverse biological activities. Metagenomics is an important omics-based culture-independent technique that is used as an effective tool to get genomic and functional information on sponge symbionts. In this study, we used metagenomic analysis of two Egyptian Red Sea sponges Hyrtios erectus and Phorbas topsenti microbiomes to study the biodiversity and the biosynthetic potential of the Red Sea sponges to produce bioactive compounds. Our data revealed high biodiversity of the two sponges' microbiota with phylum Proteobacteria as the most dominant phylum in the associated microbial community with an average of 31% and 70% respectively. The analysis also revealed high biosynthetic potential of sponge Hyrtios erectus microbiome through detecting diverse types of biosynthetic gene clusters (BGCs) with predicted cytotoxic, antibacterial and inhibitory action. Most of these BGCs were predicted to be novel as they did not show any similarity with any MIBiG database known cluster. This study highlights the importance of the microbiome of the collected Red Sea sponge Hyrtios erectus as a valuable source of new bioactive natural products.
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Affiliation(s)
- Manar El Samak
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Samar M Solyman
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai Unvirsity Elkantra Branch, Ismailia, Egypt
| | - Amro Hanora
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt.
| | - Samira Zakeer
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
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Girão M, Alexandrino DAM, Cao W, Costa I, Jia Z, Carvalho MF. Unveiling the culturable and non-culturable actinobacterial diversity in two macroalgae species from the northern Portuguese coast. Environ Microbiol 2024; 26:e16620. [PMID: 38627038 DOI: 10.1111/1462-2920.16620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/16/2024] [Indexed: 04/19/2024]
Abstract
Actinomycetota, associated with macroalgae, remains one of the least explored marine niches. The secondary metabolism of Actinomycetota, the primary microbial source of compounds relevant to biotechnology, continues to drive research into the distribution, dynamics, and metabolome of these microorganisms. In this study, we employed a combination of traditional cultivation and metagenomic analysis to investigate the diversity of Actinomycetota in two native macroalgae species from the Portuguese coast. We obtained and taxonomically identified a collection of 380 strains, which were distributed across 12 orders, 15 families, and 25 genera affiliated with the Actinomycetia class, with Streptomyces making up approximately 60% of the composition. Metagenomic results revealed the presence of Actinomycetota in both Chondrus crispus and Codium tomentosum datasets, with relative abundances of 11% and 2%, respectively. This approach identified 12 orders, 16 families, and 17 genera affiliated with Actinomycetota, with minimal overlap with the cultivation results. Acidimicrobiales emerged as the dominant actinobacterial order in both macroalgae, although no strain affiliated with this taxonomic group was successfully isolated. Our findings suggest that macroalgae represent a hotspot for Actinomycetota. The synergistic use of both culture-dependent and independent approaches proved beneficial, enabling the identification and recovery of not only abundant but also rare taxonomic members.
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Affiliation(s)
- Mariana Girão
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - Diogo A M Alexandrino
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- Department of Environmental Health, School of Health, Porto, Portugal
| | - Weiwei Cao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Isabel Costa
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Zhongjun Jia
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Maria F Carvalho
- CIIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
- ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
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Abdulrahman I, Jamal MT, Pugazhendi A, Dhavamani J, Al-Shaeri M, Al-Maaqar S, Satheesh S. Antibacterial and antibiofilm activity of extracts from sponge-associated bacterial endophytes. Prep Biochem Biotechnol 2023; 53:1143-1153. [PMID: 36840506 DOI: 10.1080/10826068.2023.2175366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Sponges forms association with many bacteria that serve as sources of new bioactive compounds. The compounds are produced in response to environmental and nutritional conditions of the environment that enable them to protect their host from colonization. In this study, three sponge bacterial endophytes were isolated, identified, and subjected to solvent extraction processes. The identified bacteria are Bacillus amyloquifaciens, Bacillus paramycoides, and Enterobacter sp. The bacteria were cultured in two different fermentation media with varying nutritional composition for the extraction process. The extracts were evaluated for antibacterial and antibiofilm activity against microfouling bacteria and the chemical composition of each extract was analyzed via gas chromatography-mass spectrometry (GC-MS). The extract from the endophytes shows varying antibacterial and antibiofilm activity against the tested strains. Several compounds were detected from the extracts including some with known antibacterial/antibiofilm activity. The results showed variations in activity and secondary metabolite production between the extracts obtained under different nutritional composition of the media. In conclusion, this study indicated the role of nutrient composition in the activity and secondary metabolites production by bacteria associated with sponge Also, this study confirmed the role of sponge bacterial endophytes as producers of bioactive compounds with potential application as antifouling (AF) agents.
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Affiliation(s)
- Idris Abdulrahman
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Department of Microbiology, Faculty of Sciences, Kaduna State University, Kaduna, Nigeria
| | - Mamdoh Taha Jamal
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Arulazhagan Pugazhendi
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Center of Excellence in Environmental Studies, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Jeyakumar Dhavamani
- Center of Excellence in Environmental Studies, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Majed Al-Shaeri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Saleh Al-Maaqar
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
- Department of Biology, Faculty of Education, Al-Baydha University, Al-Baydha, Yemen
| | - Sathianeson Satheesh
- Department of Marine Biology, Faculty of Marine Sciences, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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El Samak M, Zakeer S, Hanora A, Solyman SM. Metagenomic and metatranscriptomic exploration of the Egyptian Red Sea sponge Theonella sp. associated microbial community. Mar Genomics 2023; 70:101032. [PMID: 37084583 DOI: 10.1016/j.margen.2023.101032] [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: 02/22/2023] [Revised: 04/02/2023] [Accepted: 04/12/2023] [Indexed: 04/23/2023]
Abstract
Marine sponges associated microorganisms are considered to be prolific source of bioactive natural products. Omics-based techniques such as metagenomics and metatranscriptomics have been used as effective tools to discover natural products. In this study, we used integrated metagenomic and metatranscriptomic analysis of three samples of the Egyptian Red Sea sponge Theonella sp. microbiome to obtain a complete picture of its biosynthetic activity to produce bioactive compounds. Our data revealed high biodiversity of the Egyptian sponge microbiota represented by 38 bacterial phyla with Candidate Phylum Poribacteria as the most abundant phyla with an average of 27.5% of the microbial community. The analysis also revealed high biosynthetic activity of the sponge microbiome through detecting different types of biosynthetic gene clusters (BGCs) with predicted antibacterial, cytotoxic and inhibitory bioactivity and the majority of these clusters were found to be actively transcribed. The complete BGCs of the cytotoxic theonellamide and misakinolide were detected and found to be actively transcribed. The majority of the detected BGCs were predicted to be novel as they did not show any similarity with any known cluster in the MIBiG database.
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Affiliation(s)
- Manar El Samak
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt
| | - Samira Zakeer
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt
| | - Amro Hanora
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt.
| | - Samar M Solyman
- Department of Microbiology and Immunology, Faculty of Pharmacy, Suez Canal University, Egypt; Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University- Elkantara branch, Egypt
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Bioactivity of bacteria associated with Red Sea nudibranchs and whole genome sequence of Nocardiopsis dassonvillei RACA-4. Mar Genomics 2023; 67:101004. [PMID: 36521348 DOI: 10.1016/j.margen.2022.101004] [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: 08/17/2022] [Revised: 11/09/2022] [Accepted: 11/12/2022] [Indexed: 12/14/2022]
Abstract
Microorganisms associated with marine invertebrates consider an important source of bioactive products. This study aimed to screen for antimicrobial and anticancer activity of crude extracts of bacteria associated with Red sea nudibranchs and molecular identification of the bioactive isolates using 16Sr RNA sequencing, in addition to whole-genome sequencing of one of the most bioactive bacteria. This study showed that bacteria associated with Red sea nudibranchs are highly bioactive and 16Sr RNA sequencing results showed that two isolates belonged to Firmicutes, and two isolates belonged to Proteobacteria, and Actinobacteria. The whole genome sequence data of the isolated Nocardiopsis RACA4 isolate has an estimated genome length of 6,721,839 bp and the taxonomy showed it belongs to the bacteria Nocardiopsis dassonvillei. The De novo assembly of RACA-4 paired reads using Unicycler v0.4.8 initially yielded 97 contigs with an N50 value of 214,568 bp and L50 value of 10, The resulting assembly was further mapped to the reference genome Nocardiopsis dassonvillei strain NCTC10488 using RagTag software v.2.1.0 and a final genome assembly resulted in 39 contigs and N50 value of 6,726,007 and L50 of 1. Genome mining using anti-smash showed around 9.1% of the genome occupied with genes related to secondary metabolites biosynthesis. A wide variety of secondary metabolites belonging to Polyketides, Terpenes, and nonribosomal peptides were predicted with high degree of similarity to known compounds. Non-characterized clusters were also found which suggest new natural compounds discovered by further studies.
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Schneider YK, Hagestad OC, Li C, Hansen EH, Andersen JH. Selective isolation of Arctic marine actinobacteria and a down-scaled fermentation and extraction strategy for identifying bioactive compounds. Front Microbiol 2022; 13:1005625. [DOI: 10.3389/fmicb.2022.1005625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/21/2022] [Indexed: 11/22/2022] Open
Abstract
Actinobacteria are among the most prolific producers of bioactive secondary metabolites. In order to collect Arctic marine bacteria for the discovery of new bioactive metabolites, actinobacteria were selectively isolated during a research cruise in the Greenland Sea, Norwegian Sea and the Barents Sea. In the frame of the isolation campaign, it was investigated how different sample treatments, isolation media and sample-sources, such as animals and sediments, affected the yield of actinobacterial isolates to aid further isolation campaigns. Special attention was given to sediments, where we expected spores of spore forming bacteria to enrich. Beside actinobacteria a high share of bacilli was obtained which was not desired. An experimental protocol for down-scaled cultivation and extraction was tested and compared with an established low-throughput cultivation and extraction protocol. The heat-shock method proved suitable to enrich spore-, or endospore forming bacteria such as bacilli. Finally, a group bioactive compounds could be tentatively identified using UHPLC–MS/MS analysis of the active fractions.
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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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Marine Actinobacteria a New Source of Antibacterial Metabolites to Treat Acne Vulgaris Disease—A Systematic Literature Review. Antibiotics (Basel) 2022; 11:antibiotics11070965. [PMID: 35884220 PMCID: PMC9311749 DOI: 10.3390/antibiotics11070965] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 02/04/2023] Open
Abstract
Acne vulgaris is a multifactorial disease that remains under-explored; up to date it is known that the bacterium Cutibacterium acnes is involved in the disease occurrence, also associated with a microbial dysbiosis. Antibiotics have become a mainstay treatment generating the emergence of antibiotic-resistant bacteria. In addition, there are some reported side effects of alternative treatments, which indicate the need to investigate a different therapeutic approach. Natural products continue to be an excellent option, especially those extracted from actinobacteria, which represent a prominent source of metabolites with a wide range of biological activities, particularly the marine actinobacteria, which have been less studied than their terrestrial counterparts. Therefore, this systematic review aimed to identify and evaluate the potential anti-infective activity of metabolites isolated from marine actinobacteria strains against bacteria related to the development of acne vulgaris disease. It was found that there is a variety of compounds with anti-infective activity against Staphylococcus aureus and Staphylococcus epidermidis, bacteria closely related to acne vulgaris development; nevertheless, there is no report of a compound with antibacterial activity or quorum-sensing inhibition toward C. acnes, which is a surprising result. Since two of the most widely used antibiotics for the treatment of acne targeting C. acnes were obtained from actinobacteria of the genus Streptomyces, this demonstrates a great opportunity to pursue further studies in this field, considering the potential of marine actinobacteria to produce new anti-infective compounds.
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Sedeek AM, Ismail MM, Elsayed TR, Ramadan MA. Recent methods for discovering novel bioactive metabolites, specifically antimicrobial agents, from marine-associated microorganisms. Lett Appl Microbiol 2022; 75:511-525. [PMID: 35485872 DOI: 10.1111/lam.13728] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/08/2022] [Accepted: 04/19/2022] [Indexed: 12/01/2022]
Abstract
Marine microorganisms are a promising source for novel natural compounds with many medical and biotechnological applications. Here we demonstrate limitations and recent strategies for investigating the marine microbial community for novel bioactive metabolites, specifically those of antimicrobial potential. These strategies include culture-dependent methods such as modifying the standard culture media, including changing the gelling agent, dissolving vehicle, media supplementation, and preparation to access a broader range of bacterial diversity from marine samples. Furthermore, we discuss strategies like in situ cultivation, dilution-to-extinction cultivation, and long-term incubation. We are presenting recent applications of culture-independent methods such as genome mining, proteomics profiling, and the application of metagenomics as a novel strategy for structure confirmation in the discovery of the marine microorganism for novel antimicrobial metabolites. We present this review as a simple guide and a helpful resource for those who seek to enter the challenging field of applied marine microbiology.
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Affiliation(s)
- Abdelrahman M Sedeek
- Department of Microbiology and Immunology, Faculty of Pharmacy, Sinai University, Ismaillia, 41522, Egypt
| | - Maha M Ismail
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
| | - Tarek R Elsayed
- Department of Agricultural Microbiology, Faculty of Agriculture, Cairo University, Egypt, Giza, 12613, Egypt
| | - Mohamed A Ramadan
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, 11562, Egypt
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Anteneh YS, Yang Q, Brown MH, Franco CMM. Factors affecting the isolation and diversity of marine sponge-associated bacteria. Appl Microbiol Biotechnol 2022; 106:1729-1744. [PMID: 35103809 PMCID: PMC8882111 DOI: 10.1007/s00253-022-11791-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 12/24/2022]
Abstract
Marine sponges are an ideal source for isolating as yet undiscovered microorganisms with some sponges having about 50% of their biomass composed of microbial symbionts. This study used a variety of approaches to investigate the culturable diversity of the sponge-associated bacterial community from samples collected from the South Australian marine environment. Twelve sponge samples were selected from two sites and their bacterial population cultivated using seven different agar media at two temperatures and three oxygen levels over 3 months. These isolates were identified using microscopic, macroscopic, and 16S rRNA gene analysis. A total of 1234 bacterial colonies were isolated which consisted of four phyla: Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes, containing 21 genera. The diversity of the bacterial population was demonstrated to be influenced by the type of isolation medium, length of the incubation period and temperature, sponge type, and oxygen level. The findings of this study showed that marine sponges of South Australia can yield considerable bacterial culturable diversity if a comprehensive isolation strategy is implemented. Two sponges, with the highest and the lowest diversity of culturable isolates, were examined using next-generation sequencing to better profile the bacterial population. A marked difference in terms of phyla and genera was observed using culture-based and culture-independent approaches. This observed variation displays the importance of utilizing both methods to reflect a more complete picture of the microbial population of marine sponges. KEY POINTS: Improved bacterial diversity due to long incubations, 2 temperatures, and 3 oxygen levels. Isolates identified by morphology, restriction digests, and 16S rRNA gene sequencing. At least 70% of culturable genera were not revealed by NGS methods.
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Affiliation(s)
- Yitayal S Anteneh
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
- Department of Medical Microbiology, College of Medicine, Addis Ababa University, Addis Ababa, Ethiopia
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
| | - Qi Yang
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia
- Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Melissa H Brown
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
| | - Christopher M M Franco
- Medical Biotechnology, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA, 5042, Australia.
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Kamel HL, Hanora A, Solyman SM. Metataxanomic, bioactivity and microbiome analysis of Red Sea marine sponges from Egypt. Mar Genomics 2021; 61:100920. [PMID: 34973527 DOI: 10.1016/j.margen.2021.100920] [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: 09/13/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 10/19/2022]
Abstract
Red Sea marine sponges (phylum Porifera) and associated microorganisms harbor a wide range of microorganisms, which are considered an essential source of bioactive products. In this study, we screened both the crude extracts of Red Sea marine sponges and their associated bacterial extract for antimicrobial activity and antiviral activity. Molecular characterization of bioactive producers was performed using16S rRNA sequencing, in addition to metagenomic analysis of three representative sponges utilizing the 16S rRNA gene V3-V4 region sequencing in two different seasons. Twelve samples were collected from five different sponge species by scuba diving, and all the crude extracts of sponges showed antimicrobial activity except Negombata corticata. Moreover, 84 out of 110 bacterial isolates extracts demonstrated antimicrobial activity against at least one tested microorganism. These results revealed the bioactivity and biodiversity of the Red Sea marine invertebrates-associated bacteria. It was found that the bioactive isolates belong to several bacterial groups. The bacterial communities of Negombata magnifica, Negombata corticata, and Siphonochalina siphonella were shown with great diversity and differences in the bacterial percentage, diversity, and unique community composition at different seasons in each sponge species. Unique microenvironment for each sponge species may be linked to the production of specific bioactive product.
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Affiliation(s)
- Hasnaa L Kamel
- Department of Microbiology & Immunology, College of Pharmacy, Suez Canal University, Ismailia, Egypt; Department of Microbiology & Immunology, College of Pharmacy, Sinai University, Ismailia, Egypt.
| | - Amro Hanora
- Department of Microbiology & Immunology, College of Pharmacy, Suez Canal University, Ismailia, Egypt.
| | - Samar M Solyman
- Department of Microbiology & Immunology, College of Pharmacy, Suez Canal University, Ismailia, Egypt; Department of Microbiology & Immunology, College of Pharmacy, Sinai University, Ismailia, Egypt.
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12
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The Discovery of Actinospene, a New Polyene Macrolide with Broad Activity against Plant Fungal Pathogens and Pathogenic Yeasts. Molecules 2021; 26:molecules26227020. [PMID: 34834113 PMCID: PMC8621364 DOI: 10.3390/molecules26227020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 02/07/2023] Open
Abstract
Phytopathogenic fungi infect crops, presenting a worldwide threat to agriculture. Polyene macrolides are one of the most effective antifungal agents applied in human therapy and crop protection. In this study, we found a cryptic polyene biosynthetic gene cluster in Actinokineospora spheciospongiae by genome mining. Then, this gene cluster was activated via varying fermentation conditions, leading to the discovery of new polyene actinospene (1), which was subsequently isolated and its structure determined through spectroscopic techniques including UV, HR-MS, and NMR. The absolute configuration was confirmed by comparing the calculated and experimental electronic circular dichroism (ECD) spectra. Unlike known polyene macrolides, actinospene (1) demonstrated more versatile post-assembling decorations including two epoxide groups and an unusual isobutenyl side chain. In bioassays, actinospene (1) showed a broad spectrum of antifungal activity against several plant fungal pathogens as well as pathogenic yeasts with minimum inhibitory concentrations ranging between 2 and 10 μg/mL.
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Dat TTH, Steinert G, Cuc NTK, Smidt H, Sipkema D. Bacteria Cultivated From Sponges and Bacteria Not Yet Cultivated From Sponges-A Review. Front Microbiol 2021; 12:737925. [PMID: 34867854 PMCID: PMC8634882 DOI: 10.3389/fmicb.2021.737925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/18/2021] [Indexed: 12/21/2022] Open
Abstract
The application of high-throughput microbial community profiling as well as "omics" approaches unveiled high diversity and host-specificity of bacteria associated with marine sponges, which are renowned for their wide range of bioactive natural products. However, exploration and exploitation of bioactive compounds from sponge-associated bacteria have been limited because the majority of the bacteria remains recalcitrant to cultivation. In this review, we (i) discuss recent/novel cultivation techniques that have been used to isolate sponge-associated bacteria, (ii) provide an overview of bacteria isolated from sponges until 2017 and the associated culture conditions and identify the bacteria not yet cultured from sponges, and (iii) outline promising cultivation strategies for cultivating the uncultivated majority of bacteria from sponges in the future. Despite intensive cultivation attempts, the diversity of bacteria obtained through cultivation remains much lower than that seen through cultivation-independent methods, which is particularly noticeable for those taxa that were previously marked as "sponge-specific" and "sponge-enriched." This poses an urgent need for more efficient cultivation methods. Refining cultivation media and conditions based on information obtained from metagenomic datasets and cultivation under simulated natural conditions are the most promising strategies to isolate the most wanted sponge-associated bacteria.
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Affiliation(s)
- Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Georg Steinert
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Nguyen Thi Kim Cuc
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
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Mohamed SS, Abdelhamid SA, Ali RH. Isolation and identification of marine microbial products. J Genet Eng Biotechnol 2021; 19:162. [PMID: 34665351 PMCID: PMC8526645 DOI: 10.1186/s43141-021-00259-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/02/2021] [Indexed: 11/16/2022]
Abstract
Background The ocean is one of the world’s most important sources of bioactive chemicals in the marine environment. Microbiologists, ecologists, agronomists, taxonomists, and evolutionary biologists have been increasingly interested in marine microbial natural products (MMNPs) in recent decades. Main body Diverse marine bacteria appear to get the ability to manufacture an astounding diversity of MMNPs with a wide range of biological actions, including anti-tumor, antimicrobial, and anti-cardiovascular agents according to numerous studies. Short conclusions Innovative isolation and culture methodologies, tactics for identifying novel MMNPs via routine screens, metagenomics, genomics, combinatorial biosynthesis, and synthetic biology are all discussed in this review. There is also a discussion of potential issues and future directions for studying MMNPs.
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Affiliation(s)
- Sahar Saleh Mohamed
- Microbial Biotechnology Department, Genetic Engineering Division, National Research Centre, Cairo, Egypt
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15
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Srinivasan R, Kannappan A, Shi C, Lin X. Marine Bacterial Secondary Metabolites: A Treasure House for Structurally Unique and Effective Antimicrobial Compounds. Mar Drugs 2021; 19:md19100530. [PMID: 34677431 PMCID: PMC8539464 DOI: 10.3390/md19100530] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/12/2021] [Accepted: 09/15/2021] [Indexed: 02/06/2023] Open
Abstract
The prevalence of antimicrobial resistance reduces the effectiveness of antimicrobial drugs in preventing and treating infectious diseases caused by pathogenic organisms, such as bacteria, fungi, and viruses. Because of the burgeoning growth of microbes with antimicrobial-resistant traits, there is a dire need to identify and develop novel and effective antimicrobial agents to treat infections from antimicrobial-resistant strains. The marine environment is rich in ecological biodiversity and can be regarded as an untapped resource for prospecting novel bioactive compounds. Therefore, exploring the marine environment for antimicrobial agents plays a significant role in drug development and biomedical research. Several earlier scientific investigations have proven that bacterial diversity in the marine environment represents an emerging source of structurally unique and novel antimicrobial agents. There are several reports on marine bacterial secondary metabolites, and many are pharmacologically significant and have enormous promise for developing effective antimicrobial drugs to combat microbial infections in drug-resistant pathogens. In this review, we attempt to summarize published articles from the last twenty-five years (1996–2020) on antimicrobial secondary metabolites from marine bacteria evolved in marine environments, such as marine sediment, water, fauna, and flora.
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Affiliation(s)
- Ramanathan Srinivasan
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (R.S.); (X.L.)
| | - Arunachalam Kannappan
- State Key Laboratory of Microbial Metabolism, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (C.S.)
| | - Chunlei Shi
- State Key Laboratory of Microbial Metabolism, MOST-USDA Joint Research Center for Food Safety, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (C.S.)
| | - Xiangmin Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (R.S.); (X.L.)
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Analysis of Unusual Sulfated Constituents and Anti-infective Properties of Two Indonesian Mangroves, Lumnitzera littorea and Lumnitzera racemosa (Combretaceae). SEPARATIONS 2021. [DOI: 10.3390/separations8060082] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Lumnitzera littorea and Lumnitzera racemosa are mangrove species distributed widely along the Indonesian coasts. Besides their ecological importance, both are of interest owing to their wealth of natural products, some of which constitute potential sources for medicinal applications. We aimed to discover and characterize new anti-infective compounds, based on population-level sampling of both species from across the Indonesian Archipelago. Root metabolites were investigated by TLC, hyphenated LC-MS/MS and isolation, the internal transcribed spacer (ITS) region of rDNA was used for genetic characterization. Phytochemical characterization of both species revealed an unusual diversity in sulfated constituents with 3,3’,4’-tri-O-methyl-ellagic acid 4-sulfate representing the major compound in most samples. None of these compounds was previously reported for mangroves. Chemophenetic comparison of L. racemosa populations from different localities provided evolutionary information, as supported by molecular phylogenetic evidence. Samples of both species from particular locations exhibited anti-bacterial potential (Southern Nias Island and East Java against Gram-negative bacteria, Halmahera and Ternate Island against Gram-positive bacteria). In conclusion, Lumnitzera roots from natural mangrove stands represent a promising source for sulfated ellagic acid derivatives and further sulfur containing plant metabolites with potential human health benefits.
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17
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Shady NH, Tawfike AF, Yahia R, Fouad MA, Brachmann AO, Piel J, Abdelmohsen UR, Kamel MS. Cytotoxic activity of actinomycetes Nocardia sp. and Nocardiopsis sp. associated with marine sponge Amphimedon sp. Nat Prod Res 2021; 36:2917-2922. [PMID: 34039169 DOI: 10.1080/14786419.2021.1931865] [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: 10/21/2022]
Abstract
Cancer is a hazard life-threatening disease, which affect huge population worldwide. Marine actinomycetes are considered as promising source for potential chemotherapeutic agents. In our study, we carried out metabolic profiling for Nocardia sp. UR 86 and Nocardiopsis sp. UR 92 that were cultivated from the Red Sea sponge Amphimedon sp. to investigate their chemical diversity using different media conditions. The crude culture extracts were subjected to high-resolution mass spectrometry (HRMS) analysis. The chemical profiles of the different extracts of Nocardia sp. UR 86 and Nocardiopsis sp. UR 92 revealed their richness in diverse metabolites and consequently twenty compounds (1-20) were annotated. Moreover, the obtained extracts of the differently cultivated Nocardia sp. UR 86 and Nocardiopsis sp. UR 92 were investigated against three cell lines HepG2, MCF-7 and CACO2 and revealed the targeted cytotoxicity of Nocardia sp. and Nocardiopsis sp. metabolites against the three cell lines.
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Affiliation(s)
- Nourhan Hisham Shady
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, New Minia City, Minia, Egypt
| | - Ahmed F Tawfike
- Department of Pharmacognosy, Faculty of Pharmacy, Helwan University, Cairo, Egypt.,Molecular Discovery Group, Computational and Analytical Science Department, Rothamsted Research, Harpenden, UK
| | - Ramadan Yahia
- Department of Microbiology and immunology, Faculty of Pharmacy, Deraya University, New Minia City, Minia, Egypt
| | - Mostafa A Fouad
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Alexander O Brachmann
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, New Minia City, Minia, Egypt.,Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Mohamed Salah Kamel
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, New Minia City, Minia, Egypt.,Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
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Bio-Guided Isolation of Antimalarial Metabolites from the Coculture of Two Red Sea Sponge-Derived Actinokineospora and Rhodococcus spp. Mar Drugs 2021; 19:md19020109. [PMID: 33673168 PMCID: PMC7918646 DOI: 10.3390/md19020109] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 12/19/2022] Open
Abstract
Coculture is a productive technique to trigger microbes’ biosynthetic capacity by mimicking the natural habitats’ features principally by competition for food and space and interspecies cross-talks. Mixed cultivation of two Red Sea-derived actinobacteria, Actinokineospora spheciospongiae strain EG49 and Rhodococcus sp. UR59, resulted in the induction of several non-traced metabolites in their axenic cultures, which were detected using LC–HRMS metabolomics analysis. Antimalarial guided isolation of the cocultured fermentation led to the isolation of the angucyclines actinosporins E (1), H (2), G (3), tetragulol (5) and the anthraquinone capillasterquinone B (6), which were not reported under axenic conditions. Interestingly, actinosporins were previously induced when the axenic culture of the Actinokineospora spheciospongiae strain EG49 was treated with signalling molecule N-acetyl-d-glucosamine (GluNAc); this finding confirmed the effectiveness of coculture in the discovery of microbial metabolites yet to be discovered in the axenic fermentation with the potential that could be comparable to adding chemical signalling molecules in the fermentation flask. The isolated angucycline and anthraquinone compounds exhibited in vitro antimalarial activity and good biding affinity against lysyl-tRNA synthetase (PfKRS1), highlighting their potential developability as new antimalarial structural motif.
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19
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Liu M, Zhang W, Yao J, Niu J. Production, purification, characterization, and biological properties of Rhodosporidium paludigenum polysaccharide. PLoS One 2021; 16:e0246148. [PMID: 33513164 PMCID: PMC7845956 DOI: 10.1371/journal.pone.0246148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 01/14/2021] [Indexed: 11/18/2022] Open
Abstract
The yield of marine red yeast polysaccharide (MRYP) obtained from Rhodosporidium paludigenum was increased by optimizing fermentation conditions, and the pure polysaccharide was extracted by column chromatography. The molecular weight of pure MRYP and the ratio of mannose to glucose in components of MRYP were determined. Antioxidant and antibacterial abilities of MRYP were investigated in vitro and in vivo. The optimal fermentation parameters were as follows: Medium 4, pH = 6.72, temperature = 30.18°C, blades speed = 461.36 r/min; the optimized yield reached 4323.90 mg/L, which was 1.31 times the original yield. The sequence of factors that affected the MRYP yield was the blades speed>pH>temperature. The main components of MRYP were MYH-1 and MYH-2. The molecular weights of MYH-1 and MYH-2 were 246.92 kDa and 21.88 kDa, respectively; they accounted for 53.60% and 28.75% of total polysaccharide. In MYH-1 and MYH-2, the proportion of glucose and mannose accounted for 46.94%, 38.46%, and 67.10%, 7.17%, respectively. In vitro, the ability of scavenging DPPH•, •OH, and •O2− radical was 32.26%, 24.34%, and 22.09%; the minimum inhibitory concentration (MIC) of MRYP was 480 μg/mg. In vivo, MRYP improved the lambs’ body weight, antioxidant enzyme activity, and the number of probiotics, but it reduced the feed/gain (F/G) ratio and the number of pathogenic bacteria in 60-days-old lambs.
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Affiliation(s)
- Mengjian Liu
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - WenJu Zhang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
- * E-mail:
| | - Jun Yao
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Junli Niu
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
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20
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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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Anteneh YS, Yang Q, Brown MH, Franco CMM. Antimicrobial Activities of Marine Sponge-Associated Bacteria. Microorganisms 2021; 9:171. [PMID: 33466936 PMCID: PMC7830929 DOI: 10.3390/microorganisms9010171] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/11/2021] [Indexed: 11/17/2022] Open
Abstract
The misuse and overuse of antibiotics have led to the emergence of multidrug-resistant microorganisms, which decreases the chance of treating those infected with existing antibiotics. This resistance calls for the search of new antimicrobials from prolific producers of novel natural products including marine sponges. Many of the novel active compounds reported from sponges have originated from their microbial symbionts. Therefore, this study aims to screen for bioactive metabolites from bacteria isolated from sponges. Twelve sponge samples were collected from South Australian marine environments and grown on seven isolation media under four incubation conditions; a total of 1234 bacterial isolates were obtained. Of these, 169 bacteria were tested in media optimized for production of antimicrobial metabolites and screened against eleven human pathogens. Seventy bacteria were found to be active against at least one test bacterial or fungal pathogen, while 37% of the tested bacteria showed activity against Staphylococcus aureus including methicillin-resistant strains and antifungal activity was produced by 21% the isolates. A potential novel active compound was purified possessing inhibitory activity against S. aureus. Using 16S rRNA, the strain was identified as Streptomyces sp. Our study highlights that the marine sponges of South Australia are a rich source of abundant and diverse bacteria producing metabolites with antimicrobial activities against human pathogenic bacteria and fungi.
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Affiliation(s)
- Yitayal S. Anteneh
- College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia;
- Department of Medical Microbiology, College of Medicine, Addis Ababa University, Addis Ababa 9086, Ethiopia
| | - Qi Yang
- Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China;
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Melissa H. Brown
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia;
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22
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Abbasi S, Emtiazi G. MALDI-TOF analysis of a novel extremophile peptide purified from Halarchaeum acidiphilum ASDL78 with antiarchaeal and antibacterial activities. J Basic Microbiol 2020; 60:920-930. [PMID: 32997354 DOI: 10.1002/jobm.202000392] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/29/2020] [Accepted: 09/15/2020] [Indexed: 12/25/2022]
Abstract
In hypersaline environments, halophilic archaea synthesize antimicrobial substances called halocins. There is a promise to make new drugs for antibiotic-resistant strains. Here, we report the antibacterial activity of a new haloarchaea selected from Lut Desert, Iran. A total of 38 isolated halophilic bacteria and archaea were screened for the antagonistic activity test of each strain against other bacterial and archaeal strains. Finally, a strain, recognized as Halarchaeum acidiphilum, with a fast grown strain and high antagonistic potential against different strains was identified by morphological, physiological, and molecular characteristics. The halocin was produced in a semisolid submerge medium and partially purified by heat treatments and molecular weight ultrafiltration cutoff (3, 50, and 10 kDa). It was a cell-free, heat-resistant (85°C for 2 h) protein with a molecular mass near to 20 kDa produced at the endpoint of logarithmic growth. The molecular weight of halocin was 17 kDa, and indicated no apparent homology with known halocins, suggesting that this might be a new halocin. Therefore, a new strain belonging to Halarchaeum genus was isolated and characterized here that produced an antimicrobial and anti-haloarchaea halocin.
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Affiliation(s)
- Soheila Abbasi
- Department of Cell Biology, Molecular and Microbiology, Faculty of Biological Sciences and Technology, University of Isfahan, Isfahan, Iran
| | - Giti Emtiazi
- Department of Cell Biology, Molecular and Microbiology, Faculty of Biological Sciences and Technology, University of Isfahan, Isfahan, Iran
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Antimicrobial activity of bacteria from marine sponge Suberea mollis and bioactive metabolites of Vibrio sp. EA348. Saudi J Biol Sci 2020; 27:1139-1147. [PMID: 32256176 PMCID: PMC7105658 DOI: 10.1016/j.sjbs.2020.02.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/27/2020] [Accepted: 02/01/2020] [Indexed: 11/22/2022] Open
Abstract
Discovery of potential bioactive metabolites from sponge-associated bacteria have gained attraction in recent years. The current study explores the potential of sponge (Suberea mollis) associated bacteria against bacterial and fungal pathogens. Sponge samples were collected from Red sea in Obhur region, Jeddah, Saudi Arabia. Of 29 isolated bacteria belong to four different classes i.e. Firmicutes (62%), γ-Proteobacteria (21%), α-Proteobacteria (10%) and Actinobacteria (7%). Among them nineteen (65%) bacterial strains showed antagonistic activity against oomycetes and only 3 (10%) bacterial strains were active against human pathogenic bacteria tested. Most bioactive genera include Bacillus (55%), Pseudovibrio (13%) and Ruegeria (10%). Enzyme production (protease, lipase, amylase, cellualse) was identified in 12 (41%) bacterial strains where potential strains belonging to γ-Proteobacteria and Firmicutes groups. Production of antimicrobial metabolites and hydrolysates in these bacteria suggest their potential role in sponge against pathogens. Further bioactive metabolites from selected strain of Vibrio sp. EA348 were identified using LC-MS and GC–MS analyses. We identified many active metabolites including antibiotics such as Amifloxacin and fosfomycin. Plant growth hormones including Indoleacetic acid and Gibberellin A3 and volatile organic compound such as methyl jasmonate were also detected in this strain. Our results highlighted the importance of marine bacteria inhabiting sponges as potential source of antimicrobial compounds and plant growth hormones of pharmaceutical and agricultural significance.
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Actinobacteria from Extreme Niches in Morocco and Their Plant Growth-Promoting Potentials. DIVERSITY-BASEL 2019. [DOI: 10.3390/d11080139] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The objectives of this study were to assess actinobacterial diversity in five Moroccan extreme habitats and to evaluate their plant growth-promoting (PGP) activities. The soil samples were collected from different locations, including soils contaminated with heavy metals, from a high altitude site, from the desert, and from a marine environment. In total, 23 actinobacteria were isolated, 8 from Merzouga sand soil; 5 from Cannabis sativa rhizospheric soil; 5 from Toubkal mountain; 4 from a Draa sfar mining site; and 1 from marine soil. Based on their genotypic classification using 16S rRNA gene sequences, 19 of all belonged to the genus Streptomyces (82%) while the rest are the members of the genera Nocardioides (4.5%), Saccharomonospora (4.5%), Actinomadura (4.5%), and Prauserella (4.5%). Isolates Streptomyces sp. TNC-1 and Streptomyces sp. MNC-1 showed the highest level of phosphorus solubilization activity with 12.39 and 8.56 mg/mL, respectively. All 23 isolates were able to solubilize potassium, and 91% of them could grow under nitrogen-free conditions. The ability of the isolated actinobacteria to form indole-3-acetic acid (IAA) ranged from 6.70 to 75.54 μg/mL with Streptomyces sp. MNC-1 being the best IAA producer. In addition, all of the actinobacteria could produce siderophores, with Saccharomonospora sp. LNS-1 synthesizing the greatest amount (138.92 μg/mL). Principal coordinate analysis revealed that Streptomyces spp. MNC-1, MNT-1, MNB-2, and KNC-5; Saccharomonospora sp. LNS-1; and Nocardioides sp. KNC-3 each showed a variety of high-level plant growth-promoting activities. The extreme environments in Morocco are rich with bioactive actinobacteria that possess a variety of plant growth-promoting potentials that can further benefit green and sustainable agriculture.
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High diversity and novelty of Actinobacteria isolated from the coastal zone of the geographically remote young volcanic Easter Island, Chile. Int Microbiol 2019; 22:377-390. [PMID: 30811004 DOI: 10.1007/s10123-019-00061-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 01/08/2019] [Accepted: 01/24/2019] [Indexed: 10/27/2022]
Abstract
Easter Island is an isolated volcanic island in the Pacific Ocean. Despite the extended knowledge about its origin, flora, and fauna, little is known about the bacterial diversity inhabiting this territory. Due to its isolation, Easter Island can be considered as a suitable place to evaluate microbial diversity in a geographically isolated context, what could shed light on actinobacterial occurrence, distribution, and potential novelty. In the present study, we performed a comprehensive analysis of marine Actinobacteria diversity of Easter Island by studying a large number of coastal sampling sites, which were inoculated into a broad spectrum of different culture media, where most important variations in composition included carbon and nitrogen substrates, in addition to salinity. The isolates were characterized on the basis of 16S ribosomal RNA gene sequencing and phylogenetic analysis. High actinobacterial diversity was recovered with a total of 163 pure cultures of Actinobacteria representing 72 phylotypes and 20 genera, which were unevenly distributed in different locations of the island and sample sources. The phylogenetic evaluation indicated a high degree of novelty showing that 45% of the isolates might represent new taxa. The most abundant genera in the different samples were Micromonospora, Streptomyces, Salinispora, and Dietzia. Two aspects appear of primary importance in regard to the high degree of novelty and diversity of Actinobacteria found. First, the application of various culture media significantly increased the number of species and genera obtained. Second, the geographical isolation is considered to be of importance regarding the actinobacterial novelty found.
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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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27
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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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28
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Elsayed Y, Refaat J, Abdelmohsen UR, Othman EM, Stopper H, Fouad MA. Metabolomic profiling and biological investigation of the marine sponge-derived bacterium Rhodococcus sp. UA13. PHYTOCHEMICAL ANALYSIS : PCA 2018; 29:543-548. [PMID: 29672972 DOI: 10.1002/pca.2765] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/17/2018] [Accepted: 02/17/2018] [Indexed: 06/08/2023]
Abstract
INTRODUCTION Marine sponge-associated actinomycetes are potent sources of bioactive natural products of pharmaceutical significance. They also contributed to the discovery of several clinically relevant antimicrobials. OBJECTIVE To apply the non-targeted metabolomics approach in chemical profiling of the sponge-derived bacterium Rhodococcus sp. UA13, formerly recovered from the Red Sea sponge Callyspongia aff. Implexa, along with testing for the anti-infective potential of its different fractions. METHODOLOGY Metabolomic analysis of the crude extract was carried out using liquid chromatography with high resolution electrospray ionisation mass spectrometry (LC-HR-ESI-MS) for dereplication purposes. Besides, the three major fractions (ethyl acetate, methanol, and n-butanol) obtained by chromatographic fractionation of the crude extract were evaluated for their anti-infective properties. RESULTS A variety of metabolites, mostly peptides, were characterised herein for the first time from the genus Rhodococcus. Among the tested samples, the n-butanol fraction showed potent inhibitory activities against Staphylococcus aureus, Candida albicans, and Trypanosoma brucei brucei with IC50 values of 9.3, 6.7, and 8.7 μg/mL, respectively, whereas only the ethyl acetate fraction was active against Chlamydia trachomatis (IC50 = 18.9 μg/mL). In contrast, both fractions did not exert anti-infective actions against Enterococcus faecalis and Leishmania major, whereas the methanol fraction was totally inactive against all the tested organisms. CONCLUSION This study showed the helpfulness of the established procedure in metabolic profiling of marine actinomycetes using liquid chromatography mass spectrometry (LC-MS) data, which aids in reducing the complex isolation steps during their chemical characterisation. The anti-infective spectrum of their metabolites is also interestingly relevant to future drug development.
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Affiliation(s)
- Yasmin Elsayed
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - John Refaat
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Würzburg, Germany
| | - Eman Maher Othman
- Department of Analytical Chemistry, Faculty of Pharmacy, Minia University, Minia, Egypt
- Department of Toxicology, University of Würzburg, Würzburg, Germany
| | - Helga Stopper
- Department of Toxicology, University of Würzburg, Würzburg, Germany
| | - Mostafa Ahmed Fouad
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
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Zhao K, Li J, Zhang X, Chen Q, Liu M, Ao X, Gu Y, Liao D, Xu K, Ma M, Yu X, Xiang Q, Chen J, Zhang X, Penttinen P. Actinobacteria associated with Glycyrrhiza inflata Bat. are diverse and have plant growth promoting and antimicrobial activity. Sci Rep 2018; 8:13661. [PMID: 30209357 PMCID: PMC6135863 DOI: 10.1038/s41598-018-32097-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 09/03/2018] [Indexed: 11/09/2022] Open
Abstract
Many of the plant associated microbes may directly and indirectly contribute to plant growth and stress resistance. Our aim was to assess the plant growth-promoting and antimicrobial activities of actinobacteria isolated from Glycyrrhiza inflata Bat. plants to find strains that could be applied in agricultural industry, for example in reclaiming saline soils. We isolated 36 and 52 strains that showed morphological characteristics of actinobacteria from one year old and three year old G. inflata plants, respectively. Based on 16S rRNA gene sequence analysis, the strains represented ten actinobacterial genera. Most of the strains had plant growth promoting characteristics in vitro, tolerated 200 mM NaCl and inhibited the growth of at least one indicator organism. The eight selected Streptomyces strains increased the germination rate of G. inflata seeds under salt stress. In addition, the four best seed germination promoters promoted the growth of G. inflata in vivo. The best promoters of G. inflata growth, strains SCAU5283 and SCAU5215, inhibited a wide range of indicator organisms, and may thus be considered as promising candidates to be applied in inoculating G. inflata.
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Affiliation(s)
- Ke Zhao
- Department of Microbiology, College of Resource and Environmental Sciences, Sichuan Agricultural University, Yaan, 625000, P. R. China.
| | - Jing Li
- Department of Microbiology, College of Resource and Environmental Sciences, Sichuan Agricultural University, Yaan, 625000, P. R. China
| | - Xiaoyue Zhang
- Department of Microbiology, College of Resource and Environmental Sciences, Sichuan Agricultural University, Yaan, 625000, P. R. China
| | - Qiang Chen
- Department of Microbiology, College of Resource and Environmental Sciences, Sichuan Agricultural University, Yaan, 625000, P. R. China
| | - Maoke Liu
- Biotechnology Center, Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences, Luzhou, 646100, P. R. China
| | - Xiaolin Ao
- Department of Microbiology, College of Resource and Environmental Sciences, Sichuan Agricultural University, Yaan, 625000, P. R. China
| | - Yunfu Gu
- Department of Microbiology, College of Resource and Environmental Sciences, Sichuan Agricultural University, Yaan, 625000, P. R. China
| | - Decong Liao
- Department of Microbiology, College of Resource and Environmental Sciences, Sichuan Agricultural University, Yaan, 625000, P. R. China
| | - Kaiwei Xu
- Department of Microbiology, College of Resource and Environmental Sciences, Sichuan Agricultural University, Yaan, 625000, P. R. China
| | - Monggeng Ma
- Department of Microbiology, College of Resource and Environmental Sciences, Sichuan Agricultural University, Yaan, 625000, P. R. China
| | - Xiumei Yu
- Department of Microbiology, College of Resource and Environmental Sciences, Sichuan Agricultural University, Yaan, 625000, P. R. China
| | - Quanju Xiang
- Department of Microbiology, College of Resource and Environmental Sciences, Sichuan Agricultural University, Yaan, 625000, P. R. China
| | - Ji Chen
- Department of Microbiology, College of Resource and Environmental Sciences, Sichuan Agricultural University, Yaan, 625000, P. R. China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resource and Environmental Sciences, Sichuan Agricultural University, Yaan, 625000, P. R. China
| | - Petri Penttinen
- Zhejiang Provincial Key Laboratory of Carbon Cycling in Forest Ecosystems and Carbon Sequestration, School of Environmental & Resource Sciences, Zhejiang Agriculture & Forestry University, Linan, 311300, P. R. China. .,Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Fin-00014, Finland.
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El Samak M, Solyman SM, Hanora A. Antimicrobial activity of bacteria isolated from Red Sea marine invertebrates. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2018; 19:e00275. [PMID: 30197871 PMCID: PMC6127373 DOI: 10.1016/j.btre.2018.e00275] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 07/13/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
Abstract
Marine invertebrates-associated microorganisms were considered to be important sources of marine bioactive products. This study aims to isolate marine invertebrates associated bacteria with antimicrobial activity from the Red Sea and test their biosynthetic potential through the detection of PKS and NRPS gene clusters involved with the production of bioactive secondary metabolites. In this respect, fifty bacterial strains were isolated from eight different Red Sea marine invertebrates and screened for their antimicrobial activity against standard pathogenic bacteria (Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922, Bacillus subtilis ATCC 6633) and yeast (Candida albicans ATCC 10231) using the standard well diffusion assay. Five isolates showed antifungal activity against Candida albicans with no activity recorded against other pathogenic bacterial strains. On the other hand when these isolates were screened for the presence of biosynthetic gene clusters (PKS and NRPS) by PCR using five sets of degenerative primers, 60% of the isolates were shown to contain at least one type of PKS and NRPS gene clusters, which indicates the biosynthetic potential of these isolates even if the isolates didn't express any biological activity in vitro. Moreover the 16S rRNA molecular identification of the isolates reveal the biodiversity of the red sea marine invertebrates associated bacteria as they were found to belong to several bacterial groups present in Alphaproteobacteria, Gammaproteobacteria, Actinobacteria and Firmicutes.
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Affiliation(s)
| | | | - Amro Hanora
- Department of Microbiology & Immunology, College of Pharmacy, Suez Canal University, Ismailia, Egypt
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El-Hawary SS, Sayed AM, Mohammed R, Hassan HM, Zaki MA, Rateb ME, Mohammed TA, Amin E, Abdelmohsen UR. Epigenetic Modifiers Induce Bioactive Phenolic Metabolites in the Marine-Derived Fungus Penicillium brevicompactum. Mar Drugs 2018; 16:md16080253. [PMID: 30061488 PMCID: PMC6117726 DOI: 10.3390/md16080253] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 07/19/2018] [Accepted: 07/28/2018] [Indexed: 01/16/2023] Open
Abstract
Fungi usually contain gene clusters that are silent or cryptic under normal laboratory culture conditions. These cryptic genes could be expressed for a wide variety of bioactive compounds. One of the recent approaches to induce production of such cryptic fungal metabolites is to use histone deacetylases (HDACs) inhibitors. In the present study, the cultures of the marine-derived fungus Penicillium brevicompactum treated with nicotinamide and sodium butyrate were found to produce a lot of phenolic compounds. Nicotinamide treatment resulted in the isolation and identification of nine compounds 1–9. Sodium butyrate also enhanced the productivity of anthranilic acid (10) and ergosterol peroxide (11). The antioxidant as well as the antiproliferative activities of each metabolite were determined. Syringic acid (4), sinapic acid (5), and acetosyringone (6) exhibited potent in vitro free radical scavenging, (IC50 20 to 30 µg/mL) and antiproliferative activities (IC50 1.14 to 1.71 µM) against HepG2 cancer cell line. Furthermore, a pharmacophore model of the active compounds was generated to build up a structure-activity relationship.
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Affiliation(s)
- Seham S El-Hawary
- Pharmacognosy Department, Faculty of Pharmacy, Cairo University, Cairo 11787, Egypt.
| | - Ahmed M Sayed
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt.
- Pharmacognosy Department, Faculty of Pharmacy, Nahda University, Beni-Suef 62513, Egypt.
| | - Rabab Mohammed
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt.
| | - Hossam M Hassan
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt.
| | - Mohamed A Zaki
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt.
| | - Mostafa E Rateb
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt.
- Marine Biodiscovery Centre, University of Aberdeen, Aberdeen, Scotland AB24 3UE, UK.
- School of Computing, Engineering and Physical Sciences, University of the West of Scotland, Paisley PA1 2BE, UK.
| | - Tarek A Mohammed
- Marine Invertebrates, National Institute of Oceanography and Fisheries, Red Sea Branch, Hurghada 84511, Egypt.
| | - Elham Amin
- Pharmacognosy Department, Faculty of Pharmacy, Beni-Suef University, Beni-Suef 62514, Egypt.
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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: 26] [Impact Index Per Article: 3.7] [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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RETRACTED ARTICLE: Rhodozepinone, a new antitrypanosomal azepino-diindole alkaloid from the marine sponge-derived bacterium Rhodococcus sp. UA13. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1974-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Dashti Y, Grkovic T, Abdelmohsen UR, Hentschel U, Quinn RJ. Actinomycete Metabolome Induction/Suppression with N-Acetylglucosamine. JOURNAL OF NATURAL PRODUCTS 2017; 80:828-836. [PMID: 28355070 DOI: 10.1021/acs.jnatprod.6b00673] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The metabolite profiles of three sponge-derived actinomycetes, namely, Micromonospora sp. RV43, Rhodococcus sp. RV157, and Actinokineospora sp. EG49 were investigated after elicitation with N-acetyl-d-glucosamine. 1H NMR fingerprint methodology was utilized to study the differences in the metabolic profiles of the bacterial extracts before and after elicitation. Our study found that the addition of N-acetyl-d-glucosamine modified the secondary metabolite profiles of the three investigated actinomycete isolates. N-Acetyl-d-glucosamine induced the production of 3-formylindole (11) and guaymasol (12) in Micromonospora sp. RV43, the siderophore bacillibactin 16, and surfactin antibiotic 17 in Rhodococcus sp. RV157 and increased the production of minor metabolites actinosporins E-H (21-24) in Actinokineospora sp. EG49. These results highlight the use of NMR fingerprinting to detect changes in metabolism following addition of N-acetyl-d-glucosamine. N-Acetyl-d-glucosamine was shown to have multiple effects including suppression of metabolites, induction of new metabolites, and increased production of minor compounds.
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Affiliation(s)
- Yousef Dashti
- Eskitis Institute for Drug Discovery, Griffith University , Brisbane, QLD 4111 Australia
| | - Tanja Grkovic
- Eskitis Institute for Drug Discovery, Griffith University , Brisbane, QLD 4111 Australia
| | - Usama Ramadan Abdelmohsen
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg , Julius-von-Sachs-Platz 3, D-97082 Würzburg, Germany
| | - Ute Hentschel
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg , Julius-von-Sachs-Platz 3, D-97082 Würzburg, Germany
| | - Ronald J Quinn
- Eskitis Institute for Drug Discovery, Griffith University , Brisbane, QLD 4111 Australia
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Hassan SSU, Shaikh AL. Marine actinobacteria as a drug treasure house. Biomed Pharmacother 2017; 87:46-57. [DOI: 10.1016/j.biopha.2016.12.086] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 12/20/2016] [Accepted: 12/20/2016] [Indexed: 01/19/2023] Open
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Sreedharan V, Bhaskara Rao K. Efficacy of protease inhibitor from marine Streptomyces sp. VITBVK2 against Leishmania donovani – An in vitro study. Exp Parasitol 2017; 174:45-51. [DOI: 10.1016/j.exppara.2017.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 12/29/2016] [Accepted: 02/03/2017] [Indexed: 10/20/2022]
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Takasaka N, Kaweewan I, Ohnishi-Kameyama M, Kodani S. Isolation of a new antibacterial peptide actinokineosin fromActinokineospora spheciospongiaebased on genome mining. Lett Appl Microbiol 2016; 64:150-157. [DOI: 10.1111/lam.12693] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 10/31/2016] [Accepted: 10/31/2016] [Indexed: 11/30/2022]
Affiliation(s)
- N. Takasaka
- Graduate School of Integrated Science and Technology; Shizuoka University; Suruga-ku Shizuoka Japan
| | - I. Kaweewan
- Graduate School of Integrated Science and Technology; Shizuoka University; Suruga-ku Shizuoka Japan
| | - M. Ohnishi-Kameyama
- Food Research Institute; National Agriculture and Food Research Organization (NARO); Tsukuba Ibaraki Japan
| | - S. Kodani
- Graduate School of Integrated Science and Technology; Shizuoka University; Suruga-ku Shizuoka Japan
- College of Agriculture; Academic Institute; Shizuoka University; Suruga-ku Shizuoka Japan
- Graduate School of Science and Technology; Shizuoka University; Suruga-ku Shizuoka Japan
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The Draft Genome Sequence of Actinokineospora bangkokensis 44EHW T Reveals the Biosynthetic Pathway of the Antifungal Thailandin Compounds with Unusual Butylmalonyl-CoA Extender Units. Molecules 2016; 21:molecules21111607. [PMID: 27886115 PMCID: PMC6273641 DOI: 10.3390/molecules21111607] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/17/2016] [Accepted: 11/19/2016] [Indexed: 11/16/2022] Open
Abstract
We report the draft genome sequence of Actinokineospora bangkokensis 44EHWT, the producer of the antifungal polyene compounds, thailandins A and B. The sequence contains 7.45 Mb, 74.1% GC content and 35 putative gene clusters for the biosynthesis of secondary metabolites. There are three gene clusters encoding large polyketide synthases of type I. Annotation of the ORF functions and targeted gene disruption enabled us to identify the cluster for thailandin biosynthesis. We propose a plausible biosynthetic pathway for thailandin, where the unusual butylmalonyl-CoA extender unit is incorporated and results in an untypical side chain.
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Chen Y, Mao WJ, Yan MX, Liu X, Wang SY, Xia Z, Xiao B, Cao SJ, Yang BQ, Li J. Purification, Chemical Characterization, and Bioactivity of an Extracellular Polysaccharide Produced by the Marine Sponge Endogenous Fungus Alternaria sp. SP-32. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:301-313. [PMID: 27153822 DOI: 10.1007/s10126-016-9696-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 01/15/2016] [Indexed: 06/05/2023]
Abstract
Marine sponges are ancient and simple multicellular filter-feeding invertebrates attached to solid substrates in benthic habitats and host a variety of fungi both inside and on their surface because of its unique ingestion and digest system. Investigation on marine sponge-associated fungi mainly focused on the small molecular metabolites, yet little attention had been paid to the extracellular polysaccharides. In this study, a homogeneous extracellular polysaccharide AS2-1 was obtained from the fermented broth of the marine sponge endogenous fungus Alternaria sp. SP-32 using ethanol precipitation, anion-exchange, and size-exclusion chromatography. Results of chemical and spectroscopic analyses showed that AS2-1 was composed of mannose, glucose, and galactose with a molar ratio of 1.00:0.67:0.35, and its molecular weight was 27.4 kDa. AS2-1 consists of a mannan core and a galactoglucan chain. The mannan core is composed of (1→6)-α-Manp substituted at C-2 by (1→2)-α-Manp with different degrees of polymerization. The galactoglucan chain consists of (1→6)-α-Glcp residues with (1→6)-β-Galf residues attached to the last glucopyranose residue at C-6. (1→6)-β-Galf residues have additional branches at C-2 consisting of disaccharide units of (1→2)-β-Galf and (1→2)-α-Glcp residues. The glucopyranose residue of the galactoglucan chain is linked to the mannan core. AS2-1 possessed a high antioxidant activity as evaluated by scavenging of 1,1-diphenyl-2-picrylhydrazyl and hydroxyl radicals in vitro. AS2-1 was also evaluated for cytotoxic activity on Hela, HL-60, and K562 cell lines by the MTT and SRB methods. The investigation demonstrated that AS2-1 was a novel extracellular polysaccharide with different characterization from extracellular polysaccharides produced by other marine microorganisms.
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Affiliation(s)
- Yin Chen
- Key Laboratory of Marine Drugs, Ministry of Education, Institute of Marine Drugs and Foods, Ocean University of China, 5 Yushan Road, Qingdao, 266003, People's Republic of China
- College of Food and Pharmacy, Zhejiang Ocean University, 18 Haiyuan Road, Zhoushan, 316000, People's Republic of China
| | - Wen-Jun Mao
- Key Laboratory of Marine Drugs, Ministry of Education, Institute of Marine Drugs and Foods, Ocean University of China, 5 Yushan Road, Qingdao, 266003, People's Republic of China.
| | - Meng-Xia Yan
- Key Laboratory of Marine Drugs, Ministry of Education, Institute of Marine Drugs and Foods, Ocean University of China, 5 Yushan Road, Qingdao, 266003, People's Republic of China
| | - Xue Liu
- Key Laboratory of Marine Drugs, Ministry of Education, Institute of Marine Drugs and Foods, Ocean University of China, 5 Yushan Road, Qingdao, 266003, People's Republic of China
| | - Shu-Yao Wang
- Key Laboratory of Marine Drugs, Ministry of Education, Institute of Marine Drugs and Foods, Ocean University of China, 5 Yushan Road, Qingdao, 266003, People's Republic of China
| | - Zheng Xia
- Key Laboratory of Marine Drugs, Ministry of Education, Institute of Marine Drugs and Foods, Ocean University of China, 5 Yushan Road, Qingdao, 266003, People's Republic of China
| | - Bo Xiao
- Key Laboratory of Marine Drugs, Ministry of Education, Institute of Marine Drugs and Foods, Ocean University of China, 5 Yushan Road, Qingdao, 266003, People's Republic of China
| | - Su-Jian Cao
- Key Laboratory of Marine Drugs, Ministry of Education, Institute of Marine Drugs and Foods, Ocean University of China, 5 Yushan Road, Qingdao, 266003, People's Republic of China
| | - Bao-Qin Yang
- Key Laboratory of Marine Drugs, Ministry of Education, Institute of Marine Drugs and Foods, Ocean University of China, 5 Yushan Road, Qingdao, 266003, People's Republic of China
| | - Jie Li
- Key Laboratory of Marine Drugs, Ministry of Education, Institute of Marine Drugs and Foods, Ocean University of China, 5 Yushan Road, Qingdao, 266003, People's Republic of China
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Indraningrat AAG, Smidt H, Sipkema D. Bioprospecting Sponge-Associated Microbes for Antimicrobial Compounds. Mar Drugs 2016; 14:E87. [PMID: 27144573 PMCID: PMC4882561 DOI: 10.3390/md14050087] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/15/2016] [Accepted: 04/26/2016] [Indexed: 12/17/2022] Open
Abstract
Sponges are the most prolific marine organisms with respect to their arsenal of bioactive compounds including antimicrobials. However, the majority of these substances are probably not produced by the sponge itself, but rather by bacteria or fungi that are associated with their host. This review for the first time provides a comprehensive overview of antimicrobial compounds that are known to be produced by sponge-associated microbes. We discuss the current state-of-the-art by grouping the bioactive compounds produced by sponge-associated microorganisms in four categories: antiviral, antibacterial, antifungal and antiprotozoal compounds. Based on in vitro activity tests, identified targets of potent antimicrobial substances derived from sponge-associated microbes include: human immunodeficiency virus 1 (HIV-1) (2-undecyl-4-quinolone, sorbicillactone A and chartarutine B); influenza A (H1N1) virus (truncateol M); nosocomial Gram positive bacteria (thiopeptide YM-266183, YM-266184, mayamycin and kocurin); Escherichia coli (sydonic acid), Chlamydia trachomatis (naphthacene glycoside SF2446A2); Plasmodium spp. (manzamine A and quinolone 1); Leishmania donovani (manzamine A and valinomycin); Trypanosoma brucei (valinomycin and staurosporine); Candida albicans and dermatophytic fungi (saadamycin, 5,7-dimethoxy-4-p-methoxylphenylcoumarin and YM-202204). Thirty-five bacterial and 12 fungal genera associated with sponges that produce antimicrobials were identified, with Streptomyces, Pseudovibrio, Bacillus, Aspergillus and Penicillium as the prominent producers of antimicrobial compounds. Furthemore culture-independent approaches to more comprehensively exploit the genetic richness of antimicrobial compound-producing pathways from sponge-associated bacteria are addressed.
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Affiliation(s)
- Anak Agung Gede Indraningrat
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands.
- Department of Biology, Faculty of Mathematics and Science Education, Institut Keguruan dan Ilmu Pendidikan Persatuan Guru Republik Indonesia (IKIP PGRI) Bali, Jl. Seroja Tonja, Denpasar 80238, Indonesia.
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands.
| | - Detmer Sipkema
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands.
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41
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Saurav K, Bar-Shalom R, Haber M, Burgsdorf I, Oliviero G, Costantino V, Morgenstern D, Steindler L. In Search of Alternative Antibiotic Drugs: Quorum-Quenching Activity in Sponges and their Bacterial Isolates. Front Microbiol 2016; 7:416. [PMID: 27092109 PMCID: PMC4821063 DOI: 10.3389/fmicb.2016.00416] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/14/2016] [Indexed: 02/01/2023] Open
Abstract
Owing to the extensive development of drug resistance in pathogens against the available antibiotic arsenal, antimicrobial resistance is now an emerging major threat to public healthcare. Anti-virulence drugs are a new type of therapeutic agent aiming at virulence factors rather than killing the pathogen, thus providing less selective pressure for evolution of resistance. One promising example of this therapeutic concept targets bacterial quorum sensing (QS), because QS controls many virulence factors responsible for bacterial infections. Marine sponges and their associated bacteria are considered a still untapped source for unique chemical leads with a wide range of biological activities. In the present study, we screened extracts of 14 sponge species collected from the Red and Mediterranean Sea for their quorum-quenching (QQ) potential. Half of the species showed QQ activity in at least 2 out of 3 replicates. Six out of the 14 species were selected for bacteria isolation, to test for QQ activity also in isolates, which, once cultured, represent an unlimited source of compounds. We show that ≈20% of the isolates showed QQ activity based on a Chromobacterium violaceum CV026 screen, and that the presence or absence of QQ activity in a sponge extract did not correlate with the abundance of isolates with the same activity from the same sponge species. This can be explained by the unknown source of QQ compounds in sponge-holobionts (host or symbionts), and further by the possible non-symbiotic nature of bacteria isolated from sponges. The potential symbiotic nature of the isolates showing QQ activity was tested according to the distribution and abundance of taxonomically close bacterial Operational Taxonomic Units (OTUs) in a dataset including 97 sponge species and 178 environmental samples (i.e., seawater, freshwater, and marine sediments). Most isolates were found not to be enriched in sponges and may simply have been trapped in the filtration channels of the sponge at the time of collection. Our results highlight potential for QQ-bioactive lead molecules for anti-virulence therapy both from sponges and the bacteria isolated thereof, independently on the symbiotic nature of the latter.
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Affiliation(s)
- Kumar Saurav
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa Haifa, Israel
| | - Rinat Bar-Shalom
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa Haifa, Israel
| | - Markus Haber
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa Haifa, Israel
| | - Ilia Burgsdorf
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa Haifa, Israel
| | - Giorgia Oliviero
- The Blue Chemistry Lab Group, Department of Pharmacy, Università degli Studi di Napoli Federico II Napoli, Italy
| | - Valeria Costantino
- The Blue Chemistry Lab Group, Department of Pharmacy, Università degli Studi di Napoli Federico II Napoli, Italy
| | | | - Laura Steindler
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa Haifa, Israel
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42
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Actinobacteria and Myxobacteria—Two of the Most Important Bacterial Resources for Novel Antibiotics. Curr Top Microbiol Immunol 2016; 398:273-302. [DOI: 10.1007/82_2016_503] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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43
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Karuppiah V, Sun W, Li Z. Natural Products of Actinobacteria Derived from Marine Organisms. STUDIES IN NATURAL PRODUCTS CHEMISTRY 2016. [DOI: 10.1016/b978-0-444-63602-7.00013-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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44
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Kuang W, Li J, Zhang S, Long L. Diversity and distribution of Actinobacteria associated with reef coral Porites lutea. Front Microbiol 2015; 6:1094. [PMID: 26539166 PMCID: PMC4612714 DOI: 10.3389/fmicb.2015.01094] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 09/22/2015] [Indexed: 12/22/2022] Open
Abstract
Actinobacteria is a ubiquitous major group in coral holobiont. The diversity and spatial and temporal distribution of actinobacteria have been rarely documented. In this study, diversity of actinobacteria associated with mucus, tissue and skeleton of Porites lutea and in the surrounding seawater were examined every 3 months for 1 year on Luhuitou fringing reef. The population structures of the P. lutea-associated actinobacteria were analyzed using phylogenetic analysis of 16S rRNA gene clone libraries, which demonstrated highly diverse actinobacteria profiles in P. lutea. A total of 25 described families and 10 unnamed families were determined in the populations, and 12 genera were firstly detected in corals. The Actinobacteria diversity was significantly different between the P. lutea and the surrounding seawater. Only 10 OTUs were shared by the seawater and coral samples. Redundancy and hierarchical cluster analyses were performed to analyze the correlation between the variations of actinobacteria population within the divergent compartments of P. lutea, seasonal changes, and environmental factors. The actinobacteria communities in the same coral compartment tended to cluster together. Even so, an extremely small fraction of OTUs was common in all three P. lutea compartments. Analysis of the relationship between actinobacteria assemblages and the environmental parameters showed that several genera were closely related to specific environmental factors. This study highlights that coral-associated actinobacteria populations are highly diverse, and spatially structured within P. lutea, and they are distinct from which in the ambient seawater.
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Affiliation(s)
- Weiqi Kuang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou, China ; College of Earth Science, University of Chinese Academy of Sciences Beijing, China
| | - Jie Li
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou, China
| | - Lijuan Long
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences Guangzhou, China
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45
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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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46
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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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47
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Mining Genomes of Three Marine Sponge-Associated Actinobacterial Isolates for Secondary Metabolism. GENOME ANNOUNCEMENTS 2015; 3:3/5/e01106-15. [PMID: 26430030 PMCID: PMC4591302 DOI: 10.1128/genomea.01106-15] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the draft genome sequences of three actinobacterial isolates, Micromonospora sp. RV43, Rubrobacter sp. RV113, and Nocardiopsis sp. RV163 that had previously been isolated from Mediterranean sponges. The draft genomes were analyzed for the presence of gene clusters indicative of secondary metabolism using antiSMASH 3.0 and NapDos pipelines. Our findings demonstrated the chemical richness of sponge-associated actinomycetes and the efficacy of genome mining in exploring the genomic potential of sponge-derived actinomycetes.
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48
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Cheng C, MacIntyre L, Abdelmohsen UR, Horn H, Polymenakou PN, Edrada-Ebel R, Hentschel U. Biodiversity, Anti-Trypanosomal Activity Screening, and Metabolomic Profiling of Actinomycetes Isolated from Mediterranean Sponges. PLoS One 2015; 10:e0138528. [PMID: 26407167 PMCID: PMC4583450 DOI: 10.1371/journal.pone.0138528] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 09/01/2015] [Indexed: 01/22/2023] Open
Abstract
Marine sponge–associated actinomycetes are considered as promising sources for the discovery of novel biologically active compounds. In the present study, a total of 64 actinomycetes were isolated from 12 different marine sponge species that had been collected offshore the islands of Milos and Crete, Greece, eastern Mediterranean. The isolates were affiliated to 23 genera representing 8 different suborders based on nearly full length 16S rRNA gene sequencing. Four putatively novel species belonging to genera Geodermatophilus, Microlunatus, Rhodococcus and Actinomycetospora were identified based on a 16S rRNA gene sequence similarity of < 98.5% to currently described strains. Eight actinomycete isolates showed bioactivities against Trypanosma brucei brucei TC221 with half maximal inhibitory concentration (IC50) values <20 μg/mL. Thirty four isolates from the Milos collection and 12 isolates from the Crete collection were subjected to metabolomic analysis using high resolution LC-MS and NMR for dereplication purposes. Two isolates belonging to the genera Streptomyces (SBT348) and Micromonospora (SBT687) were prioritized based on their distinct chemistry profiles as well as their anti-trypanosomal activities. These findings demonstrated the feasibility and efficacy of utilizing metabolomics tools to prioritize chemically unique strains from microorganism collections and further highlight sponges as rich source for novel and bioactive actinomycetes.
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Affiliation(s)
- Cheng Cheng
- Dept. of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Würzburg, Germany
| | - Lynsey MacIntyre
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Usama Ramadan Abdelmohsen
- Dept. of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Würzburg, Germany
| | - Hannes Horn
- Dept. of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Würzburg, Germany
| | - Paraskevi N. Polymenakou
- Hellenic Centre for Marine Research, Institute of Marine Biology, Biotechnology and Aquaculture, Gournes Pediados, Heraklion, Crete, Greece
| | - RuAngelie Edrada-Ebel
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
- * E-mail: (RE-E); (UH)
| | - Ute Hentschel
- Dept. of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Würzburg, Germany
- * E-mail: (RE-E); (UH)
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49
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Claverías FP, Undabarrena A, González M, Seeger M, Cámara B. Culturable diversity and antimicrobial activity of Actinobacteria from marine sediments in Valparaíso bay, Chile. Front Microbiol 2015; 6:737. [PMID: 26284034 PMCID: PMC4516979 DOI: 10.3389/fmicb.2015.00737] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 07/06/2015] [Indexed: 12/21/2022] Open
Abstract
Marine-derived Actinobacteria are a source of a broad variety of secondary metabolites with diverse biological activities, such as antibiotics and antitumorals; many of which have been developed for clinical use. Rare Actinobacteria represent an untapped source of new bioactive compounds that have been scarcely recognized. In this study, rare Actinobacteria from marine sediments were isolated from the Valparaíso bay, Chile, and their potential to produce antibacterial compounds was evaluated. Different culture conditions and selective media that select the growth of Actinobacteria were used leading to the isolation of 68 bacterial strains. Comparative analysis of the 16S rRNA gene sequences led to identifying isolates that belong to the phylum Actinobacteria with genetic affiliations to 17 genera: Aeromicrobium, Agrococcus, Arthrobacter, Brachybacterium, Corynebacterium, Dietzia, Flaviflexus, Gordonia, Isoptericola, Janibacter, Microbacterium, Mycobacterium, Ornithinimicrobium, Pseudonocardia, Rhodococcus, Streptomyces, and Tessaracoccus. Also, one isolate could not be consistently classified and formed a novel phylogenetic branch related to the Nocardiopsaceae family. The antimicrobial activity of these isolates was evaluated, demonstrating the capability of specific novel isolates to inhibit the growth of Gram-positive and Gram-negative bacteria. In conclusion, this study shows a rich biodiversity of culturable Actinobacteria, associated to marine sediments from Valparaíso bay, highlighting novel rare Actinobacteria, and their potential for the production of biologically active compounds.
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Affiliation(s)
| | | | | | | | - Beatriz Cámara
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa MaríaValparaíso, Chile
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50
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Inhibitory activities of the marine streptomycete-derived compound SF2446A2 against Chlamydia trachomatis and Schistosoma mansoni. J Antibiot (Tokyo) 2015; 68:674-9. [PMID: 25990954 DOI: 10.1038/ja.2015.54] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 03/24/2015] [Accepted: 04/03/2015] [Indexed: 12/18/2022]
Abstract
Infectious diseases caused by chlamydia or schistosomes are a major health problem worldwide, and particularly so in developing countries. The lack of appropriate vaccines renders the search for potent natural products against these disease-causing agents an urgent endeavor. Sponge-associated actinomycetes represent a rich reservoir for natural products. Among them, members of the genus Streptomyces are capable of synthesizing an impressive array of diverse natural products with a wide variety of biological activities. The naphthacene glycoside SF2446A2 was isolated from the calcium alginate beads culture of Streptomyces sp. strain RV15 that had originally been obtained from the Mediterranean sponge Dysidea tupha. Its structure was identified by spectroscopic analysis and MS and comparison with the literature data. SF2446A2 showed inhibitory activity against Chlamydia trachomatis and was able to inhibit the primary infection in a dose-dependent manner, as well as progeny formation. Moreover, it caused disruptive effects on the surface area of Schistosoma mansoni and affected the gonads by impairing oogenesis and spermatogenesis. Our current study demonstrates that sponge-associated actinomycetes are capable of providing compounds with new pharmacological activities and with relevance to drug discovery.
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