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Nugraha AP, Sibero MT, Farabi K, Surboyo MDC, Ernawati DS, Ahmad Noor TNEBT. Marine Ascomycetes Extract Antifungal Susceptibility against Candida spp. Isolates from Oral Candidiasis HIV/AIDS Patient: An In Vitro Study. Eur J Dent 2024; 18:624-631. [PMID: 38387624 PMCID: PMC11132786 DOI: 10.1055/s-0043-1768466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024] Open
Abstract
OBJECTIVE The etiology of oral candidiasis (OC) was Candida albicans, C. krusei, C. dubliniensis, C. tropicalis that are frequently found in human immunodeficiency virus/ acquired immunodeficiency syndrome (HIV/AIDS) patients. Marine ascomycetes (MA) have been widely reported as an important producer of various antibiotic compounds. However, there is limited study of antifungal compounds from MA against Candida species. The aim of this study was to investigate the antifungal susceptibility of MA against Candida spp. isolates from OC HIV/AIDS patient. MATERIALS AND METHODS Trichoderma sp. is a sponge-associated fungus collected from Karimunjawa National Park, Central Java, Indonesia. The validation of C. albicans, C. krusei, C. dubliniensis, C. tropicalis. was done by ChromAgar. This study was true experimental with post-test only control group design; the sample was four replications for each group. Nystatin administration (K +), the golden standard antifungal drug, was used. The minimum fungicidal concentration (MFC), minimum inhibitory concentration (MIC), and diffusion zone methods were done. Analysis of variance difference test, and post-hoc Tukey's honest significant different were done to analyze the significant different between groups (p ≤ 0.05). RESULTS The MFC and MIC of MA against C. albicans, C. krusei, C. dubliniensis, and C. tropicalis were found at 12.5%. In addition, the greatest diffusion zone of MA against C. albicans, C. krusei, C. dubliniensis, and C. tropicalis was found at 12.5%. There is no appreciable difference in antifungal activity between K + and 12.5% of MA extract (p ≥ 0.05). CONCLUSION Concentration of 12.5% MA extract has antifungal susceptibility against Candida spp. isolates from OC HIV/AIDS patient.
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Affiliation(s)
- Alexander Patera Nugraha
- Department of Orthodontic, Faculty of Dental Medicine - Universitas Airlangga, Surabaya, Indonesia
- Immunology Study Programme, Postgraduate School, Universitas Airlangga, Surabaya, Indonesia
| | - Mada Triandala Sibero
- Department of Marine Science, Fac. of Fisheries and Marine Science, Diponegoro University, Semarang, Indonesia
| | - Kindi Farabi
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Indonesia
| | | | - Diah Savitri Ernawati
- Department of Oral Medicine, Faculty of Dental Medicine - Universitas Airlangga, Surabaya, Indonesia
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Steiner LX, Wiese J, Rahn T, Borchert E, Slaby BM, Hentschel U. Maribacter halichondriae sp. nov., isolated from the marine sponge Halichondria panicea, displays features of a sponge-associated life style. Antonie Van Leeuwenhoek 2024; 117:56. [PMID: 38489089 PMCID: PMC10942906 DOI: 10.1007/s10482-024-01950-4] [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: 12/15/2023] [Accepted: 02/16/2024] [Indexed: 03/17/2024]
Abstract
A new member of the family Flavobacteriaceae (termed Hal144T) was isolated from the marine breadcrumb sponge Halichondria panicea. Sponge material was collected in 2018 at Schilksee which is located in the Kiel Fjord (Baltic Sea, Germany). Phylogenetic analysis of the full-length Hal144T 16S rRNA gene sequence revealed similarities from 94.3 to 96.6% to the nearest type strains of the genus Maribacter. The phylogenetic tree of the 16S rRNA gene sequences depicted a cluster of strain Hal144T with its closest relatives Maribacter aestuarii GY20T (96.6%) and Maribacter thermophilus HT7-2T (96.3%). Genome phylogeny showed that Maribacter halichondriae Hal144T branched from a cluster consisting of Maribacter arenosus, Maribacter luteus, and Maribacter polysiphoniae. Genome comparisons of strain Maribacter halichondriae Hal144T with Maribacter sp. type strains exhibited average nucleotide identities in the range of 75-76% and digital DNA-DNA hybridisation values in the range of 13.1-13.4%. Compared to the next related type strains, strain Hal144T revealed unique genomic features such as phosphoenolpyruvate-dependent phosphotransferase system pathway, serine-glyoxylate cycle, lipid A 3-O-deacylase, 3-hexulose-6-phosphate synthase, enrichment of pseudogenes and of genes involved in cell wall and envelope biogenesis, indicating an adaptation to the host. Strain Hal144T was determined to be Gram-negative, mesophilic, strictly aerobic, flexirubin positive, resistant to aminoglycoside antibiotics, and able to utilize N-acetyl-β-D-glucosamine. Optimal growth occurred at 25-30 °C, within a salinity range of 2-6% sea salt, and a pH range between 5 and 8. The major fatty acids identified were C17:0 3-OH, iso-C15:0, and iso-C15:1 G. The DNA G + C content of strain Hal144T was 41.4 mol%. Based on the polyphasic approach, strain Hal144T represents a novel species of the genus Maribacter, and we propose the name Maribacter halichondriae sp. nov. The type strain is Hal144T (= DSM 114563T = LMG 32744T).
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Affiliation(s)
- Leon X Steiner
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RU Marine Ecology, RD3 Marine Symbioses, Wischhofstraße 1-3, 24148, Kiel, Germany
| | - Jutta Wiese
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RU Marine Ecology, RD3 Marine Symbioses, Wischhofstraße 1-3, 24148, Kiel, Germany.
| | - Tanja Rahn
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RU Marine Ecology, RD3 Marine Symbioses, Wischhofstraße 1-3, 24148, Kiel, Germany
| | - Erik Borchert
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RU Marine Ecology, RD3 Marine Symbioses, Wischhofstraße 1-3, 24148, Kiel, Germany
| | - Beate M Slaby
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RU Marine Ecology, RD3 Marine Symbioses, Wischhofstraße 1-3, 24148, Kiel, Germany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research Kiel, RU Marine Ecology, RD3 Marine Symbioses, Wischhofstraße 1-3, 24148, Kiel, Germany
- Christian-Albrechts-University (CAU) of Kiel, Kiel, Germany
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3
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El-Hawary SS, Hassan MHA, Hudhud AO, Al-Karmalawy AA, Mustafa M, Hamed EAE, Abdelmohsen UR, Mohammed R. LC-HRMS Profiling and Cytotoxic Potential of Actinomycetes Associated with the Red Sea Soft Coral Sarcophyton glaucum: In vitro and In silico Studies. Chem Biodivers 2024; 21:e202301617. [PMID: 38193652 DOI: 10.1002/cbdv.202301617] [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: 10/14/2023] [Revised: 12/31/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024]
Abstract
In the current study, the actinomycetes associated with the red sea-derived soft coral Sarcophyton glaucum were investigated in terms of biological and chemical diversity. Four different media, M1, ISP2, Marine Agar (MA), and Actinomycete isolation agar (AIA) were used for the isolation of three strains of actinomycetes that were identified as Streptomyces sp. UR 25, Micromonospora sp. UR32 and Saccharomonospora sp. UR 19. LC-HRMS analysis was used to investigate the chemical diversity of the isolated actinobacteria. The LC-HRMS data were statistically processed using MetaboAnalyst 5.0 viz to differentiate the extract groups and determine the optimal growth culturing conditions. Multivariate data statistical analysis revealed that the Micromonospora sp. extract cultured on (MA) medium is the most distinctive extract in terms of chemical composition. While, the Streptomyces sp. UR 25 extracts are differ significantly from Micromonospora sp. UR32 and Saccharomonospora sp. UR 19. Biological investigation using in vitro cytotoxic assay for actinobacteria extracts revealed the prominent potentiality of the Streptomyces sp. UR 25 cultured on oligotrophic medium against human hepatoma (HepG2), human breast adenocarcinoma (MCF-7) and human colon adenocarcinoma (CACO2) cell lines (IC50 =3.3, 4.2 and 6.8 μg/mL, respectively). SwissTarget Prediction speculated that among the identified compounds, 16-deethyl, indanomycin (8) could have reasonable affinity on HDM2 active site. In this respect, molecular docking study was performed for compound (8) to reveal a substantial affinity on HDM2 active site. In addition, molecular dynamics simulations were carried out at 200 ns for the most active compound (8) compared to the co-crystallized inhibitor DIZ giving deeper information regarding their thermodynamic and dynamic properties as well.
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Affiliation(s)
- Seham S El-Hawary
- Department of Pharmacognosy, Faculty of Pharmacy, Cairo University, Cairo, 11511, Egypt
| | - Marwa H A Hassan
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt
| | - Ahmed O Hudhud
- Department of Pharmacognosy, Faculty of Pharmacy, Merit University, Sohag, 82511, Egypt
| | - Ahmed A Al-Karmalawy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta, 34518, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ahram Canadian University, 6th of October City, Giza, 12566, Egypt
| | - Muhamad Mustafa
- IBMM, CNRS, ENSCM, Université de Montpellier, Montpellier, 34095, France
- Department of Medicinal Chemistry, Faculty of Pharmacy, Deraya University, Minia, 61111, Egypt
| | - Elsayed A E Hamed
- National institute of oceanography and Fisheries, Hurghada-Red Sea (NIOF), 84511, Egypt
| | - Usama Ramadan Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, 61519, Egypt
- Department of Pharmacognosy, Faculty of Pharmacy, Deraya University, New Minia, 61111, Egypt
| | - Rabab Mohammed
- Department of Pharmacognosy, Faculty of Pharmacy, Beni-Suef University, Beni-Suef, 62511, Egypt
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Wu Q, Zhu H, Sun C, Zhou L, Wang H, Shi S, Tian X, Ju J. Halo- and Thiocarbazomycins from Coral- and Coral Reef Sands-Derived Actinomycetes. Mar Drugs 2022; 20:md20080537. [PMID: 36005541 PMCID: PMC9410401 DOI: 10.3390/md20080537] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Four actinomycete strains isolated from the coral Acropora austera and coral sand samples from the South China Sea, were found to produce a series of halogenated compounds baring similar ultraviolet absorption based on the analysis of HPLC and LC-MS. The production titers of halogenated compounds from Streptomyces diacarni SCSIO 64983 exceeded those of other similar strains leading us to focus on SCSIO 64983. Four new thiocarbazomycins A–B (1–2), chlocarbazomycin E (3), and brocarbazomycin A (4), together with three known chlocarbazomycins A–C (5–7) containing a carbazole core were identified, and their structures were determined using a combination of spectroscopic analysis including HRESIMS, 1D and 2D NMR. Structurally speaking, compounds 1 and 2 have the rare sulfur-containing carbazole nuclei, and 3 and 4 contain Cl and Br atoms, respectively. Although these compounds have not yet been found to have obvious biological activity, their discovery highlights the role of molecular libraries in subsequent drug discovery campaigns.
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Affiliation(s)
- Qiaoling Wu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 110039, China
| | - Hongjie Zhu
- School of Pharmaceutical Sciences, Shandong University, Jinan 250012, China
| | - Changli Sun
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Le Zhou
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Huimin Wang
- School of Pharmacy, Institute of Marine Drug, Guangxi University of Traditional Chinese Medicine, Nanning 530200, China
| | - Songbiao Shi
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 110039, China
| | - Xinpeng Tian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Jianhua Ju
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, RNAM Center for Marine Microbiology, Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 110039, China
- Correspondence: ; Tel.: +86-20-8902-3028
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Shi SB, Cui LQ, Zeng Q, Long LJ, Tian XP. Nocardioides coralli sp. nov., an actinobacterium isolated from stony coral in the South China Sea. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005342] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, aerobic, non-pigmented and non-motile actinobacterium, designated strain SCSIO 67246T, was isolated from a stony coral sample collected from the Sanya sea area, Hainan province, China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain SCSIO 67246T shared the highest similarities with
Nocardioides rotundus
MCCC 1A10561T (96.5 %) and
Nocardioides sonneratiae
KCTC 39565T (96.1%). The novel strain grew at 15–37 °C, at pH 5.0–10.0 and in the presence of 0–10 % (w/v) NaCl. The genome length of strain SCSIO 67246T was 3.52 Mbp with a DNA G+C content of 72.0 mol% and 3397 protein-coding genes. The novel strain showed an average nucleotide identity value of 76.5 % and a digital DNA–DNA hybridization value of 20.1 % with
N. rotundus
MCCC 1A10561T. Strain SCSIO 67246T contained MK-8(H4) as the major menaquinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and five phospholipids. The major cellular fatty acids were iso-C16 : 0, C17 : 1
ω8c and summed feature 9 (iso-C17 : 1
ω9c/10-methyl C16 : 0). ll-2,6-Diaminopimelic acid was the diagnostic diamino acid. The whole-cell sugars were galactose, glucose and ribose. Based on this polyphasic taxonomic study, strain SCSIO 67246T represents a novel species of the genus
Nocardioides
, for which the name Nocardioides coralli sp. nov. is proposed. The type strain is SCSIO 67246T (=MCCC 1K06251T=KCTC 49719T).
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Affiliation(s)
- Song-Biao Shi
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, SCSIO, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Lin-Qing Cui
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, SCSIO, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Qi Zeng
- University of Chinese Academy of Sciences, Beijing 100049, PR China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, SCSIO, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Li-Juan Long
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, PR China
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, SCSIO, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
| | - Xin-Peng Tian
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, Sanya Institute of Oceanology, SCSIO, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong 510301, PR China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, PR China
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Chen J, Xu L, Zhou Y, Han B. Natural Products from Actinomycetes Associated with Marine Organisms. Mar Drugs 2021; 19:md19110629. [PMID: 34822500 PMCID: PMC8621598 DOI: 10.3390/md19110629] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 12/15/2022] Open
Abstract
The actinomycetes have proven to be a rich source of bioactive secondary metabolites and play a critical role in the development of pharmaceutical researches. With interactions of host organisms and having special ecological status, the actinomycetes associated with marine animals, marine plants, macroalgae, cyanobacteria, and lichens have more potential to produce active metabolites acting as chemical defenses to protect the host from predators as well as microbial infection. This review focuses on 536 secondary metabolites (SMs) from actinomycetes associated with these marine organisms covering the literature to mid-2021, which will highlight the taxonomic diversity of actinomycetes and the structural classes, biological activities of SMs. Among all the actinomycetes listed, members of Streptomyces (68%), Micromonospora (6%), and Nocardiopsis (3%) are dominant producers of secondary metabolites. Additionally, alkaloids (37%), polyketides (33%), and peptides (15%) comprise the largest proportion of natural products with mostly antimicrobial activity and cytotoxicity. Furthermore, the data analysis and clinical information of SMs have been summarized in this article, suggesting that some of these actinomycetes with multiple host organisms deserve more attention to their special ecological status and genetic factors.
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Yu X, Yu K, Liao Z, Chen B, Deng C, Yu J, Yao Q, Qin Z, Liang J. Seasonal fluctuations in symbiotic bacteria and their role in environmental adaptation of the scleractinian coral Acropora pruinosa in high-latitude coral reef area of the South China Sea. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 792:148438. [PMID: 34153755 DOI: 10.1016/j.scitotenv.2021.148438] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/09/2021] [Accepted: 06/09/2021] [Indexed: 06/13/2023]
Abstract
Coral-associated bacterial communities are paramount for coral ecosystems and holobiont health. However, the role of symbiotic bacteria in the adaptation of high-latitude corals to seasonal fluctuations remains underexplored. Therefore, we used 16S rRNA-based high-throughput sequencing to analyze the symbiotic bacterial diversity, composition, and core bacterial community in high-latitude coral and explored the seasonal fluctuation characteristics of symbiotic bacterial communities. We found that bacterial richness and α-diversity changed significantly across different seasons. Additionally, the community structure recombined seasonally, with different dominant bacterial phyla and genera in different seasons. However, the symbiotic bacterial community structures of Acropora pruinosa in winter and spring were similar. Proteobacteria were the dominant bacteria in spring, autumn, and winter. In summer, the dominant bacterial taxa were Bacteroidota and Proteobacteria. Ralstonia was the dominant bacterial genus in spring and winter, whereas in autumn, BD1-7_clade was dominant. Linear discriminant analysis effect size identified 20 abundant genera between the different groups. Core microbiome analysis revealed that 12 core bacterial operational taxonomic units were associated with A. pruinosa in all seasons, seven of which varied with the seasons, changing between dominant and rare. Distance-based redundancy and variation partitioning analyses revealed that sea surface temperature was the major contributor of variation in the microbial community structure. We hypothesized that the high diversity and abundance of symbiotic bacteria and the increase in Prosthecochloris abundance in coral in summer can help A. pruinosa maintain its physiological functions, ameliorating the negative physiological effects of the decrease in Symbiodiniaceae density under high-temperature stress. Thus, the rapid reorganization of the symbiotic bacterial community structure and core microflora in different seasons may allow the corals to adapt to large seasonal environmental fluctuations. In conclusion, seasonal variation of bacteria plays an important role in coral adaptation to large environmental fluctuations.
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Affiliation(s)
- Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), China.
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Chuanqi Deng
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiaoyang Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Qiucui Yao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
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Feng WM, Liu P, Yan H, Zhang S, Shang EX, Yu G, Jiang S, Qian DW, Ma JW, Duan JA. Impact of Bacillus on Phthalides Accumulation in Angelica sinensis (Oliv.) by Stoichiometry and Microbial Diversity Analysis. Front Microbiol 2021; 11:611143. [PMID: 33488552 PMCID: PMC7819887 DOI: 10.3389/fmicb.2020.611143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
Plant-microorganism interaction in the rhizosphere is thought to play an important role in the formation of soil fertility, transformation and absorption of nutrients, growth and development of medicinal plants, and accumulation of medicinal ingredients. Yet, the role that they play in the phthalides accumulation of Angelica sinensis (Oliv.) Diels remains unclear. In the present study, we report a correlative analysis between rhizosphere microorganisms and phthalides accumulation in A. sinensis from Gansu, China where was the major production areas. Meanwhile, Bacillus was explored the potential functions in the plant growth and phthalide accumulation. Results revealed that the common bacterial species detected in six samples comprised 1150 OTUs which were involved in 368 genera, and predominant taxa include Actinobacteria, Acidobacteria, and Proteobacteria. The average contents of the six phthalides were 4.0329 mg/g. The correlation analysis indicated that 20 high abundance strains showed positive or negative correlations with phthalides accumulation. Flavobacterium, Nitrospira, Gaiella, Bradyrhizobium, Mycobacterium, Bacillus, RB41, Blastococcus, Nocardioides, and Solirubrobacter may be the key strains that affect phthalides accumulation on the genus level. By the plant-bacterial co-culture and fermentation, Bacillus which were isolated from rhizosphere soils can promote the plant growth, biomass accumulation and increased the contents of the butylidenephthalide (36∼415%) while the ligustilide (12∼67%) was decreased. Altogether, there is an interaction between rhizosphere microorganisms and phthalides accumulation in A. sinensis, Bacillus could promote butylidenephthalide accumulation while inhibiting ligustilide accumulation.
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Affiliation(s)
- Wei-Meng Feng
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Pei Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hui Yan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Sen Zhang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Er-Xin Shang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Guang Yu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shu Jiang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Da-Wei Qian
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jun-Wei Ma
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jin-Ao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, China
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Modolon F, Barno AR, Villela HDM, Peixoto RS. Ecological and biotechnological importance of secondary metabolites produced by coral-associated bacteria. J Appl Microbiol 2020; 129:1441-1457. [PMID: 32627318 DOI: 10.1111/jam.14766] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/20/2020] [Accepted: 06/28/2020] [Indexed: 12/16/2022]
Abstract
Symbiotic relationships between corals and their associated micro-organisms are essential to maintain host homeostasis. Coral-associated bacteria (CAB) can have different beneficial roles in the coral metaorganism, such as metabolizing essential nutrients for the coral host and protecting the coral from pathogens. Many CAB exert these functions via secondary metabolites, which include antibacterial, antifouling, antitumour, antiparasitic and antiviral compounds. This review describes how analysis of CAB has led to the discovery of secondary metabolites with potential biotechnological applications. The most commonly found types of secondary metabolites, antimicrobial and antibiofilm compounds, are emphasized and described. Recently developed methods that can be applied to enhance the culturing of CAB from shallow-water reefs and the less-studied deep-sea coral reefs are also discussed. Last, we suggest how the combined use of meta-omics and innovative growth-diffusion techniques can vastly improve the discovery of novel compounds in coral environments.
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Affiliation(s)
- F Modolon
- Department of Microbiology, Paulo de Góes Microbiology Institute, Federal University of Rio De Janeiro, Rio de Janeiro, RJ, Brazil
| | - A R Barno
- Department of Microbiology, Paulo de Góes Microbiology Institute, Federal University of Rio De Janeiro, Rio de Janeiro, RJ, Brazil
| | - H D M Villela
- Department of Microbiology, Paulo de Góes Microbiology Institute, Federal University of Rio De Janeiro, Rio de Janeiro, RJ, Brazil
| | - R S Peixoto
- Department of Microbiology, Paulo de Góes Microbiology Institute, Federal University of Rio De Janeiro, Rio de Janeiro, RJ, Brazil.,IMAM-AquaRio - Rio de Janeiro Aquarium Research Center, Rio de Janeiro, RJ, Brazil
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10
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Actinomycetes from the Red Sea Sponge Coscinoderma mathewsi: Isolation, Diversity, and Potential for Bioactive Compounds Discovery. Microorganisms 2020; 8:microorganisms8050783. [PMID: 32456212 PMCID: PMC7285244 DOI: 10.3390/microorganisms8050783] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 12/26/2022] Open
Abstract
The diversity of actinomycetes associated with the marine sponge Coscinoderma mathewsi collected from Hurghada (Egypt) was studied. Twenty-three actinomycetes were separated and identified based on the 16S rDNA gene sequence analysis. Out of them, three isolates were classified as novel species of the genera Micromonospora, Nocardia, and Gordonia. Genome sequencing of actinomycete strains has revealed many silent biosynthetic gene clusters and has shown their exceptional capacity for the production of secondary metabolites, not observed under classical cultivation conditions. Therefore, the effect of mycolic-acid-containing bacteria or mycolic acid on the biosynthesis of cryptic natural products was investigated. Sponge-derived actinomycete Micromonospora sp. UA17 was co-cultured using liquid fermentation with two mycolic acid-containing actinomycetes (Gordonia sp. UA19 and Nocardia sp. UA 23), or supplemented with pure mycolic acid. LC-HRESIMS data were analyzed to compare natural production across all crude extracts. Micromonospora sp. UA17 was rich with isotetracenone, indolocarbazole, and anthracycline analogs. Some co-culture extracts showed metabolites such as a chlorocardicin, neocopiamycin A, and chicamycin B that were not found in the respective monocultures, suggesting a mycolic acid effect on the induction of cryptic natural product biosynthetic pathways. The antibacterial, antifungal, and antiparasitic activities for the different cultures extracts were also tested.
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11
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Abstract
The marine environment encompasses a huge biological diversity and can be considered as an underexplored location for prospecting bioactive molecules. In this review, the current state of art about antimicrobial molecules from marine bacteria has been summarized considering the main phylum and sources evolved in a marine environment. Considering the last two decades, we have found as most studied group of bacteria producers of substances with antimicrobial activity is the Firmicutes phylum, in particular strains of the Bacillus genus. The reason for that can be attributed to the difficult cultivation of typical Actinobacteria from a marine sediment, whose members are the major producers of antimicrobial substances in land environments. However, a reversed trend has been observed in recent years with an increasing number of reports settling on Actinobacteria. Great diversity of chemical structures have been identified, such as fijimicyns and lynamicyns from Actinomycetes and macrolactins produced by Bacillus.
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Affiliation(s)
- Paolo Stincone
- Laboratório de Bioquímica e Microbiologia Aplicada, Departamento de Ciência de Alimentos, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Adriano Brandelli
- Laboratório de Bioquímica e Microbiologia Aplicada, Departamento de Ciência de Alimentos, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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12
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Raimundo I, Silva SG, Costa R, Keller-Costa T. Bioactive Secondary Metabolites from Octocoral-Associated Microbes-New Chances for Blue Growth. Mar Drugs 2018; 16:E485. [PMID: 30518125 PMCID: PMC6316421 DOI: 10.3390/md16120485] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 11/25/2018] [Accepted: 11/29/2018] [Indexed: 12/14/2022] Open
Abstract
Octocorals (Cnidaria, Anthozoa Octocorallia) are magnificent repositories of natural products with fascinating and unusual chemical structures and bioactivities of interest to medicine and biotechnology. However, mechanistic understanding of the contribution of microbial symbionts to the chemical diversity of octocorals is yet to be achieved. This review inventories the natural products so-far described for octocoral-derived bacteria and fungi, uncovering a true chemical arsenal of terpenes, steroids, alkaloids, and polyketides with antibacterial, antifungal, antiviral, antifouling, anticancer, anti-inflammatory, and antimalarial activities of enormous potential for blue growth. Genome mining of 15 bacterial associates (spanning 12 genera) cultivated from Eunicella spp. resulted in the identification of 440 putative and classifiable secondary metabolite biosynthetic gene clusters (BGCs), encompassing varied terpene-, polyketide-, bacteriocin-, and nonribosomal peptide-synthase BGCs. This points towards a widespread yet uncharted capacity of octocoral-associated bacteria to synthetize a broad range of natural products. However, to extend our knowledge and foster the near-future laboratory production of bioactive compounds from (cultivatable and currently uncultivatable) octocoral symbionts, optimal blending between targeted metagenomics, DNA recombinant technologies, improved symbiont cultivation, functional genomics, and analytical chemistry are required. Such a multidisciplinary undertaking is key to achieving a sustainable response to the urgent industrial demand for novel drugs and enzyme varieties.
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Affiliation(s)
- Inês Raimundo
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
| | - Sandra G Silva
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
| | - Rodrigo Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
| | - Tina Keller-Costa
- Institute for Bioengineering and Biosciences (iBB), Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001 Lisbon, Portugal.
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13
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Babu DT, Archana K, Kachiprath B, Solomon S, Jayanath G, Singh ISB, Philip R. Marine actinomycetes as bioremediators in Penaeus monodon rearing system. FISH & SHELLFISH IMMUNOLOGY 2018; 75:231-242. [PMID: 29407617 DOI: 10.1016/j.fsi.2018.01.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 01/15/2018] [Accepted: 01/25/2018] [Indexed: 06/07/2023]
Abstract
Actinomycetes (277 Nos) isolated from marine environment and shrimp culture pond sediments were tested for hydrolytic enzyme production and biogranulation property. Potential isolates were screened for their efficacy in bioremediation of shrimp culture system. Based on the BOD reduction efficiency and water quality parameters, five actinomycete isolates viz., Streptomyces coelicoflavus (A6), Streptomyces diastaticus (A44), Nocardiopsis alba (A55), Streptomyces parvus (A56) and Streptomyces champavatii (R32) were subjected for tertiary screening in Penaeus monodon larval rearing system and the animals were challenged with white spot syndrome virus (WSSV). The bioremediating effect of actinomycete treatments were assessed by analysing the expression profile of five antimicrobial peptide (AMP) genes viz., anti-lipopolysaccharide factor (ALF), crustin-2, crustin-3, penaeidin-3 and penaeidin-5 and eight immune genes viz., alpha-2-macroglobulin (α-2-M), astakine, glutathione-S-transferase, haemocyanin, peroxinectin, pmCathepsinC, prophenol oxidase (proPO) and Rab-7. Expression of eight WSSV genes viz., DNA polymerase, endonuclease, protein kinase, immediate early gene, latency related gene, ribonucleotide reductase, thymidine kinase and VP28 were also analyzed to detect the presence and intensity of viral infection in the experimental animals post-challenge. Theapplication of consortia (1 g/5 L water) yields better results in terms of significant reduction in BOD of shrimp rearing system showing the bioremediation potential of the marine actinomycete strains. The application of marine actinomycetes viz., Streptomyces coelicoflavus (A6), Streptomyces diastaticus (A44), Nocardiopsis alba (A55), Streptomyces parvus (A56) and Streptomyces champavatii (R32) in granulated form were found to be potential bioremediators in shrimp rearing system.
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Affiliation(s)
- Divya T Babu
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi-682016, Kerala, India
| | - K Archana
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi-682016, Kerala, India
| | - Bhavya Kachiprath
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi-682016, Kerala, India
| | - Solly Solomon
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi-682016, Kerala, India
| | - G Jayanath
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi-682016, Kerala, India
| | - I S Bright Singh
- National Centre for Aquatic Animal Health, Cochin University of Science and Technology, Fine Arts Avenue, Kochi-682016, Kerala, India
| | - Rosamma Philip
- Department of Marine Biology, Microbiology and Biochemistry, School of Marine Sciences, Cochin University of Science and Technology, Fine Arts Avenue, Kochi-682016, Kerala, India.
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14
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Cuadrat RRC, Ionescu D, Dávila AMR, Grossart HP. Recovering Genomics Clusters of Secondary Metabolites from Lakes Using Genome-Resolved Metagenomics. Front Microbiol 2018. [PMID: 29515540 PMCID: PMC5826242 DOI: 10.3389/fmicb.2018.00251] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Metagenomic approaches became increasingly popular in the past decades due to decreasing costs of DNA sequencing and bioinformatics development. So far, however, the recovery of long genes coding for secondary metabolites still represents a big challenge. Often, the quality of metagenome assemblies is poor, especially in environments with a high microbial diversity where sequence coverage is low and complexity of natural communities high. Recently, new and improved algorithms for binning environmental reads and contigs have been developed to overcome such limitations. Some of these algorithms use a similarity detection approach to classify the obtained reads into taxonomical units and to assemble draft genomes. This approach, however, is quite limited since it can classify exclusively sequences similar to those available (and well classified) in the databases. In this work, we used draft genomes from Lake Stechlin, north-eastern Germany, recovered by MetaBat, an efficient binning tool that integrates empirical probabilistic distances of genome abundance, and tetranucleotide frequency for accurate metagenome binning. These genomes were screened for secondary metabolism genes, such as polyketide synthases (PKS) and non-ribosomal peptide synthases (NRPS), using the Anti-SMASH and NAPDOS workflows. With this approach we were able to identify 243 secondary metabolite clusters from 121 genomes recovered from our lake samples. A total of 18 NRPS, 19 PKS, and 3 hybrid PKS/NRPS clusters were found. In addition, it was possible to predict the partial structure of several secondary metabolite clusters allowing for taxonomical classifications and phylogenetic inferences. Our approach revealed a high potential to recover and study secondary metabolites genes from any aquatic ecosystem.
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Affiliation(s)
- Rafael R C Cuadrat
- Bioinformatics Core Facility, Max Plank Institute for Biology of Ageing, Köln, Germany.,Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
| | - Danny Ionescu
- Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Alberto M R Dávila
- Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Hans-Peter Grossart
- Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany.,Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
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15
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Sowani H, Kulkarni M, Zinjarde S. An insight into the ecology, diversity and adaptations of Gordonia species. Crit Rev Microbiol 2017; 44:393-413. [PMID: 29276839 DOI: 10.1080/1040841x.2017.1418286] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The bacterial genus Gordonia encompasses a variety of versatile species that have been isolated from a multitude of environments. Gordonia was described as a genus about 20 years ago, and to date, 39 different species have been identified. Gordonia is recognized for symbiotic associations with multiple hosts, including aquatic (marine and fresh water) biological forms and terrestrial invertebrates. Some Gordonia species isolated from clinical specimens are known to be opportunistic human pathogens causing secondary infections in immunocompromised and immunosuppressive individuals. They are also predominant in mangrove ecosystems and terrestrial sites. Members of the genus Gordonia are ecologically adaptable and show marked variations in their properties and products. They generate diverse bioactive compounds and produce a variety of extracellular enzymes. In addition, production of surface active compounds and carotenoid pigments allows this group of microorganisms to grow under different conditions. Several isolates from water and soil have been implicated in bioremediation of different environments and plant associated species have been explored for agricultural applications. This review highlights the prevalence of the members of this versatile genus in diverse environments, details its associations with living forms, summarizes the biotechnologically relevant products that can be obtained and discusses the salient genomic features that allow this Actinomycete to survive in different ecological niches.
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Affiliation(s)
- Harshada Sowani
- a Department of Chemistry , Biochemistry Division Savitribai Phule Pune University , Pune , India
| | - Mohan Kulkarni
- a Department of Chemistry , Biochemistry Division Savitribai Phule Pune University , Pune , India
| | - Smita Zinjarde
- b Institute of Bioinformatics and Biotechnology , Savitribai Phule Pune University , Pune , India.,c Department of Microbiology , Savitribai Phule Pune University , Pune , India
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16
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Sarmiento-Vizcaíno A, González V, Braña AF, Palacios JJ, Otero L, Fernández J, Molina A, Kulik A, Vázquez F, Acuña JL, García LA, Blanco G. Pharmacological Potential of Phylogenetically Diverse Actinobacteria Isolated from Deep-Sea Coral Ecosystems of the Submarine Avilés Canyon in the Cantabrian Sea. MICROBIAL ECOLOGY 2017; 73:338-352. [PMID: 27614749 DOI: 10.1007/s00248-016-0845-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 08/24/2016] [Indexed: 06/06/2023]
Abstract
Marine Actinobacteria are emerging as an unexplored source for natural product discovery. Eighty-seven deep-sea coral reef invertebrates were collected during an oceanographic expedition at the submarine Avilés Canyon (Asturias, Spain) in a range of 1500 to 4700 m depth. From these, 18 cultivable bioactive Actinobacteria were isolated, mainly from corals, phylum Cnidaria, and some specimens of phyla Echinodermata, Porifera, Annelida, Arthropoda, Mollusca and Sipuncula. As determined by 16S rRNA sequencing and phylogenetic analyses, all isolates belong to the phylum Actinobacteria, mainly to the Streptomyces genus and also to Micromonospora, Pseudonocardia and Myceligenerans. Production of bioactive compounds of pharmacological interest was investigated by high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS) techniques and subsequent database comparison. Results reveal that deep-sea isolated Actinobacteria display a wide repertoire of secondary metabolite production with a high chemical diversity. Most identified products (both diffusible and volatiles) are known by their contrasted antibiotic or antitumor activities. Bioassays with ethyl acetate extracts from isolates displayed strong antibiotic activities against a panel of important resistant clinical pathogens, including Gram-positive and Gram-negative bacteria, as well as fungi, all of them isolated at two main hospitals (HUCA and Cabueñes) from the same geographical region. The identity of the active extracts components of these producing Actinobacteria is currently being investigated, given its potential for the discovery of pharmaceuticals and other products of biotechnological interest.
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Affiliation(s)
- Aida Sarmiento-Vizcaíno
- Departamento de Biología Funcional, Área de Microbiología, e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Verónica González
- Departamento de Biología Funcional, Área de Microbiología, e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Alfredo F Braña
- Departamento de Biología Funcional, Área de Microbiología, e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006, Oviedo, Spain
| | - Juan J Palacios
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
| | - Luis Otero
- Servicio de Microbiología Hospital de Cabueñes, Gijón, Spain
| | - Jonathan Fernández
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
| | - Axayacatl Molina
- Departamento de Biología de Organismos y Sistemas. Área de Ecología, Universidad de Oviedo, Oviedo, Spain
| | - Andreas Kulik
- Microbial Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Fernando Vázquez
- Departamento de Biología Funcional, Área de Microbiología, e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006, Oviedo, Spain
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
| | - José L Acuña
- Departamento de Biología de Organismos y Sistemas. Área de Ecología, Universidad de Oviedo, Oviedo, Spain
| | - Luis A García
- Departamento de Ingeniería Química y Tecnología del Medio Ambiente. Área de Ingeniería Química, Universidad de Oviedo, Oviedo, Spain
| | - Gloria Blanco
- Departamento de Biología Funcional, Área de Microbiología, e Instituto Universitario de Oncología del Principado de Asturias, Universidad de Oviedo, 33006, Oviedo, Spain.
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17
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Padmanaban VP, Verma P, Venkatabaskaran S, Keppayan T, Gopal D, Sekar AK, Ramalingam K. Antimicrobial potential and taxonomic investigation of piezotolerant Streptomyces sp. NIOT-Ch-40 isolated from deep-sea sediment. World J Microbiol Biotechnol 2017; 33:27. [DOI: 10.1007/s11274-016-2193-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/20/2016] [Indexed: 11/28/2022]
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18
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Zhao K, Zhao C, Liao P, Zhang Q, Li Y, Liu M, Ao X, Gu Y, Liao D, Xu K, Yu X, Xiang Q, Huang C, Chen Q, Zhang L, Zhang X, Penttinen P. Isolation and antimicrobial activities of actinobacteria closely associated with liquorice plants Glycyrrhiza glabra L. and Glycyrrhiza inflate BAT. in Xinjiang, China. MICROBIOLOGY-SGM 2016; 162:1135-1146. [PMID: 27145982 DOI: 10.1099/mic.0.000301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A total of 218 actinobacteria strains were isolated from wild perennial liquorice plants Glycyrrhiza glabra L. and Glycyrrhiza. inflate BAT. Based on morphological characteristics, 45 and 32 strains from G. inflate and G. glabra, respectively, were selected for further analyses. According to 16S rRNA sequence analysis, most of the strains belonged to genus Streptomyces and a few strains represented the rare actinobacteria Micromonospora, Rhodococcus and Tsukamurella. A total of 39 strains from G. inflate and 27 strains from G. glabra showed antimicrobial activity against at least one indicator organism. The range of the antimicrobial activity of the strains isolated from G. glabra and G. inflate was similar. A total of 34 strains from G. inflate and 29 strains from G. glabra carried at least one of the genes encoding polyketide synthases, non-ribosomal peptide synthetase and FADH2-dependent halogenase. In the type II polyketide synthase KSα gene phylogenetic analysis, the strains were divided into two major clades: one included known spore pigment production-linked KSα sequences and other sequences were linked to the production of different types of aromatic polyketide antibiotics. Based on the antimicrobial range, the isolates that carried different KSα types were not separated from each other or from the isolates that did not carry KSα. The incongruent phylogenies of 16S rRNA and KSα genes indicated that the KSα genes were possibly horizontally transferred. In all, the liquorice plants were a rich source of biocontrol agents that may produce novel bioactive compounds.
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Affiliation(s)
- Ke Zhao
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Yaan 625000, China.,Xinjiang Production & Construction Corps, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar 843300, China
| | - Chong Zhao
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Yaan 625000, China
| | - Ping Liao
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Yaan 625000, China
| | - Qin Zhang
- Xinjiang Production & Construction Corps, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar 843300, China
| | - Yanbing Li
- Xinjiang Production & Construction Corps, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar 843300, China
| | - Maoke Liu
- Biotechnology Center, Rice and Sorghum Research Institute, Sichuan Academy of Agricultural Sciences, Luzhou 646100, China
| | - Xiaoling Ao
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Yaan 625000, China
| | - Yunfu Gu
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Yaan 625000, China
| | - Decong Liao
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Yaan 625000, China
| | - Kaiwei Xu
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Yaan 625000, China
| | - Xiumei Yu
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Yaan 625000, China
| | - Quanju Xiang
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Yaan 625000, China
| | - Chengyi Huang
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Yaan 625000, China
| | - Qiang Chen
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Yaan 625000, China
| | - Lili Zhang
- Xinjiang Production & Construction Corps, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar 843300, China
| | - Xiaoping Zhang
- Department of Microbiology, College of Resource, Sichuan Agricultural University, Yaan 625000, China
| | - Petri Penttinen
- Department of Environmental Sciences, University of Helsinki, Helsinki, Fin-00014, Finland
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19
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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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20
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Cuadrat RRC, Cury JC, Dávila AMR. Metagenomic Analysis of Upwelling-Affected Brazilian Coastal Seawater Reveals Sequence Domains of Type I PKS and Modular NRPS. Int J Mol Sci 2015; 16:28285-95. [PMID: 26633360 PMCID: PMC4691048 DOI: 10.3390/ijms161226101] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 11/23/2022] Open
Abstract
Marine environments harbor a wide range of microorganisms from the three domains of life. These microorganisms have great potential to enable discovery of new enzymes and bioactive compounds for industrial use. However, only ~1% of microorganisms from the environment can currently be identified through cultured isolates, limiting the discovery of new compounds. To overcome this limitation, a metagenomics approach has been widely adopted for biodiversity studies on samples from marine environments. In this study, we screened metagenomes in order to estimate the potential for new natural compound synthesis mediated by diversity in the Polyketide Synthase (PKS) and Nonribosomal Peptide Synthetase (NRPS) genes. The samples were collected from the Praia dos Anjos (Angel’s Beach) surface water—Arraial do Cabo (Rio de Janeiro state, Brazil), an environment affected by upwelling. In order to evaluate the potential for screening natural products in Arraial do Cabo samples, we used KS (keto-synthase) and C (condensation) domains (from PKS and NRPS, respectively) to build Hidden Markov Models (HMM) models. From both samples, a total of 84 KS and 46 C novel domain sequences were obtained, showing the potential of this environment for the discovery of new genes of biotechnological interest. These domains were classified by phylogenetic analysis and this was the first study conducted to screen PKS and NRPS genes in an upwelling affected sample
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Affiliation(s)
- Rafael R C Cuadrat
- Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, Fiocruz, Avenida Brasil 4365, Rio de Janeiro CEP 21040-360, Brazil.
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, OT Neuglobsow, Stechlin 16775, Germany.
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straße 6-8, Berlin 14195, Germany.
| | - Juliano C Cury
- Molecular Microbiology Laboratory, Federal University of São João del-Rei, Sete Lagoas Campus Rua Sétimo Moreira Martins 188, Itapoã II, Sete Lagoas CEP 35702-031, Brazil.
| | - Alberto M R Dávila
- Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, Fiocruz, Avenida Brasil 4365, Rio de Janeiro CEP 21040-360, Brazil.
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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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Braña AF, Fiedler HP, Nava H, González V, Sarmiento-Vizcaíno A, Molina A, Acuña JL, García LA, Blanco G. Two Streptomyces species producing antibiotic, antitumor, and anti-inflammatory compounds are widespread among intertidal macroalgae and deep-sea coral reef invertebrates from the central Cantabrian Sea. MICROBIAL ECOLOGY 2015; 69:512-524. [PMID: 25319239 DOI: 10.1007/s00248-014-0508-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 09/30/2014] [Indexed: 06/04/2023]
Abstract
Streptomycetes are widely distributed in the marine environment, although only a few studies on their associations to algae and coral ecosystems have been reported. Using a culture-dependent approach, we have isolated antibiotic-active Streptomyces species associated to diverse intertidal marine macroalgae (Phyllum Heterokontophyta, Rhodophyta, and Chlorophyta), from the central Cantabrian Sea. Two strains, with diverse antibiotic and cytotoxic activities, were found to inhabit these coastal environments, being widespread and persistent over a 3-year observation time frame. Based on 16S rRNA sequence analysis, the strains were identified as Streptomyces cyaneofuscatus M-27 and Streptomyces carnosus M-40. Similar isolates to these two strains were also associated to corals and other invertebrates from deep-sea coral reef ecosystem (Phyllum Cnidaria, Echinodermata, Arthropoda, Sipuncula, and Anelida) living up to 4.700-m depth in the submarine Avilés Canyon, thus revealing their barotolerant feature. These two strains were also found to colonize terrestrial lichens and have been repeatedly isolated from precipitations from tropospheric clouds. Compounds with antibiotic and cytotoxic activities produced by these strains were identified by high-performance liquid chromatography (HPLC) and database comparison. Antitumor compounds with antibacterial activities and members of the anthracycline family (daunomycin, cosmomycin B, galtamycin B), antifungals (maltophilins), anti-inflamatory molecules also with antituberculosis properties (lobophorins) were identified in this work. Many other compounds produced by the studied strains still remain unidentified, suggesting that Streptomyces associated to algae and coral ecosystems might represent an underexplored promising source for pharmaceutical drug discovery.
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Bernal MG, Campa-Córdova ÁI, Saucedo PE, González MC, Marrero RM, Mazón-Suástegui JM. Isolation and in vitro selection of actinomycetes strains as potential probiotics for aquaculture. Vet World 2015; 8:170-6. [PMID: 27047067 PMCID: PMC4774698 DOI: 10.14202/vetworld.2015.170-176] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/25/2014] [Accepted: 01/03/2015] [Indexed: 01/14/2023] Open
Abstract
AIM This study was designed to describe a series of in vitro tests that may aid the discovery of probiotic strains from actinomycetes. MATERIALS AND METHODS Actinomycetes were isolated from marine sediments using four different isolation media, followed by antimicrobial activity and toxicity assessment by the agar diffusion method and the hemolysis of human blood cells, respectively. Extracellular enzymatic production was monitored by the hydrolysis of proteins, lipids and carbohydrates. Tolerance to different pH values and salt concentrations was also determined, followed by hydrophobicity analysis and genetic identification of the most promising strains. RESULTS Five out of 31 isolated strains showed antimicrobial activity against three Vibrio species. Three non-hemolytic strains (N7, RL8 and V4) among these active isolates yielded positive results in hydrophobicity tests and exhibited good growth at salt concentrations ranging from 0% to 10%, except strain RL8, which required a salt concentration >0.6%. Although these strains did not grow at pH<3, they showed different enzymatic activities. Phylogenetic analysis revealed that strains N7 and V4 have more than 99% identity with several Streptomyces species, whereas the closest matches to strain RL8 are Streptomyces panacagri and Streptomyces flocculus, with 98% and 98.2% similarity, respectively. CONCLUSION Three actinomycetes strains showing probiotic-like properties were discovered using several in vitro tests that can be easily implemented in different institutions around the world.
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Affiliation(s)
- Milagro García Bernal
- Department of Microbiology, Center for the Study of Bioactive Chemicals (CBQ), Central University “Marta Abreu” of Las Villas. Road to Camajuaní Km 5½. Santa Clara 54830. Villa Clara. Cuba
| | - Ángel Isidro Campa-Córdova
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita Sur, C.P. 23090. La Paz, Baja California Sur, México
| | - Pedro Enrique Saucedo
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita Sur, C.P. 23090. La Paz, Baja California Sur, México
| | - Marlen Casanova González
- Department of Microbiology, Center for the Study of Bioactive Chemicals (CBQ), Central University “Marta Abreu” of Las Villas. Road to Camajuaní Km 5½. Santa Clara 54830. Villa Clara. Cuba
| | - Ricardo Medina Marrero
- Department of Microbiology, Center for the Study of Bioactive Chemicals (CBQ), Central University “Marta Abreu” of Las Villas. Road to Camajuaní Km 5½. Santa Clara 54830. Villa Clara. Cuba
| | - José Manuel Mazón-Suástegui
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita Sur, C.P. 23090. La Paz, Baja California Sur, México
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Li J, Dong JD, Yang J, Luo XM, Zhang S. Detection of polyketide synthase and nonribosomal peptide synthetase biosynthetic genes from antimicrobial coral-associated actinomycetes. Antonie van Leeuwenhoek 2014; 106:623-35. [DOI: 10.1007/s10482-014-0233-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/06/2014] [Indexed: 11/29/2022]
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Valliappan K, Sun W, Li Z. Marine actinobacteria associated with marine organisms and their potentials in producing pharmaceutical natural products. Appl Microbiol Biotechnol 2014; 98:7365-77. [PMID: 25064352 DOI: 10.1007/s00253-014-5954-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/10/2014] [Accepted: 07/11/2014] [Indexed: 01/09/2023]
Abstract
Actinobacteria are ubiquitous in the marine environment, playing an important ecological role in the recycling of refractory biomaterials and producing novel natural products with pharmic applications. Actinobacteria have been detected or isolated from the marine creatures such as sponges, corals, mollusks, ascidians, seaweeds, and seagrass. Marine organism-associated actinobacterial 16S rRNA gene sequences, i.e., 3,003 sequences, deposited in the NCBI database clearly revealed enormous numbers of actinobacteria associated with marine organisms. For example, RDP classification of these sequences showed that 112 and 62 actinobacterial genera were associated with the sponges and corals, respectively. In most cases, it is expected that these actinobacteria protect the host against pathogens by producing bioactive compounds. Natural products investigation and functional gene screening of the actinobacteria associated with the marine organisms revealed that they can synthesize numerous natural products including polyketides, isoprenoids, phenazines, peptides, indolocarbazoles, sterols, and others. These compounds showed anticancer, antimicrobial, antiparasitic, neurological, antioxidant, and anti-HIV activities. Therefore, marine organism-associated actinobacteria represent an important resource for marine drugs. It is an upcoming field of research to search for novel actinobacteria and pharmaceutical natural products from actinobacteria associated with the marine organisms. In this review, we attempt to summarize the present knowledge on the diversity and natural products production of actinobacteria associated with the marine organisms, based on the publications from 1991 to 2013.
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Affiliation(s)
- Karuppiah Valliappan
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, 200240, Shanghai, China
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Abdelmohsen UR, Yang C, Horn H, Hajjar D, Ravasi T, Hentschel U. Actinomycetes from Red Sea sponges: sources for chemical and phylogenetic diversity. Mar Drugs 2014; 12:2771-89. [PMID: 24824024 PMCID: PMC4052315 DOI: 10.3390/md12052771] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 04/10/2014] [Accepted: 04/14/2014] [Indexed: 02/01/2023] Open
Abstract
The diversity of actinomycetes associated with marine sponges collected off Fsar Reef (Saudi Arabia) was investigated in the present study. Forty-seven actinomycetes were cultivated and phylogenetically identified based on 16S rRNA gene sequencing and were assigned to 10 different actinomycete genera. Eight putatively novel species belonging to genera Kocuria, Mycobacterium, Nocardia, and Rhodococcus were identified based on sequence similarity values below 98.2% to other 16S rRNA gene sequences available in the NCBI database. PCR-based screening for biosynthetic genes including type I and type II polyketide synthases (PKS-I, PKS-II) as well as nonribosomal peptide synthetases (NRPS) showed that 20 actinomycete isolates encoded each at least one type of biosynthetic gene. The organic extracts of nine isolates displayed bioactivity against at least one of the test pathogens, which were Gram-positive and Gram-negative bacteria, fungi, human parasites, as well as in a West Nile Virus protease enzymatic assay. These results emphasize that marine sponges are a prolific resource for novel bioactive actinomycetes with potential for drug discovery.
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Affiliation(s)
- Usama Ramadan Abdelmohsen
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, Würzburg D-97082, Germany.
| | - Chen Yang
- Division of Chemical & Life Sciences and Engineering and Division of Applied Mathematics and Computer Science, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Hannes Horn
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, Würzburg D-97082, Germany.
| | - Dina Hajjar
- Division of Chemical & Life Sciences and Engineering and Division of Applied Mathematics and Computer Science, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Timothy Ravasi
- Division of Chemical & Life Sciences and Engineering and Division of Applied Mathematics and Computer Science, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Ute Hentschel
- Department of Botany II, Julius-von-Sachs Institute for Biological Sciences, University of Würzburg, Julius-von-Sachs-Platz 3, Würzburg D-97082, Germany.
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27
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Sun W, Zhang F, He L, Li Z. Pyrosequencing reveals diverse microbial community associated with the zoanthid Palythoa australiae from the South China Sea. MICROBIAL ECOLOGY 2014; 67:942-950. [PMID: 24682342 DOI: 10.1007/s00248-014-0395-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 02/10/2014] [Indexed: 06/03/2023]
Abstract
Diverse sessile organisms inhabit the coral reef ecosystems, including corals, sponges, and sea anemones. In the past decades, scleractinian corals (Cnidaria, Anthozoa, Scleractinia) and their associated microorganisms have attracted much attention. Zoanthids (Cnidaria, Anthozoa, Zoanthidea) are commonly found in coral reefs. However, little is known about the community structure of zoanthid-associated microbiota. In this study, the microbial community associated with the zoanthid Palythoa australiae in the South China Sea was investigated by 454 pyrosequencing. As a result, 2,353 bacterial, 583 archaeal, and 36 eukaryotic microbial ribotypes were detected, respectively. A total of 22 bacterial phyla (16 formally described phyla and six candidate phyla) were recovered. Proteobacteria was the most abundant group, followed by Chloroflexi and Actinobacteria. High-abundance Rhizobiales and diverse Chloroflexi were observed in the bacterial community. The archaeal population was composed of Crenarchaeota and Euryarchaeota, with Marine Group I as the dominant lineage. In particular, Candidatus Nitrosopumilus dominated the archaeal community. Besides bacteria and archaea, the zoanthid harbored eukaryotic microorganisms including fungi and algae though their diversity was very low. This study provided the first insights into the microbial community associated with P. australiae by 454 pyrosequencing, consequently laid a basis for the understanding of the association of P. australiae-microbes symbioses.
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Affiliation(s)
- Wei Sun
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
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Sato S, Iwata F, Fukae T, Katayama M. Neomacquarimicin: a new macquarimicin analog from marine-derived actinomycete. J Antibiot (Tokyo) 2014; 67:479-82. [DOI: 10.1038/ja.2014.17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 01/16/2014] [Accepted: 02/02/2014] [Indexed: 11/09/2022]
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29
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Boddy CN. Bioinformatics tools for genome mining of polyketide and non-ribosomal peptides. ACTA ACUST UNITED AC 2014; 41:443-50. [DOI: 10.1007/s10295-013-1368-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 10/14/2013] [Indexed: 12/12/2022]
Abstract
Abstract
Microbial natural products have played a key role in the development of clinical agents in nearly all therapeutic areas. Recent advances in genome sequencing have revealed that there is an incredible wealth of new polyketide and non-ribosomal peptide natural product diversity to be mined from genetic data. The diversity and complexity of polyketide and non-ribosomal peptide biosynthesis has required the development of unique bioinformatics tools to identify, annotate, and predict the structures of these natural products from their biosynthetic gene clusters. This review highlights and evaluates web-based bioinformatics tools currently available to the natural product community for genome mining to discover new polyketides and non-ribosomal peptides.
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Affiliation(s)
- Christopher N Boddy
- grid.28046.38 0000000121822255 Departments of Chemistry and Biology, Center for Advanced Research in Environmental Genomics University of Ottawa K1N 6N5 Ottawa ON Canada
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30
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Abdelmohsen UR, Bayer K, Hentschel U. Diversity, abundance and natural products of marine sponge-associated actinomycetes. Nat Prod Rep 2014; 31:381-99. [DOI: 10.1039/c3np70111e] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
This review discusses the diversity, abundance and natural products repertoire of actinomycetes associated with marine sponges. Comprehensive phylogenetic analysis was carried out and qPCR data on actinomycete abundances in sponge ecosystems are presented.
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Affiliation(s)
- Usama Ramadan Abdelmohsen
- Department of Botany II
- Julius-von-Sachs-Institute for Biological Sciences
- University of Würzburg
- 97082 Würzburg, Germany
- Department of Pharmacognosy
| | - Kristina Bayer
- Department of Botany II
- Julius-von-Sachs-Institute for Biological Sciences
- University of Würzburg
- 97082 Würzburg, Germany
| | - Ute Hentschel
- Department of Botany II
- Julius-von-Sachs-Institute for Biological Sciences
- University of Würzburg
- 97082 Würzburg, Germany
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Graça AP, Bondoso J, Gaspar H, Xavier JR, Monteiro MC, de la Cruz M, Oves-Costales D, Vicente F, Lage OM. Antimicrobial activity of heterotrophic bacterial communities from the marine sponge Erylus discophorus (Astrophorida, Geodiidae). PLoS One 2013; 8:e78992. [PMID: 24236081 PMCID: PMC3827338 DOI: 10.1371/journal.pone.0078992] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/25/2013] [Indexed: 12/17/2022] Open
Abstract
Heterotrophic bacteria associated with two specimens of the marine sponge Erylus discophorus were screened for their capacity to produce bioactive compounds against a panel of human pathogens (Staphylococcus aureus wild type and methicillin-resistant S. aureus (MRSA), Bacillus subtilis, Pseudomonas aeruginosa, Acinetobacter baumanii, Candida albicans and Aspergillus fumigatus), fish pathogen (Aliivibrio fischeri) and environmentally relevant bacteria (Vibrio harveyi). The sponges were collected in Berlengas Islands, Portugal. Of the 212 isolated heterotrophic bacteria belonging to Alpha- and Gammaproteobacteria, Actinobacteria and Firmicutes, 31% produced antimicrobial metabolites. Bioactivity was found against both Gram positive and Gram negative and clinically and environmentally relevant target microorganisms. Bioactivity was found mainly against B. subtilis and some bioactivity against S. aureus MRSA, V. harveyi and A. fisheri. No antifungal activity was detected. The three most bioactive genera were Pseudovibrio (47.0%), Vibrio (22.7%) and Bacillus (7.6%). Other less bioactive genera were Labrenzia, Acinetobacter, Microbulbifer, Pseudomonas, Gordonia, Microbacterium, Micrococcus and Mycobacterium, Paenibacillus and Staphylococcus. The search of polyketide I synthases (PKS-I) and nonribosomal peptide synthetases (NRPSs) genes in 59 of the bioactive bacteria suggested the presence of PKS-I in 12 strains, NRPS in 3 strains and both genes in 3 strains. Our results show the potential of the bacterial community associated with Erylus discophorus sponges as producers of bioactive compounds.
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Affiliation(s)
- Ana Patrícia Graça
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIMAR/CIIMAR), Porto, Portugal
| | - Joana Bondoso
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIMAR/CIIMAR), Porto, Portugal
| | - Helena Gaspar
- Centro de Química e Bioquímica e Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa Campo Grande, Lisboa, Portugal
| | - Joana R. Xavier
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Pólo dos Açores – Departamento de Biologia da Universidade dos Açores, Ponta Delgada, Portugal
- CEAB, Centre d'Estudis Avançats de Blanes, (CSIC), Blanes (Girona), Spain
| | - Maria Cândida Monteiro
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Armilla, Granada, Spain
| | - Mercedes de la Cruz
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Armilla, Granada, Spain
| | - Daniel Oves-Costales
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Armilla, Granada, Spain
| | - Francisca Vicente
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Parque Tecnológico de Ciencias de la Salud, Armilla, Granada, Spain
| | - Olga Maria Lage
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIMAR/CIIMAR), Porto, Portugal
- * E-mail:
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32
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Yang S, Sun W, Tang C, Jin L, Zhang F, Li Z. Phylogenetic diversity of actinobacteria associated with soft coral Alcyonium gracllimum and stony coral Tubastraea coccinea in the East China Sea. MICROBIAL ECOLOGY 2013; 66:189-199. [PMID: 23503990 DOI: 10.1007/s00248-013-0205-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 02/21/2013] [Indexed: 06/01/2023]
Abstract
Actinobacteria are widely distributed in the marine environment. To date, few studies have been performed to explore the coral-associated Actinobacteria, and little is known about the diversity of coral-associated Actinobacteria. In this study, the actinobacterial diversity associated with one soft coral Alcyonium gracllimum and one stony coral Tubastraea coccinea collected from the East China Sea was investigated using both culture-independent and culture-dependent approaches. A total of 19 actinobacterial genera were detected in these two corals, among which nine genera (Corynebacterium, Dietzia, Gordonia, Kocuria, Microbacterium, Micrococcus, Mycobacterium, Streptomyces, and Candidatus Microthrix) were common, three genera (Cellulomonas, Dermatophilus, and Janibacter) were unique to the soft coral, and seven genera (Brevibacterium, Dermacoccus, Leucobacter, Micromonospora, Nocardioides, Rhodococcus, and Serinicoccus) were unique to the stony coral. This finding suggested that highly diverse Actinobacteria were associated with different types of corals. In particular, five actinobacterial genera (Cellulomonas, Dermacoccus, Gordonia, Serinicoccus, and Candidatus Microthrix) were recovered from corals for the first time, extending the known diversity of coral-associated Actinobacteria. This study shows that soft and stony corals host diverse Actinobacteria and can serve as a new source of marine actinomycetes.
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Affiliation(s)
- Shan Yang
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic of China
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