1
|
Alloun W, Berkani M, Shavandi A, Beddiar A, Pellegrini M, Garzia M, Lakhdari D, Ganachari SV, Aminabhavi TM, Vasseghian Y, Muddapur U, Chaouche NK. Harnessing artificial intelligence-driven approach for enhanced indole-3-acetic acid from the newly isolated Streptomyces rutgersensis AW08. ENVIRONMENTAL RESEARCH 2024; 252:118933. [PMID: 38642645 DOI: 10.1016/j.envres.2024.118933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 03/28/2024] [Accepted: 04/12/2024] [Indexed: 04/22/2024]
Abstract
Indole-3-acetic acid (IAA) derived from Actinobacteria fermentations on agro-wastes constitutes a safer and low-cost alternative to synthetic IAA. This study aims to select a high IAA-producing Streptomyces-like strain isolated from Lake Oubeira sediments (El Kala, Algeria) for further investigations (i.e., 16S rRNA gene barcoding and process optimization). Subsequently, artificial intelligence-based approaches were employed to maximize IAA bioproduction on spent coffee grounds as high-value-added feedstock. The specificity was the novel application of the Limited-Memory Broyden-Fletcher-Goldfarb-Shanno Box (L-BFGS-B) optimization algorithm. The new strain AW08 was a significant producer of IAA (26.116 ± 0.61 μg/mL) and was identified as Streptomyces rutgersensis by 16S rRNA gene barcoding and phylogenetic inquiry. The empirical data involved the inoculation of AW08 in various cultural conditions according to a four-factor Box Behnken Design matrix (BBD) of Response surface methodology (RSM). The input parameters and regression equation extracted from the RSM-BBD were the basis for implementing and training the L-BFGS-B algorithm. Upon training the model, the optimal conditions suggested by the BBD and L-BFGS-B algorithm were, respectively, L-Trp (X1) = 0.58 %; 0.57 %; T° (X2) = 26.37 °C; 28.19 °C; pH (X3) = 7.75; 8.59; and carbon source (X4) = 30 %; 33.29 %, with the predicted response IAA (Y) = 152.8; 169.18 μg/mL). Our findings emphasize the potential of the multifunctional S. rutgersensis AW08, isolated and reported for the first time in Algeria, as a robust producer of IAA. Validation investigations using the bioprocess parameters provided by the L-BFGS-B and the BBD-RSM models demonstrate the effectiveness of AI-driven optimization in maximizing IAA output by 5.43-fold and 4.2-fold, respectively. This study constitutes the first paper reporting a novel interdisciplinary approach and providing insights into biotechnological advancements. These results support for the first time a reasonable approach for valorizing spent coffee grounds as feedstock for sustainable and economic IAA production from S. rutgersensis AW08.
Collapse
Affiliation(s)
- Wiem Alloun
- Laboratory of Mycology, Biotechnology and Microbial Activity, Department of Applied Biology, BP, 325 Aïn El Bey Road, Constantine 25017, Algeria; The BioMatter Lab, École Polytechnique de Bruxelles, Université Libre de Bruxelles (ULB), Avenue F.D. Roosevelt, 50-CP 165/61, 1050 Brussels, Belgium; Department of Life, Health and Environmental Sciences, University of L'Aquila, Coppito, 67100 L'Aquila, Italy
| | - Mohammed Berkani
- Biotechnology Laboratory, Higher National School of Biotechnology Taoufik KHAZNADAR, Nouveau Pôle universitaire Ali Mendjeli, BP. E66, Constantine, 25100, Algeria.
| | - Amin Shavandi
- The BioMatter Lab, École Polytechnique de Bruxelles, Université Libre de Bruxelles (ULB), Avenue F.D. Roosevelt, 50-CP 165/61, 1050 Brussels, Belgium
| | - Adlène Beddiar
- Department of Web Development and Artificial Intelligence, University of Mohammed Cherif Messaadia, Souk-Ahras, Algeria
| | - Marika Pellegrini
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Coppito, 67100 L'Aquila, Italy
| | - Matteo Garzia
- Department of Life, Health and Environmental Sciences, University of L'Aquila, Coppito, 67100 L'Aquila, Italy
| | - Delloula Lakhdari
- Biotechnology Laboratory, Higher National School of Biotechnology Taoufik KHAZNADAR, Nouveau Pôle universitaire Ali Mendjeli, BP. E66, Constantine, 25100, Algeria; Research Center in Industrial Technologies CRTI, P.O. Box 64, Cheraga 16014, Algiers, Algeria
| | - Sharanabasava V Ganachari
- Center for Energy and Environment, School of Advanced Sciences, KLE Technological University, Hubballi, Karnataka, 580 031, India
| | - Tejraj M Aminabhavi
- Center for Energy and Environment, School of Advanced Sciences, KLE Technological University, Hubballi, Karnataka, 580 031, India; School of Engineering, University of Petroleum and Energy Studies (UPES) Uttarakhand, Dehradun, 248 007, India; Korea University, Seoul, South Korea.
| | - Yasser Vasseghian
- Department of Chemistry, Soongsil University, Seoul, 06978, South Korea; University Centre for Research & Development, Department of Mechanical Engineering, Chandigarh University, Gharuan, Mohali, Punjab 140413, India; The University of Johannesburg, Department of Chemical Engineering, P.O. Box 17011, Doornfontein, 2088, South Africa.
| | - Uday Muddapur
- Department of Biotechnology, KLE Technological University, Hubballi, Karnataka, 580 031, India
| | - Noreddine Kacem Chaouche
- Laboratory of Mycology, Biotechnology and Microbial Activity, Department of Applied Biology, BP, 325 Aïn El Bey Road, Constantine 25017, Algeria
| |
Collapse
|
2
|
Zhang Z, Li D, Xie F, Zhang H. The causal relationship between gut microbiota and neuroblastoma: a bidirectional Mendelian randomization analysis and meta-analysis. Microbiol Spectr 2024; 12:e0365623. [PMID: 38411074 PMCID: PMC10986465 DOI: 10.1128/spectrum.03656-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/07/2024] [Indexed: 02/28/2024] Open
Abstract
Neuroblastoma (NB) is a type of neuroectodermal tumor that originates from primitive sympathetic ganglion cells. Although many risk factors contributing to the occurrence of NB have been reported in recent years, the role of the gut microbiota in its development remains unclear. A bidirectional Mendelian randomization (MR) analysis was conducted to elucidate the causal relationship between the gut microbiota and NB. In the MR analysis, we employed the inverse-variance weighted (IVW) method as the primary criterion for assessing causality, while also utilizing three additional approaches, including MR-Egger, weighted median model, and weighted mode, for comprehensive evaluation. For gut microbiota that were causally associated with NB, a reverse MR was also used to assess the stability of this causal relationship. Finally, we also used external cohorts for validation and performed a meta-analysis of the results. The IVW results indicated a causal relationship between six gut microbiota and NB. Among the six gut microbiota, genus Lachnospiraceae [IVW odds ratio (OR): 2.66, 95% confidence interval (CI): 1.09-6.51, P value: 0.03] exhibited a detrimental effect against NB. On the other hand, the class Actinobacteria (IVW OR: 0.24, 95% CI: 0.07-0.77, P value: 0.02), the family Bifidobacteriaceae (IVW OR: 0.40, 95% CI: 0.17-0.96, P value: 0.04), the genus Desulfovibrio (IVW OR: 0.50, 95% CI: 0.25-0.97, P value: 0.04), the genus Bifidobacterium (IVW OR: 0.39, 95% CI: 0.16-0.92, P value: 0.03), and the genus Howardella (IVW OR: 0.55, 95% CI: 0.31-0.97, P value: 0.04) displayed a protective effect on NB. A reverse MR analysis did not reveal a causality between NB and the six gut microbiota. Meta-analysis showed that genus Bifidobacterium (meta OR: 0.41, 95% CI: 0.22-0.75, P < 0.01) and genus Lachnospiraceae (meta OR: 2.20, 95% CI: 1.01-4.79, P < 0.05) were still significant. IMPORTANCE Bidirectional Mendelian randomization was used to explore the causality between gut microbiota and neuroblastoma (NB). The results showed that there is a causal relationship between the six gut microbiota and NB, of which two gut microbiota were further confirmed in the meta-analysis. This may provide a new perspective on the prevention and treatment of NB.
Collapse
Affiliation(s)
- Zexin Zhang
- The Second Clinical School of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Dongting Li
- The Affiliated Guangzhou Hospital of TCM of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fengxi Xie
- Maoming Hospital of Guangzhou University of Chinese Medicine, Maoming, China
| | - Haibo Zhang
- The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- Guangdong Key Laboratory of Clinical Research of Chinese Medicine, Guangzhou, China
- Guangdong Joint Laboratory of Guangdong, Hong Kong and Macao Chinese Medicine and Immune Diseases, Guangzhou, China
- State Key Laboratory of Wet Certificate of Chinese Medicine Jointly Built by the Province and the Ministry, Guangzhou, China
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Girão M, Freitas S, Martins TP, Urbatzka R, Carvalho MF, Leão PN. Decylprodigiosin: a new member of the prodigiosin family isolated from a seaweed-associated Streptomyces. Front Pharmacol 2024; 15:1347485. [PMID: 38576493 PMCID: PMC10991731 DOI: 10.3389/fphar.2024.1347485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/11/2024] [Indexed: 04/06/2024] Open
Abstract
Bioprospecting actinobacterial secondary metabolism from untapped marine sources may lead to the discovery of biotechnologically-relevant compounds. While studying the diversity and bioactive potential of Actinomycetota associated with Codium tomentosum, a green seaweed collected in the northern Portuguese cost, strain CT-F61, identified as Streptomyces violaceoruber, was isolated. Its extracts displayed a strong anticancer activity on breast carcinoma T-47D and colorectal carcinoma HCT116 cells, being effective as well against a panel of human and fish pathogenic bacteria. Following a bioactivity-guided isolation pipeline, a new analogue of the red-pigmented family of the antibiotics prodigiosins, decylprodigiosin (1), was identified and chemically characterized. Despite this family of natural products being well-known for a long time, we report a new analogue and the first evidence for prodigiosins being produced by a seaweed-associated actinomycete.
Collapse
Affiliation(s)
- Mariana Girão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
- School of Medicine and Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Sara Freitas
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Teresa P. Martins
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Ralph Urbatzka
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| | - Maria F. Carvalho
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
- School of Medicine and Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Pedro N. Leão
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos, Portugal
| |
Collapse
|
5
|
Guan L, Wang H, Chen J, Yang F, Yang J, Li J, Jin L. Isolation and Identification of Culturable Bacteria from South China Seawater and Preliminary Screening of Marine Biocontrol Bacteria. Microorganisms 2023; 11:2933. [PMID: 38138077 PMCID: PMC10746102 DOI: 10.3390/microorganisms11122933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
Marine microorganisms have evolved special metabolic pathways to produce numerous bioactive substances with novel structures and unique functions. This study analyzed the diversity of culturable bacteria in marine water samples from the South China Sea and screened the isolated bacteria with pathogenic fungi. A total of 200 culturable strains of 72 different bacteria were obtained from 56 water samples from the South China Sea. They belonged to three phyla and four classes, namely Gammaproteobacteria, Alphaproteobacteria, Bacilli and Actinomycetia. Bacilli was the dominant class, comprising up to 59.72%, followed by Gammaproteobacteria (20.83%). Bacillus, Pseudomonas, Paenibacillus and Rhizobium were the most dominant genera. Among these strains, HY-88 and HY-91 encoding BamC, FenB and PKSI genes were selected and identified as Bacillus subtilis. The respective inhibition rates of the HY-88 caused by plate confrontation against Magnaporthe grisea, Fusarium oxysporum, Botrytis cinerea, anthrax and Botrytis cinerea were 90.91%, 54.29%, 52.17% and 51.72%, in comparison with HY-91 86.36%, 48.57%, 47.83% and 34.48%. In addition, the supernatant of HY-88 showed a lesion inhibition rate of 74.5%, which was significantly higher than HY-91 (60.55%). In addition, HY-88 and HY-91 showed strong antifungal activity to Colletotrichum viniferum on detached Shine Muscat grapes. Tolerance tests showed that the HY-88 and HY-91 grew at 10-40 °C, 7-10% NaCl and pH 3-11. HY-88 and HY-91 could inhibit various fungal plant diseases, which lays a foundation for the development of new biopesticides.
Collapse
Affiliation(s)
- Limei Guan
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
| | - Hongxiu Wang
- Institute of Microbiology, Jiangxi Academy of Sciences, Nanchang 330029, China;
| | - Junhui Chen
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
| | - Feiying Yang
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
| | - Jian Yang
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
| | - Jianghuai Li
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
| | - Liang Jin
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330029, China; (L.G.); (J.C.); (F.Y.); (J.Y.); (J.L.)
| |
Collapse
|
6
|
Rathinam AJ, Santhaseelan H, Dahms HU, Dinakaran VT, Murugaiah SG. Bioprospecting of unexplored halophilic actinobacteria against human infectious pathogens. 3 Biotech 2023; 13:398. [PMID: 37974926 PMCID: PMC10645811 DOI: 10.1007/s13205-023-03812-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 10/08/2023] [Indexed: 11/19/2023] Open
Abstract
Human pathogenic diseases received much attention recently due to their uncontrolled spread of antimicrobial resistance (AMR) which causes several threads every year. Effective alternate antimicrobials are urgently required to combat those disease causing infectious microbes. Halophilic actinobacteria revealed huge potentials and unexplored cultivable/non-cultivable actinobacterial species producing enormous antimicrobials have been proved in several genomics approaches. Potential gene clusters, PKS and NRPKS from Nocardia, Salinospora, Rhodococcus, and Streptomyces have wide range coding genes of secondary metabolites. Biosynthetic pathways identification via various approaches like genome mining, In silico, OSMAC (one strain many compound) analysis provides better identification of knowing the active metabolites using several databases like AMP, APD and CRAMPR, etc. Genome constellations of actinobacteria particularly the prediction of BGCs (Biosynthetic Gene Clusters) to mine the bioactive molecules such as pigments, biosurfactants and few enzymes have been reported for antimicrobial activity. Saltpan, saltlake, lagoon and haloalkali environment exploring potential actinobacterial strains Micromonospora, Kocuria, Pseudonocardia, and Nocardiopsis revealed several acids and ester derivatives with antimicrobial potential. Marine sediments and marine macro organisms have been found as significant population holders of potential actinobacterial strains. Deadly infectious diseases (IDs) including tuberculosis, ventilator-associated pneumonia and Candidiasis, have been targeted by halo-actinobacterial metabolites with promising results. Methicillin resistant Staphylococus aureus and virus like Encephalitic alphaviruses were potentially targeted by halophilic actinobacterial metabolites by the compound Homoseongomycin from sponge associated antinobacterium. In this review, we discuss the potential antimicrobial properties of various biomolecules extracted from the unexplored halophilic actinobacterial strains specifically against human infectious pathogens along with prospective genomic constellations.
Collapse
Affiliation(s)
- Arthur James Rathinam
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Henciya Santhaseelan
- Department of Marine Science, Bharathidasan University, Tiruchirappalli, 620 024 India
| | - Hans-Uwe Dahms
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, 80708 Taiwan
| | | | | |
Collapse
|
7
|
Deutsch Y, Samara M, Nasser A, Berman-Frank I, Ezra D. Kocuria flava, a Bacterial Endophyte of the Marine Macroalga Bryopsis plumosa, Emits 8-Nonenoic Acid Which Inhibits the Aquaculture Pathogen Saprolegnia parasitica. Mar Drugs 2023; 21:476. [PMID: 37755090 PMCID: PMC10532832 DOI: 10.3390/md21090476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/28/2023] Open
Abstract
Secondary metabolites-organic compounds that are often bioactive-produced by endophytes, among others, provide a selective advantage by increasing the organism's survivability. Secondary metabolites mediate the symbiotic relationship between endophytes and their host, potentially providing the host with tolerance to, and protection against biotic and abiotic stressors. Secondary metabolites can be secreted as a dissolved substance or emitted as a volatile. In a previous study, we isolated bioactive endophytes from several macroalgae and tested them in vitro for their ability to inhibit major disease-causing pathogens of aquatic animals in the aquaculture industry. One endophyte (isolate Abp5, K. flava) inhibited and killed, in vitro, the pathogen Saprolegnia parasitica, an oomycete that causes saprolegniasis-a disease affecting a wide range of aquatic animals. Here, using analytical chemistry tools, we found that Abp5 produces the volatile organic compound (VOC) 8-nonenoic acid. Once we confirmed the production of this compound by the endophyte, we tested the compound's ability to treat S. parasitica in in vitro and in vivo bioassays. In the latter, we found that 5 mg/L of the compound improves the survival of larvae challenged with S. parasitica by 54.5%. Our isolation and characterization of the VOC emitted by the endophytic K. flava establish the groundwork for future studies of endophytic biocontrol agents from macroalgae. Use of this compound could enable managing oomycete agricultural pathogens in general, and S. parasitica in particular, a major causal agent in aquaculture diseases.
Collapse
Affiliation(s)
- Ynon Deutsch
- Department of Plant Pathology and Weed Research, The Volcani Institute, Agricultural Research Organization, Rishon LeZion 7528809, Israel;
- Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, Haifa 3103301, Israel;
| | - Mohamed Samara
- The Inter-Institutional Analytical Instrumentation Unit (IU), The Volcani Institute, Agricultural Research Organization, Rishon LeZion 7528809, Israel; (M.S.); (A.N.)
| | - Ahmed Nasser
- The Inter-Institutional Analytical Instrumentation Unit (IU), The Volcani Institute, Agricultural Research Organization, Rishon LeZion 7528809, Israel; (M.S.); (A.N.)
| | - Ilana Berman-Frank
- Leon H. Charney School of Marine Sciences, Department of Marine Biology, University of Haifa, Haifa 3103301, Israel;
| | - David Ezra
- Department of Plant Pathology and Weed Research, The Volcani Institute, Agricultural Research Organization, Rishon LeZion 7528809, Israel;
| |
Collapse
|
8
|
Xiong Z, Wang R, Xia T, Zhang S, Ma S, Guo Z. Natural Products and Biological Activity from Actinomycetes Associated with Marine Algae. Molecules 2023; 28:5138. [PMID: 37446800 DOI: 10.3390/molecules28135138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Marine natural products have been recognized as the most promising source of bioactive substances for drug discovery research. This review illustrates the diversity of culturable actinobacteria associated with marine algae, their bioactivity and metabolites, and approaches to their isolation and determination of their biological properties. Furthermore, actinobacteria associated with marine algae are presented as a new subject for an extensive investigation to find novel and active natural products, which make them a potentially rich and innovative source for new drug development deserving more attention and exploration.
Collapse
Affiliation(s)
- Zijun Xiong
- Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Rong Wang
- Hainan Provincial Key Laboratory of Tropical Maricultural Technologies, Hainan Academy of Ocean and Fisheries Sciences, Haikou 571126, China
| | - Tengfei Xia
- Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou 571100, China
| | - Shiqing Zhang
- Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Shuai Ma
- Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| | - Zhikai Guo
- Hainan Key Laboratory of Tropical Microbe Resources, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute for Tropical Agricultural Resources, Haikou 571101, China
| |
Collapse
|
9
|
Alloun W, Berkani M, Benaissa A, Shavandi A, Gares M, Danesh C, Lakhdari D, Ghfar AA, Chaouche NK. Waste valorization as low-cost media engineering for auxin production from the newly isolated Streptomyces rubrogriseus AW22: Model development. CHEMOSPHERE 2023; 326:138394. [PMID: 36925000 DOI: 10.1016/j.chemosphere.2023.138394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/26/2023] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
Indole-3-acetic acid (IAA) represents a crucial phytohormone regulating specific tropic responses in plants and functions as a chemical signal between plant hosts and their symbionts. The Actinobacteria strain of AW22 with high IAA production ability was isolated in Algeria for the first time and was characterized as Streptomyces rubrogriseus through chemotaxonomic analysis and 16 S rDNA sequence alignment. The suitable medium for a maximum IAA yield was engineered in vitro and in silico using machine learning-assisted modeling. The primary low-cost feedstocks comprised various concentrations of spent coffee grounds (SCGs) and carob bean grounds (CBGs) extracts. Further, we combined the Box-Behnken design from response surface methodology (BBD-RSM) with artificial neural networks (ANNs) coupled with the genetic algorithm (GA). The critical process parameters screened via Plackett-Burman design (PBD) served as BBD and ANN-GA inputs, with IAA yield as the output variable. Analysis of the putative IAA using thin-layer chromatography (TLC) and (HPLC) revealed Rf values equal to 0.69 and a retention time of 3.711 min, equivalent to the authentic IAA. AW 22 achieved a maximum IAA yield of 188.290 ± 0.38 μg/mL using the process parameters generated by the ANN-GA model, consisting of L-Trp, 0.6%; SCG, 30%; T°, 25.8 °C; and pH 9, after eight days of incubation. An R2 of 99.98%, adding to an MSE of 1.86 × 10-5 at 129 epochs, postulated higher reliability of ANN-GA-approach in predicting responses, compared with BBD-RSM modeling exhibiting an R2 of 76.28%. The validation experiments resulted in a 4.55-fold and 4.46-fold increase in IAA secretion, corresponding to ANN-GA and BBD-RSM models, respectively, confirming the validity of both models.
Collapse
Affiliation(s)
- Wiem Alloun
- Laboratory of Mycology, Biotechnology and Microbial Activity (LaMyBAM), Department of Applied Biology, Constantine 1 University, BP, 325, Aïn El Bey, Constantine, 25017, Algeria.
| | - Mohammed Berkani
- Biotechnology Laboratory, National Higher School of Biotechnology, Ali Mendjeli University City, BP E66, 25100, Constantine, Algeria.
| | - Akila Benaissa
- Pharmaceutical Research and Sustainable Development Laboratory (ReMeDD), Department of Pharmaceutical Engineering, Faculty of Process Engineering, Constantine 3 University, Constantine, 25000, Algeria
| | - Amin Shavandi
- 3BIO-BioMatter Unit, École Polytechnique de Bruxelles, Université Libre de Bruxelles (ULB), Avenue F.D. Roosevelt, 50-CP 165/61, 1050, Brussels, Belgium
| | - Maroua Gares
- Laboratory of Mycology, Biotechnology and Microbial Activity (LaMyBAM), Department of Applied Biology, Constantine 1 University, BP, 325, Aïn El Bey, Constantine, 25017, Algeria
| | - Camellia Danesh
- The University of Johannesburg, Department of Chemical Engineering, P.O. Box 17011, Doornfontein, 2088, South Africa.
| | - Delloula Lakhdari
- Biotechnology Laboratory, National Higher School of Biotechnology, Ali Mendjeli University City, BP E66, 25100, Constantine, Algeria; Research Center in Industrial Technologies CRTI, P.O. Box 64, Cheraga 16014, Algiers, Algeria
| | - Ayman A Ghfar
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Noreddine Kacem Chaouche
- Laboratory of Mycology, Biotechnology and Microbial Activity (LaMyBAM), Department of Applied Biology, Constantine 1 University, BP, 325, Aïn El Bey, Constantine, 25017, Algeria
| |
Collapse
|
10
|
Elshafie HS, De Martino L, Formisano C, Caputo L, De Feo V, Camele I. Chemical Identification of Secondary Metabolites from Rhizospheric Actinomycetes Using LC-MS Analysis: In Silico Antifungal Evaluation and Growth-Promoting Effects. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091869. [PMID: 37176926 PMCID: PMC10181443 DOI: 10.3390/plants12091869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023]
Abstract
The rhizosphere is a rich source of actinomycetes which can produce several potential biologically active secondary metabolites. The principal goal for this research is to extract, purify, and characterize the bioactive secondary metabolites produced by three different strains of actinomycetes isolated from the rhizosphere of rosemary, black locust, and olive. The plant growth-promoting effect (PGPE) of the studied strains of actinomycetes on Ocimum basilicum L. (basil) and the disease-control effect on necrotic stem lesions of "black leg" caused by Fusarium tabacinum on basil were evaluated in silico. The cell-free culture filtrates from the studied actinomycetes isolates were evaluated in vitro for their antimicrobial activity against some common phytopathogens. The secondary metabolites obtained from the cell-free culture filtrates have been chemically characterized using high-resolution electrospray ionization of liquid-chromatography/mass-spectrometric detection (ESI-(HR)Orbitrap-MS). Results of the in silico trial showed that all studied isolates demonstrated PGPE on basil seedlings, improved some eco-physiological characteristics, and reduced the disease incidence of F. tabacinum. The extracted metabolites from the studied actinomycetes demonstrated antimicrobial activity in a Petri-plates assay. The chemical analysis revealed the presence of 20 different components. This research emphasizes how valuable the examined isolates are for producing bioactive compounds, indicating their putative antimicrobial activity and their potential employment as fungal biocontrol agents. In particular, the obtained results revealed the possibility of green synthesis of some important secondary metabolites, such as N-Acetyl-l-histidinol, Rhizocticin A, and Eponemycin, from actinomycetes. The bioactive metabolites may be successively used to develop novel bio-formulations for both crop protection and/or PGPE.
Collapse
Affiliation(s)
- Hazem S Elshafie
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, 85100 Potenza, Italy
| | - Laura De Martino
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy
| | - Carmen Formisano
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Montesano 49, 80131 Naples, Italy
| | - Lucia Caputo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy
| | - Vincenzo De Feo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy
| | - Ippolito Camele
- School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata, 85100 Potenza, Italy
| |
Collapse
|
11
|
Pyrrole-Containing Alkaloids from a Marine-Derived Actinobacterium Streptomyces zhaozhouensis and Their Antimicrobial and Cytotoxic Activities. Mar Drugs 2023; 21:md21030167. [PMID: 36976216 PMCID: PMC10054583 DOI: 10.3390/md21030167] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Two new alkaloids, streptopyrroles B and C (1 and 2), were discovered through a chemical investigation of the ethyl acetate (EtOAc) extract from a marine-derived actinomycete, Streptomyces zhaozhouensis, along with four known analogs (3–6). The structures of the new compounds were elucidated by spectroscopic analysis (HR-ESIMS, 1D, and 2D NMR) and a comparison of their experimental data with literature values. The new compounds were evaluated for their antimicrobial activity by standard broth dilution assay, and the tested compounds showed significant activity against Gram-positive bacteria with minimum inhibitory concentration (MIC) values ranging from 0.7 to 2.9 µM, and kanamycin was used as a positive control with MIC values ranging from <0.5 to 4.1 µM. Additionally, 1, 3, and 5 were evaluated for their cytotoxicity against six tumor cell lines by sulforhodamine B (SRB) assay, and these compounds displayed cytotoxic activities against all the tested cell lines, with concentration causing 50% cell growth inhibition (GI50) values ranging from 4.9 to 10.8 µM, while a positive control, adriamycin, showed GI50 values of 0.13–0.17 µM.
Collapse
|
12
|
Quach NT, Nguyen Vu TH, Bui TL, Pham AT, An Nguyen TT, Xuan Le TT, Thuy Ta TT, Dudhagara P, Phi QT. Genome-Guided Investigation Provides New Insights into Secondary Metabolites of Streptomyces parvulus SX6 from Aegiceras corniculatum. Pol J Microbiol 2022; 71:381-394. [DOI: 10.33073/pjm-2022-034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/13/2022] [Indexed: 11/07/2022] Open
Abstract
Abstract
Whole-genome sequencing and genome mining are recently considered an efficient approach to shine more light on the underlying secondary metabolites of Streptomyces. The present study unearths the biosynthetic potential of endophytic SX6 as a promising source of biologically active substances and plant-derived compounds for the first time. Out of 38 isolates associated with Aegiceras corniculatum (L.) Blanco, Streptomyces parvulus SX6 was highly active against Pseudomonas aeruginosa ATCC® 9027™ and methicillin-resistant Staphylococcus epidermidis (MRSE) ATCC® 35984™. Additionally, S. parvulus SX6 culture extract showed strong cytotoxicity against Hep3B, MCF-7, and A549 cell lines at a concentration of 30 μg/ml, but not in non-cancerous HEK-293 cells. The genome contained 7.69 Mb in size with an average G + C content of 72.8% and consisted of 6,779 protein-coding genes. AntiSMASH analysis resulted in the identification of 29 biosynthetic gene clusters (BGCs) for secondary metabolites. Among them, 4 BGCs showed low similarity (28–67% of genes show similarity) to actinomycin, streptovaricin, and polyoxypeptin gene clusters, possibly attributed to antibacterial and anticancer activities observed. In addition, the complete biosynthetic pathways of plant-derived compounds, including daidzein and genistein were identified using genome mining and HPLC-DAD-MS analysis. These findings portray an exciting avenue for future characterization of promising secondary metabolites from mangrove endophytic S. parvulus.
Collapse
Affiliation(s)
- Ngoc Tung Quach
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | - Thi Hanh Nguyen Vu
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | - Thi Lien Bui
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | - Anh Tuan Pham
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | - Thi Thu An Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | - Thi Thanh Xuan Le
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| | | | - Pravin Dudhagara
- Department of Biosciences (UGC-SAP-II and DST-FIST-I), Veer Narmad South Gujarat University , Surat , India
| | - Quyet-Tien Phi
- Graduate University of Science and Technology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
- Institute of Biotechnology, Vietnam Academy of Science and Technology , Hanoi , Vietnam
| |
Collapse
|
13
|
dos Santos JDN, João SA, Martín J, Vicente F, Reyes F, Lage OM. iChip-Inspired Isolation, Bioactivities and Dereplication of Actinomycetota from Portuguese Beach Sediments. Microorganisms 2022; 10:microorganisms10071471. [PMID: 35889190 PMCID: PMC9319460 DOI: 10.3390/microorganisms10071471] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/13/2022] [Accepted: 07/19/2022] [Indexed: 02/01/2023] Open
Abstract
Oceans hold a stunning number of unique microorganisms, which remain unstudied by culture-dependent methods due to failures in establishing the right conditions for these organisms to grow. In this work, an isolation effort inspired by the iChip was performed using marine sediments from Memoria beach, Portugal. The isolates obtained were identified by 16S rRNA gene analysis, fingerprinted using BOX-PCR and ERIC-PCR, searched for the putative presence of secondary metabolism genes associated with polyketide synthase I (PKS-I) and non-ribosomal peptide synthetases (NRPS), screened for antimicrobial activity against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 29213, and had bioactive extracts dereplicated by LC/HRMS. Of the 158 isolated strains, 96 were affiliated with the phylum Actinomycetota, PKS-I and NRPS genes were detected in 53 actinomycetotal strains, and 11 proved to be bioactive (10 against E. coli, 1 against S. aureus and 1 against both pathogens). Further bioactivities were explored using an “one strain many compounds” approach, with six strains showing continued bioactivity and one showing a novel one. Extract dereplication showed the presence of several known bioactive molecules and potential novel ones in the bioactive extracts. These results indicate the use of the bacteria isolated here as sources of new bioactive natural products.
Collapse
Affiliation(s)
- José Diogo Neves dos Santos
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal; (S.A.J.); (O.M.L.)
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
- Correspondence: ; Tel.: +351-910903938
| | - Susana Afonso João
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal; (S.A.J.); (O.M.L.)
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Granada, Spain; (J.M.); (F.V.); (F.R.)
| | - Francisca Vicente
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Granada, Spain; (J.M.); (F.V.); (F.R.)
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avenida del Conocimiento, 34 Parque Tecnológico de Ciencias de la Salud, 18016 Granada, Spain; (J.M.); (F.V.); (F.R.)
| | - Olga Maria Lage
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal; (S.A.J.); (O.M.L.)
- Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, 4450-208 Matosinhos, Portugal
| |
Collapse
|
14
|
Rhizospheric Actinomycetes Revealed Antifungal and Plant-Growth-Promoting Activities under Controlled Environment. PLANTS 2022; 11:plants11141872. [PMID: 35890505 PMCID: PMC9317816 DOI: 10.3390/plants11141872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 12/25/2022]
Abstract
Actinomycetes has large habitats and can be isolated from terrestrial soil, rhizospheres of plant roots, and marine sediments. Actinomycetes produce several bioactive secondary metabolites with antibacterial, antifungal, and antiviral properties. In this study, some Actinomycetes strains were isolated from the rhizosphere zone of four different plant species: rosemary, acacia, strawberry, and olive. The antagonistic activity of all isolates was screened in vitro against Escherichia coli and Bacillus megaterium. Isolates with the strongest bioactivity potential were selected and molecularly identified as Streptomyces sp., Streptomyces atratus, and Arthrobacter humicola. The growth-promoting activity of the selected Actinomycetes isolates was in vivo evaluated on tomato plants and for disease control against Sclerotinia sclerotiorum. The results demonstrated that all bacterized plants with the studied Actinomycetes isolates were able to promote the tomato seedlings’ growth, showing high values of ecophysiological parameters. In particular, the bacterized seedlings with Streptomyces sp. and A. humicola showed low disease incidence of S. sclerotiorum infection (0.3% and 0.2%, respectively), whereas those bacterized with S. atratus showed a moderate disease incidence (7.6%) compared with the positive control (36.8%). In addition, the ability of the studied Actinomycetes to produce extracellular hydrolytic enzymes was verified. The results showed that A. humicola was able to produce chitinase, glucanase, and protease, whereas Streptomyces sp. and S. atratus produced amylase and pectinase at high and moderate levels, respectively. This study highlights the value of the studied isolates in providing bioactive metabolites and extracellular hydrolytic enzymes, indicating their potential application as fungal-biocontrol agents.
Collapse
|
15
|
Alaidaroos BA. Rare Actinomycetes from Undiscovered Sources as a Source of Novel Antimicrobial Agents to Control Multidrug-Resistant Bacteria. INTERNATIONAL JOURNAL OF PHARMACEUTICAL RESEARCH AND ALLIED SCIENCES 2022. [DOI: 10.51847/dpfaj9fiep] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
16
|
Ferreira L, Morais J, Preto M, Silva R, Urbatzka R, Vasconcelos V, Reis M. Uncovering the Bioactive Potential of a Cyanobacterial Natural Products Library Aided by Untargeted Metabolomics. Mar Drugs 2021; 19:633. [PMID: 34822504 PMCID: PMC8624515 DOI: 10.3390/md19110633] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 01/18/2023] Open
Abstract
The Blue Biotechnology and Ecotoxicology Culture Collection (LEGE-CC) holds a vast number of cyanobacteria whose chemical richness is still largely unknown. To expedite its bioactivity screening we developed a natural products library. Sixty strains and four environmental samples were chromatographed, using a semiautomatic HPLC system, yielding 512 fractions that were tested for their cytotoxic activity against 2D and 3D models of human colon carcinoma (HCT 116), and non-cancerous cell line hCMEC/D3. Six fractions showed high cytotoxicity against 2D and 3D cell models (group A), and six other fractions were selected by their effects on 3D cells (group B). The metabolome of each group was organized and characterized using the MolNetEnhancer workflow, and its processing with MetaboAnalyst allowed discrimination of the mass features with the highest fold change, and thus the ones that might be bioactive. Of those, mass features without precedented identification were mostly found in group A, indicating seven possible novel bioactive molecules, alongside in silico putative annotation of five cytotoxic compounds. Manual dereplication of group B tentatively identified nine pheophytin and pheophorbide derivatives. Our approach enabled the selection of 7 out of 60 cyanobacterial strains for anticancer drug discovery, providing new data concerning the chemical composition of these cyanobacteria.
Collapse
Affiliation(s)
- Leonor Ferreira
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, University of Porto, 4450-208 Matosinhos, Portugal; (L.F.); (J.M.); (M.P.); (R.S.); (R.U.); (V.V.)
| | - João Morais
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, University of Porto, 4450-208 Matosinhos, Portugal; (L.F.); (J.M.); (M.P.); (R.S.); (R.U.); (V.V.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
| | - Marco Preto
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, University of Porto, 4450-208 Matosinhos, Portugal; (L.F.); (J.M.); (M.P.); (R.S.); (R.U.); (V.V.)
| | - Raquel Silva
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, University of Porto, 4450-208 Matosinhos, Portugal; (L.F.); (J.M.); (M.P.); (R.S.); (R.U.); (V.V.)
| | - Ralph Urbatzka
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, University of Porto, 4450-208 Matosinhos, Portugal; (L.F.); (J.M.); (M.P.); (R.S.); (R.U.); (V.V.)
| | - Vitor Vasconcelos
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, University of Porto, 4450-208 Matosinhos, Portugal; (L.F.); (J.M.); (M.P.); (R.S.); (R.U.); (V.V.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
| | - Mariana Reis
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, Terminal de Cruzeiros do Porto de Leixões, University of Porto, 4450-208 Matosinhos, Portugal; (L.F.); (J.M.); (M.P.); (R.S.); (R.U.); (V.V.)
| |
Collapse
|
17
|
Genome information of the cellulolytic soil actinobacterium Isoptericola dokdonensis DS-3 and comparative genomic analysis of the genus Isoptericola. J Microbiol 2021; 59:1010-1018. [PMID: 34724179 DOI: 10.1007/s12275-021-1452-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/15/2021] [Accepted: 09/15/2021] [Indexed: 10/20/2022]
Abstract
The actinobacterial group is regarded as a reservoir of biologically active natural products and hydrolytic enzymes with the potential for biomedical and industrial applications. Here, we present the complete genome sequence of Isoptericola dokdonensis DS-3 isolated from soil in Dokdo, small islets in the East Sea of Korea. This actinomycete harbors a large number of genes encoding carbohydrate-degrading enzymes, and its activity to degrade carboxymethyl cellulose into glucose was experimentally evaluated. Since the genus Isoptericola was proposed after reclassification based on phylogenetic analysis, strains of Isoptericola have been continuously isolated from diverse environments and the importance of this genus in the ecosystem has been suggested by recent culturomic or metagenomic studies. The phylogenic relationships of the genus tended to be closer among strains that had been isolated from similar habitats. By analyzing the properties of published genome sequences of seven defined species in the genus, a large number of genes for carbohydrate hydrolysis and utilization, as well as several biosynthetic gene clusters for secondary metabolites, were identified. Genomic information of I. dokdonensis DS-3 together with comparative analysis of the genomes of Isoptericola provides insights into understanding this actinobacterial group with a potential for industrial applications.
Collapse
|
18
|
Integrated mass spectrometry-based multi-omics for elucidating mechanisms of bacterial virulence. Biochem Soc Trans 2021; 49:1905-1926. [PMID: 34374408 DOI: 10.1042/bst20191088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 11/17/2022]
Abstract
Despite being considered the simplest form of life, bacteria remain enigmatic, particularly in light of pathogenesis and evolving antimicrobial resistance. After three decades of genomics, we remain some way from understanding these organisms, and a substantial proportion of genes remain functionally unknown. Methodological advances, principally mass spectrometry (MS), are paving the way for parallel analysis of the proteome, metabolome and lipidome. Each provides a global, complementary assay, in addition to genomics, and the ability to better comprehend how pathogens respond to changes in their internal (e.g. mutation) and external environments consistent with infection-like conditions. Such responses include accessing necessary nutrients for survival in a hostile environment where co-colonizing bacteria and normal flora are acclimated to the prevailing conditions. Multi-omics can be harnessed across temporal and spatial (sub-cellular) dimensions to understand adaptation at the molecular level. Gene deletion libraries, in conjunction with large-scale approaches and evolving bioinformatics integration, will greatly facilitate next-generation vaccines and antimicrobial interventions by highlighting novel targets and pathogen-specific pathways. MS is also central in phenotypic characterization of surface biomolecules such as lipid A, as well as aiding in the determination of protein interactions and complexes. There is increasing evidence that bacteria are capable of widespread post-translational modification, including phosphorylation, glycosylation and acetylation; with each contributing to virulence. This review focuses on the bacterial genotype to phenotype transition and surveys the recent literature showing how the genome can be validated at the proteome, metabolome and lipidome levels to provide an integrated view of organism response to host conditions.
Collapse
|
19
|
Al-shaibani MM, Radin Mohamed RMS, Sidik NM, Enshasy HAE, Al-Gheethi A, Noman E, Al-Mekhlafi NA, Zin NM. Biodiversity of Secondary Metabolites Compounds Isolated from Phylum Actinobacteria and Its Therapeutic Applications. Molecules 2021; 26:molecules26154504. [PMID: 34361657 PMCID: PMC8347454 DOI: 10.3390/molecules26154504] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 07/14/2021] [Accepted: 07/22/2021] [Indexed: 12/08/2022] Open
Abstract
The current review aims to summarise the biodiversity and biosynthesis of novel secondary metabolites compounds, of the phylum Actinobacteria and the diverse range of secondary metabolites produced that vary depending on its ecological environments they inhabit. Actinobacteria creates a wide range of bioactive substances that can be of great value to public health and the pharmaceutical industry. The literature analysis process for this review was conducted using the VOSviewer software tool to visualise the bibliometric networks of the most relevant databases from the Scopus database in the period between 2010 and 22 March 2021. Screening and exploring the available literature relating to the extreme environments and ecosystems that Actinobacteria inhabit aims to identify new strains of this major microorganism class, producing unique novel bioactive compounds. The knowledge gained from these studies is intended to encourage scientists in the natural product discovery field to identify and characterise novel strains containing various bioactive gene clusters with potential clinical applications. It is evident that Actinobacteria adapted to survive in extreme environments represent an important source of a wide range of bioactive compounds. Actinobacteria have a large number of secondary metabolite biosynthetic gene clusters. They can synthesise thousands of subordinate metabolites with different biological actions such as anti-bacterial, anti-parasitic, anti-fungal, anti-virus, anti-cancer and growth-promoting compounds. These are highly significant economically due to their potential applications in the food, nutrition and health industries and thus support our communities' well-being.
Collapse
Affiliation(s)
- Muhanna Mohammed Al-shaibani
- Micro-Pollutant Research Centre (MPRC), Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor, Malaysia;
- Center for Diagnostic, Therapeutic and Investigative Studies, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia;
| | - Radin Maya Saphira Radin Mohamed
- Micro-Pollutant Research Centre (MPRC), Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor, Malaysia;
- Correspondence: (R.M.S.R.M.); (N.M.S.); (A.A.-G.)
| | - Nik Marzuki Sidik
- Faculty of Agro-Based Industry, Universiti Malaysia Kelantan, Jeli 17600, Kelantan, Malaysia
- Correspondence: (R.M.S.R.M.); (N.M.S.); (A.A.-G.)
| | - Hesham Ali El Enshasy
- Institute of Bioproducts Development (IBD), Universiti Teknologi Malaysia (UTM), Skudai 81310, Johor, Malaysia;
- City of Scientific Research and Technology Applications (SRTA), 21934 New Burg Al Arab, Alexandria, Egypt
| | - Adel Al-Gheethi
- Micro-Pollutant Research Centre (MPRC), Faculty of Civil Engineering and Built Environment, Universiti Tun Hussein Onn Malaysia, Parit Raja 86400, Johor, Malaysia;
- Correspondence: (R.M.S.R.M.); (N.M.S.); (A.A.-G.)
| | - Efaq Noman
- Applied Microbiology Department, Faculty of Applied Sciences, Taiz University, Taiz 6803, Yemen;
| | - Nabil Ali Al-Mekhlafi
- Atta-ur-Rahman Institute for Natural Product Discovery, UiTM, Puncak Alam Campus, Bandar Puncak Alam 42300, Selangor, Malaysia;
- Biochemical Technology Program, Department of Chemistry Faculty of Applied Science, Thamar University, Thamar P.O. Box 87246, Yemen
| | - Noraziah Mohamad Zin
- Center for Diagnostic, Therapeutic and Investigative Studies, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia;
| |
Collapse
|
20
|
Goel N, Fatima SW, Kumar S, Sinha R, Khare SK. Antimicrobial resistance in biofilms: Exploring marine actinobacteria as a potential source of antibiotics and biofilm inhibitors. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 30:e00613. [PMID: 33996521 PMCID: PMC8105627 DOI: 10.1016/j.btre.2021.e00613] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/19/2021] [Accepted: 03/21/2021] [Indexed: 12/12/2022]
Abstract
Antimicrobial resistance (AMR) is one of the serious global public health threats that require immediate action. With the emergence of new resistance mechanisms in infection-causing microorganisms such as bacteria, fungi, and viruses, AMR threatens the effective prevention and treatment of diseases caused by them. This has resulted in prolonged illness, disability, and death. It has been predicted that AMR will lead to over ten million deaths by 2050. The rapid spread of multidrug-resistant bacteria is also causing old antibiotics to become ineffective. Among the diverse factors contributing to AMR, intrinsic biofilm development has been highlighted as an essential contributing facet. Moreover, biofilm-derived antibiotic tolerance leads to serious recurrent chronic infections. Therefore, the discovery of novel bioactive molecules is a potential solution that can help combat AMR. To achieve this, sustained mining of novel antimicrobial leads from actinobacteria, particularly marine actinobacteria, can be a promising strategy. Given their vast diversity and different habitats, the extraordinary capacity of actinobacteria can be tapped to synthesize new antibiotics or bioactive molecules for biofilm inhibition. Advanced screening strategies and novel approaches in the field of modern biochemical and molecular biology can be used to detect such new compounds. In view of this, the present review focuses on understanding some of the recent strategies to inhibit biofilm formation and explores the potential role of marine actinobacteria as sources of novel antibiotics and biofilm inhibitor molecules.
Collapse
Affiliation(s)
- Nikky Goel
- Department of Chemistry, Indian Institute of Technology Delhi, India
| | | | - Sumit Kumar
- Department of Chemistry, Indian Institute of Technology Delhi, India
| | | | - Sunil K. Khare
- Department of Chemistry, Indian Institute of Technology Delhi, India
| |
Collapse
|
21
|
An Analysis of Biosynthesis Gene Clusters and Bioactivity of Marine Bacterial Symbionts. Curr Microbiol 2021; 78:2522-2533. [PMID: 34041587 DOI: 10.1007/s00284-021-02535-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 05/05/2021] [Indexed: 01/28/2023]
Abstract
Symbiotic marine bacteria have a pivotal role in drug discovery due to the synthesis of diverse biologically potential compounds. The marine bacterial phyla proteobacteria, actinobacteria and firmicutes are commonly associated with marine macro organisms and frequently reported as dominant bioactive compound producers. They can produce biologically active compounds that possess antimicrobial, antiviral, antitumor, antibiofilm and antifouling properties. Synthesis of these bioactive compounds is controlled by a set of genes of their genomes that is known as biosynthesis gene clusters (BGCs). The development in the field of biotechnology and bioinformatics has uncovered the potential BGCs of the bacterial genome and its functions. Now-a-days researchers have focused their attention on the identification of potential BGCs for the discovery of novel bioactive compounds using advanced technology. This review highlights the marine bacterial symbionts and their BGCs which are responsible for the synthesis of bioactive compounds.
Collapse
|
22
|
Assad BM, Savi DC, Biscaia SMP, Mayrhofer BF, Iantas J, Mews M, de Oliveira JC, Trindade ES, Glienke C. Endophytic actinobacteria of Hymenachne amplexicaulis from the Brazilian Pantanal wetland produce compounds with antibacterial and antitumor activities. Microbiol Res 2021; 248:126768. [PMID: 33873141 DOI: 10.1016/j.micres.2021.126768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 02/28/2021] [Accepted: 04/03/2021] [Indexed: 12/24/2022]
Abstract
The increase in the number of deaths from infections caused by multidrug-resistant bacteria and cancer diseases highlights the need for new molecules with biological activity. Actinobacteria represent a potential source of new compounds, as these microorganisms have already produced a great diversity of clinically employed antibiotics. Endophytes from unexplored biomes, such as the Pantanal (the largest wetland in the world), can be a source of new molecules. Hymenachne amplexicaulis is among the unexplored native plants of the Pantanal in terms of its endophytic community. This plant is considered a weed in other countries due to its ability to adapt and compete with native plants, and there is evidence to suggest that the endophytic community of H. amplexicaulis plays an important role in this competitiveness. To explore its therapeutic potential, the present study isolated, identified (using partial sequence of the 16S rDNA) and bioprospected H. amplexicaulis endophytic actinobacteria. Ten isolates belonging to the genera Streptomyces, Microbispora, Leifsonia, and Verrucosispora were obtained from root fragments. The susceptibility profile of the isolates to the different classes of antibiotics was evaluated, with 80 % of the isolates showing resistance to the antibiotics Nalidixic Acid, Ampicillin, Chloramphenicol, Oxacillin, and Rifampicin. To assess antibacterial and antitumor activities, methanolic extracts were obtained by fermentation in SG culture medium at 36 °C at 180 rpm for 10 days. The extract produced from the S. albidoflavus CMRP4854 isolate was the only one to show activity against the Gram-negative bacterium Acinetobacter baumanii. Due to the great clinical importance of this pathogen and the difficulty in obtaining active compounds against it, the CMRP4854 isolate should be further investigated for the identification of active compounds and mode of action. We also emphasize the results obtained by the extract of the isolates Streptomyces albidoflavus CMRP4852 and Verrucosispora sp. CMRP4860 that presented antibacterial effect against Methicilin-resistant Staphylococcus aureus (MRSA) (MIC: 1.5 μg/mL and 13 μg/mL, respectively) and Vancomycin-resistant Enterococcus (VRE) (MIC: 40 μg/mL for both extracts). Extracts (200 μg/mL) of these two endophytes also showed selective cytotoxicity action against murine B16-F10 melanoma cells. However, the CMRP4852 extract also affected the density of normal cells. Due to these results, the crude extract of isolate CMRP4860 Verrucosispora sp., which was the only one that presented cytotoxicity and reduced cell density only in tumor cells, was selected for subsequent analysis involving scale-up fermentation of the CMRP4860 resulting in 9 fractions that were tested against both bacteria and tumor cells, with particular fractions showing promise and meriting further investigation. Taken together, the results of this study not only show for the first time that the endophytic community of H. amplexicaulis actinobacteria can produce secondary metabolites that potentially possess important antibacterial and cytotoxic properties, but also reinforce the pressing need to conserve biomes such as the Brazilian Pantanal.
Collapse
Affiliation(s)
- Beatriz M Assad
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990, Curitiba, Paraná State, Brazil
| | - Daiani C Savi
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990, Curitiba, Paraná State, Brazil; University Center - Católica de Santa Catarina, Joinville, SC, Brazil
| | - Stellee M P Biscaia
- Postgraduate Program in Cell and Molecular Biology, Department of Cellular Biology, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100. CEP, 81531-970, Curitiba, PR, Brazil
| | - Bárbara F Mayrhofer
- Postgraduate Program in Microbiology, Department of Pathology, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990, Curitiba, Paraná State, Brazil
| | - Jucelia Iantas
- Postgraduate Program in Microbiology, Department of Pathology, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990, Curitiba, Paraná State, Brazil
| | - Mathias Mews
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990, Curitiba, Paraná State, Brazil
| | - Jaqueline C de Oliveira
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990, Curitiba, Paraná State, Brazil
| | - Edvaldo S Trindade
- Postgraduate Program in Cell and Molecular Biology, Department of Cellular Biology, Federal University of Parana, Av. Coronel Francisco Heráclito dos Santos, 100. CEP, 81531-970, Curitiba, PR, Brazil
| | - Chirlei Glienke
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990, Curitiba, Paraná State, Brazil; Postgraduate Program in Microbiology, Department of Pathology, Federal University of Paraná (UFPR), Centro Politécnico, Jardim das Américas, 81531-990, Curitiba, Paraná State, Brazil.
| |
Collapse
|
23
|
Jose PA, Maharshi A, Jha B. Actinobacteria in natural products research: Progress and prospects. Microbiol Res 2021; 246:126708. [PMID: 33529791 DOI: 10.1016/j.micres.2021.126708] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/12/2021] [Accepted: 01/16/2021] [Indexed: 12/15/2022]
Abstract
Actinobacteria are well-recognised biosynthetic factories that produce an extensive spectrum of secondary metabolites. Recent genomic insights seem to impact the exploitation of these metabolically versatile bacteria in several aspects. Notably, from the isolation of novel taxa to the discovery of new compounds, different approaches evolve at a steady pace. Here, we systematically discuss the enduring importance of Actinobacteria in the field of drug discovery, the current focus of isolation efforts targeting bioactive Actinobacteria from diverse sources, recent discoveries of novel compounds with different bioactivities, and the relative employment of different strategies in the search for novel compounds. Ultimately, we highlight notable progress that will have profound impacts on future quests for secondary metabolites of Actinobacteria.
Collapse
Affiliation(s)
- Polpass Arul Jose
- Marine Biotechnology and Ecology Division, CSIR- Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India.
| | - Anjisha Maharshi
- Marine Biotechnology and Ecology Division, CSIR- Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India
| | - Bhavanath Jha
- Marine Biotechnology and Ecology Division, CSIR- Central Salt and Marine Chemicals Research Institute, G. B. Marg, Bhavnagar, Gujarat, 364002, India; Academy of Scientific and Innovative Research (AcSIR), CSIR, India.
| |
Collapse
|
24
|
Karim MRU, Harunari E, Sharma AR, Oku N, Akasaka K, Urabe D, Sibero MT, Igarashi Y. Nocarimidazoles C and D, antimicrobial alkanoylimidazoles from a coral-derived actinomycete Kocuria sp.: application of 1 J C,H coupling constants for the unequivocal determination of substituted imidazoles and stereochemical diversity of anteisoalkyl chains in microbial metabolites. Beilstein J Org Chem 2020; 16:2719-2727. [PMID: 33214797 PMCID: PMC7653330 DOI: 10.3762/bjoc.16.222] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/20/2020] [Indexed: 11/23/2022] Open
Abstract
Chemical investigation of secondary metabolites from a marine-derived actinomycete strain of the genus Kocuria, isolated from a stony coral Mycedium sp., led to the identification of two new alkanoylimidazoles, nocarimidazoles C (1) and D (2) as well as three known congeners, nocarimidazoles A (3) and B (4) and bulbimidazole A (5). Structure analysis of 1 and 2 by NMR and MS revealed that both are 4-alkanoyl-5-aminoimidazoles with a 6-methyloctanoyl or decanoyl chain, respectively. Two possible positions of the amino group on the imidazole rings (C-2 and C-5) posed a challenge in the structure study, which was settled by the measurement of 1JC,H coupling constants for comparison with those of synthetically prepared model imidazoles. The absolute configurations of the anteisoalkanoyl group present in 1, 4, and 5 were determined by low-temperature HPLC analysis of the degradation products labeled with a chiral anthracene reagent, which revealed that 1 is a mixture of the R- and S-enantiomers with a ratio of 73:27, 4 is the pure (S)-enantiomer, and 5 is the (S)-enantiomer with 98% ee. The present study illustrates the diversity in the stereochemistry of anteiso branching in bacterial metabolites. Compounds 1−4 were moderately antimicrobial against Gram-positive bacteria and fungi, with MIC ranges of 6.25–25 μg/mL.
Collapse
Affiliation(s)
- Md Rokon Ul Karim
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Enjuro Harunari
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Amit Raj Sharma
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Naoya Oku
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Kazuaki Akasaka
- Shokei Gakuin University, 4-10-1 Yurigaoka, Natori, Miyagi 981-1295, Japan
| | - Daisuke Urabe
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| | - Mada Triandala Sibero
- Department of Marine Science, Faculty of Fisheries and Marine Science, Diponegoro University, Semarang, Central Java 50275, Indonesia
| | - Yasuhiro Igarashi
- Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan
| |
Collapse
|
25
|
Diversity and Bioactive Potential of Actinobacteria Isolated from a Coastal Marine Sediment in Northern Portugal. Microorganisms 2020; 8:microorganisms8111691. [PMID: 33143202 PMCID: PMC7692593 DOI: 10.3390/microorganisms8111691] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/20/2020] [Accepted: 10/27/2020] [Indexed: 12/22/2022] Open
Abstract
Natural compounds have had increasing applications in the biotechnological sector, with a large fraction of these substances being channeled to the pharmaceutical industry due to their important pharmacological properties. The discovery of new bioactive molecules with novel mechanisms of action constitutes a promising solution for the design of alternative therapeutic solutions. Actinobacteria are a large group of morphologically and physiologically diverse bacteria well known for their production of biotechnologically relevant compounds. The Portuguese coast is scantly explored in terms of Actinobacteria diversity and respective bioactive potential, offering a good opportunity to find new Actinobacteria taxa and bioactive natural products. In this study, we investigated the Actinobacteria diversity associated with a sediment sample collected from the intertidal zone of a beach in northern Portugal, through a cultivation-dependent approach, and screened its antimicrobial and cytotoxic potential. A total of 52 Actinobacteria strains were recovered from the marine sediment, with the largest fraction of the isolates belonging to the genus Micromonospora. Bioactivity screening assays identified crude extracts of six Streptomyces strains active against C. albicans, exhibiting minimum inhibition concentration (MIC) values in the range of 3.90-125 μg mL-1. Twenty-five Actinobacteria crude extracts (obtained from strains of the genera Micromonospora, Streptomyces and Actinomadura) exhibited significant effects on the viability of at least one tested cancer cell line (breast ductal carcinoma T-47D and liver hepatocellular carcinoma HepG2). The Actinobacteria extracts demonstrating activity in the antimicrobial and/or cytotoxic assays were subjected to metabolomic analysis (Mass spectrometry (MS)-based dereplication and molecular networking analyses), indicating the presence of four clusters that may represent new natural products. The results obtained demonstrate the importance of bioprospecting underexplored environments, like the Portuguese coast, for enhancing the discovery of new natural products, and call attention to the relevance of preserving the natural genetic diversity of coastal environments.
Collapse
|
26
|
Bioactive metabolites produced from Streptomyces enissocaesilis SSASC10 against fish pathogens. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
27
|
Silva LJ, Crevelin EJ, Souza DT, Lacerda-Júnior GV, de Oliveira VM, Ruiz ALTG, Rosa LH, Moraes LAB, Melo IS. Actinobacteria from Antarctica as a source for anticancer discovery. Sci Rep 2020; 10:13870. [PMID: 32807803 PMCID: PMC7431910 DOI: 10.1038/s41598-020-69786-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 07/03/2020] [Indexed: 01/09/2023] Open
Abstract
Although many advances have been achieved to treat aggressive tumours, cancer remains a leading cause of death and a public health problem worldwide. Among the main approaches for the discovery of new bioactive agents, the prospect of microbial secondary metabolites represents an effective source for the development of drug leads. In this study, we investigated the actinobacterial diversity associated with an endemic Antarctic species, Deschampsia antarctica, by integrated culture-dependent and culture-independent methods and acknowledged this niche as a reservoir of bioactive strains for the production of antitumour compounds. The 16S rRNA-based analysis showed the predominance of the Actinomycetales order, a well-known group of bioactive metabolite producers belonging to the Actinobacteria phylum. Cultivation techniques were applied, and 72 psychrotolerant Actinobacteria strains belonging to the genera Actinoplanes, Arthrobacter, Kribbella, Mycobacterium, Nocardia, Pilimelia, Pseudarthrobacter, Rhodococcus, Streptacidiphilus, Streptomyces and Tsukamurella were identified. The secondary metabolites were screened, and 17 isolates were identified as promising antitumour compound producers. However, the bio-guided assay showed a pronounced antiproliferative activity for the crude extracts of Streptomyces sp. CMAA 1527 and Streptomyces sp. CMAA 1653. The TGI and LC50 values revealed the potential of these natural products to control the proliferation of breast (MCF-7), glioblastoma (U251), lung/non-small (NCI-H460) and kidney (786-0) human cancer cell lines. Cinerubin B and actinomycin V were the predominant compounds identified in Streptomyces sp. CMAA 1527 and Streptomyces sp. CMAA 1653, respectively. Our results suggest that the rhizosphere of D. antarctica represents a prominent reservoir of bioactive actinobacteria strains and reveals it as an important environment for potential antitumour agents.
Collapse
Affiliation(s)
- Leonardo Jose Silva
- College of Agriculture "Luiz de Queiroz", University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Eduardo José Crevelin
- Laboratory of Mass Spectrometry Applied To Natural Products Chemistry, Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP), University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Danilo Tosta Souza
- Laboratory of Mass Spectrometry Applied To Natural Products Chemistry, Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP), University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Gileno Vieira Lacerda-Júnior
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation (EMBRAPA) - Embrapa Environment, Jaguariúna, SP, Brazil
| | - Valeria Maia de Oliveira
- Microbial Resourses Division, Research Center for Chemistry, Biology and Agriculture (CPQBA), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | | | - Luiz Henrique Rosa
- Department of Microbiology, Biological Sciences Institute - Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Luiz Alberto Beraldo Moraes
- Laboratory of Mass Spectrometry Applied To Natural Products Chemistry, Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP), University of São Paulo (USP), Ribeirão Preto, SP, Brazil
| | - Itamar Soares Melo
- Laboratory of Environmental Microbiology, Brazilian Agricultural Research Corporation (EMBRAPA) - Embrapa Environment, Jaguariúna, SP, Brazil.
| |
Collapse
|
28
|
Axenov-Gribanov DV, Kostka DV, Vasilieva UА, Shatilina ZM, Krasnova ME, Pereliaeva EV, Zolotovskaya ED, Morgunova MM, Rusanovskaya OO, Timofeyev MA. Cultivable Actinobacteria First Found in Baikal Endemic Algae Is a New Source of Natural Products with Antibiotic Activity. Int J Microbiol 2020; 2020:5359816. [PMID: 32802070 PMCID: PMC7403937 DOI: 10.1155/2020/5359816] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/02/2020] [Indexed: 02/08/2023] Open
Abstract
Inadequate use of antibiotics has led to spread of microorganisms resistant to effective antimicrobial compounds for humans and animals. This study was aimed to isolate cultivable strains of actinobacteria associated with Baikal endemic alga Draparnaldioides baicalensis and estimate their antibiotic properties. During this study, we isolated both widespread and dominant strains related to the genus Streptomyces and representatives of the genera Saccharopolyspora, Nonomuraea, Rhodococcus, and Micromonospora. For the first time, actinobacteria belonging to the genera Nonomuraea and Saccharopolyspora were isolated from Baikal ecosystem. Also, it was the first time when actinobacteria of the genus Nonomuraea were isolated from freshwater algae. Some rare strains demonstrated activity inhibiting growth of bacteria and yeasts. Also, it has been shown that the strains associated with Baikal alga D. baicalensis are active against both Gram-positive and Gram-negative bacteria. According to this study and previously published materials, diversity of cultivable actinobacteria and rare strains isolated from D. baicalensis is comparable to that of cultivable actinobacteria previously isolated from plant sources of Lake Baikal. Also, it exceeds the cultivable actinobacteria diversity previously described for macroinvertebrates, water, or sediments of Lake Baikal. The large number of rare and active strains associated with the endemic alga D. baicalensis could be the promising sources for biopharmaceutical and biotechnological developments and discovery of new natural compounds.
Collapse
Affiliation(s)
| | - Daria V. Kostka
- Irkutsk State University, Karl Marx St. 1, 664003 Irkutsk, Russia
- Irkutsk Regional Clinical Advisory and Diagnostic Center, Baykalskaya Str., 109 Irkutsk, Russia
| | - Ulyana А. Vasilieva
- Irkutsk State University, Karl Marx St. 1, 664003 Irkutsk, Russia
- Siberian Institute of Plant Physiology and Biochemistry, 132 Lermontov Str., 664033 Irkutsk, Russia
| | | | | | | | | | | | | | - Maxim A. Timofeyev
- Irkutsk State University, Karl Marx St. 1, 664003 Irkutsk, Russia
- Baikal Research Centre, Lenin Str. 21, 664003 Irkutsk, Russia
| |
Collapse
|
29
|
Shi Y, Xu J, Ding B, Chen G, Jin L, Ke L, Xu X, Wang J, Sun Q, Xu X. Gastrointestinal Motility and Improvement Efficacy of Shenhuang Plaster Application on Shenque: Identification, Evaluation, and Mechanism. J Immunol Res 2020; 2020:2383970. [PMID: 32733972 PMCID: PMC7369653 DOI: 10.1155/2020/2383970] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/09/2020] [Indexed: 12/22/2022] Open
Abstract
Constipation, a gastrointestinal function disorder, is one of the side effects of paclitaxel (PTX) chemotherapy. Shenhuang plaster (SHP) application on the Shenque acupoint promotes gut motility in clinical settings. In this study, we elucidated the ingredients in SHP and evaluated its effects on PTX-induced constipation using a tumour-bearing mouse model. SHP was prepared using the traditional Chinese plaster preparation method. The ingredients were analysed using UPLC-MS/MS and identified via screening in a standard drug database. The gastrointestinal transit was evaluated by the movement of a fluorescein-labelled dextran in the gastrointestinal tract. A histological study of the mucosa was carried out after haematoxylin and eosin staining. mRNA expression was assessed using real-time RT-PCR, and the foetal microbiota composition was elucidated through 16 s rDNA sequencing and BLAST analysis. Our results indicate that the application of SHP attenuated weight gain inhibition by PTX; however, no inhibitory effect was observed on tumour growth. PTX-induced sluggish intestine, villus, and mucosal base layer damage were significantly improved following the application of SHP. Further, SHP enhanced the stimulation efficiency of PTX on TLR4 and its downstream cytokines, as well as on IL-1β in intestinal cells. SHP combined with PTX reshaped the microbiota, which showed beneficial effects on health. Hence, these results provide evidence that SHP alleviates PTX-induced constipation and intestinal morphological damage but augments the effects of PTX on the expression of cytokines in the TLR4 pathway and IL-1β. Therefore, we propose that SHP stimulates the host immune response to eradicate cancer cells.
Collapse
Affiliation(s)
- Yanan Shi
- The College of Nursing, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Jingming Xu
- The First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Bin Ding
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Guiping Chen
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310018, China
| | - Lu Jin
- School of Second Clinical Medical, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Liang Ke
- The First Affiliated Hospital of Nanchang University, Nanchang 830052, China
| | - Xiao Xu
- The College of Nursing, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - JingXia Wang
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310018, China
| | - Qiuhua Sun
- The College of Nursing, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xiaohong Xu
- The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou 310018, China
| |
Collapse
|
30
|
Ye Y, Anwar N, Mao X, Wu S, Yan C, Zhao Z, Zhang R, Nie Y, Zhang J, Wang J, Wu M. Discovery of Three 22-Membered Macrolides by Deciphering the Streamlined Genome of Mangrove-Derived Streptomyces sp. HM190. Front Microbiol 2020; 11:1464. [PMID: 32676068 PMCID: PMC7333363 DOI: 10.3389/fmicb.2020.01464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/04/2020] [Indexed: 11/13/2022] Open
Abstract
Strain HM190, a moderate halophile, was isolated from rhizosphere soil of the mangrove Kandelia obovata in Fugong village, China. The 16S ribosomal RNA (rRNA) gene sequence and the results of phylogenetic analysis revealed that strain HM190 belonged to the genus Streptomyces and had the highest sequence similarity of 99.79% to Streptomyces heilongjiangensis NEAU-W2T. The complete genome of strain HM190 comprised 7,762,826 bp in a linear chromosome with 71.97% G + C content. According to antiSMASH analysis, a total of 30 biosynthetic gene clusters (BGCs) were predicted to be involved in secondary metabolism, 12 of which were responsible for the production of polyketide- and non-ribosomal peptide-derived secondary metabolites. Gene cluster 5 was responsible for macrolide biosynthesis in a strain-specific 126,331-bp genomic island belonging to the left-arm region. Combined genomics–metabolomics analysis led to the discovery of three 22-membered macrolides (compounds 1–3). Their structures were elucidated by using spectroscopic techniques including high-resolution electrospray ionization mass spectroscopy (HRESIMS) and nuclear magnetic resonance (NMR). The absolute configurations of compounds 1–3 were determined by the X-ray single crystal diffraction and NMR data analysis. All three compounds displayed moderate cytotoxic activities toward tumor cell lines HepG2, A549, and HCT116.
Collapse
Affiliation(s)
- Yanghui Ye
- Ocean College, Zhejiang University, Hangzhou, China
| | - Nusratgul Anwar
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xuming Mao
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shihua Wu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Cen Yan
- Ocean College, Zhejiang University, Hangzhou, China
| | - Zhe Zhao
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ran Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yanfang Nie
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jianwei Zhang
- Cardiovascular Health Department, AstraZeneca Trading Co., Ltd., Wuxi, China
| | - Jidong Wang
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou, China
| | - Min Wu
- Ocean College, Zhejiang University, Hangzhou, China
| |
Collapse
|
31
|
Isolation and Characterization of a New Endophytic Actinobacterium Streptomyces californicus Strain ADR1 as a Promising Source of Anti-Bacterial, Anti-Biofilm and Antioxidant Metabolites. Microorganisms 2020; 8:microorganisms8060929. [PMID: 32575628 PMCID: PMC7355773 DOI: 10.3390/microorganisms8060929] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/01/2020] [Accepted: 06/05/2020] [Indexed: 11/29/2022] Open
Abstract
In view of the fast depleting armamentarium of drugs against significant pathogens, like methicillin-resistant Staphylococcus aureus (MRSA) and others due to rapidly emerging drug-resistance, the discovery and development of new drugs need urgent action. In this endeavor, a new strain of endophytic actinobacterium was isolated from the plant Datura metel, which produced secondary metabolites with potent anti-infective activities. The isolate was identified as Streptomyces californicus strain ADR1 based on 16S rRNA gene sequence analysis. Metabolites produced by the isolate had been investigated for their antibacterial attributes against important pathogens: S. aureus, MRSA, S. epidermis, Enterococcus faecium and E. faecalis. Minimum inhibitory concentration (MIC90) values against these pathogens varied from 0.23 ± 0.01 to 5.68 ± 0.20 μg/mL. The metabolites inhibited biofilm formation by the strains of S. aureus and MRSA (Biofilm inhibitory concentration [BIC90] values: 0.74 ± 0.08–4.92 ± 0.49 μg/mL). The BIC90 values increased in the case of pre-formed biofilms. Additionally, the metabolites possessed good antioxidant properties, with an inhibitory concentration (IC90) value of 217.24 ± 6.77 µg/mL for 1, 1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging. An insight into different classes of compounds produced by the strain ADR1 was obtained by chemical profiling and GC-MS analysis, wherein several therapeutic classes, for example, alkaloids, phenolics, terpenes, terpenoids and glycosides, were discovered.
Collapse
|
32
|
Zheng X, Sun X, Liu Q, Huang Y, Yuan Y. The Composition Alteration of Respiratory Microbiota in Lung Cancer. Cancer Invest 2020; 38:158-168. [PMID: 32073913 DOI: 10.1080/07357907.2020.1732405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Background: Previous studies have reported mixed results regarding the composition of respiratory microbiota in lung cancer patients. Therefore, relying on previously published studies, we sought to estimate the relative proportion of respiratory microbiota between lung cancer cases and controls.Methods: MEDLINE, Embase, The Cochrane Library, and Web of Science online databases were systematically searched from inception up to October 14, 2019, to retrieve relevant studies. The relative abundance of each predominant taxon of respiratory microbiota in lung cancer patients and controls was pooled using the reported outcome data.Results: A total of 8 studies comprising 530 participants were included in the final analysis. The pooled phylum level analysis revealed that Bacteroidetes and Proteobacteria were the most abundant bacterial phyla among all participants, recording 17.5%, 47.5% in lung cancer patients, 28.2%, 39.27% in patients with benign pulmonary diseases and 40.62%, 32.09% in healthy controls, respectively. In addition, Actinobacteria and Firmicutes phyla were abundant in lung cancer cases compared to other groups (14.8%, 17.62% for lung cancer versus 13.04%, 13.16% for benign pulmonary nodules and 12.43%, 12.45% for healthy controls). At genus level, Prevotella was predominant in all the participants, and its proportion was relatively lower in cancer patients (25.74% for lung cancer versus 35.59% and 36.75% for benign pulmonary nodules and healthy controls, respectively). Comparatively, Streptococcus was more abundant in lung cancer cases (9.65% in lung cancer versus 7.98%, 7.26% in benign pulmonary nodules and healthy controls).Conclusions: The respiratory microbiota composition of respiratory microbiota significantly differs between lung cancer patients and healthy individuals, and may be used as potential biomarker of lung cancer. In addition, larger sample size, standardized procedures, dynamic monitoring, metabolomics, and culturomics are needed to confirm these results.
Collapse
Affiliation(s)
- Xi Zheng
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaochi Sun
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Qinye Liu
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Yue Huang
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Yong Yuan
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
33
|
Soumare A, Boubekri K, Lyamlouli K, Hafidi M, Ouhdouch Y, Kouisni L. From Isolation of Phosphate Solubilizing Microbes to Their Formulation and Use as Biofertilizers: Status and Needs. Front Bioeng Biotechnol 2020; 7:425. [PMID: 31998701 PMCID: PMC6962098 DOI: 10.3389/fbioe.2019.00425] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 12/02/2019] [Indexed: 11/13/2022] Open
Abstract
The production of biofertilizers at industrial level is a bottleneck because bacterial strains are generally developed and managed by research laboratories and not by production units. A seamless transition from laboratory to field application is, therefore necessary. This review provides an overview of the constraints that limiting the application or the implementation of Actinobacteria based biofertilizers especially in agricultural field and suggests solutions to overcome some of these limits. General processes of making and controlling the quality of the inoculum are briefly described. In addition, the paper underlines the opportunity of biofertilizers alone or in combination with chemical fertilizers. This review also, highlights the latest studies (until June 2019) and focuses on P-solubilization microorganisms mainly Actinobacteria. The biotechnology of these bacteria is a glimmer of hope for rock phosphate (RP) bioformulation. Since direct application of RP fertilizer is not always agronomically effective due to its sparse solubility.
Collapse
Affiliation(s)
- Abdoulaye Soumare
- AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco.,Université Cheikh Anta Diop, Laboratoire Commun de Microbiologie IRD/ISRA/UCAD, Centre de Recherche de Bel Air, Dakar, Senegal
| | - Kenza Boubekri
- AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco.,Faculté des Sciences Semlalia, Université Cadi Ayyad, Laboratoire of Microbial Biotechnologies, Agrosciences and Environment, Marrakesh, Morocco
| | - Karim Lyamlouli
- AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco
| | - Mohamed Hafidi
- AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco.,Faculté des Sciences Semlalia, Université Cadi Ayyad, Laboratoire of Microbial Biotechnologies, Agrosciences and Environment, Marrakesh, Morocco
| | - Yedir Ouhdouch
- AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco.,Faculté des Sciences Semlalia, Université Cadi Ayyad, Laboratoire of Microbial Biotechnologies, Agrosciences and Environment, Marrakesh, Morocco
| | - Lamfeddal Kouisni
- AgroBioSciences Program, Mohammed VI Polytechnic University (UM6P), Benguerir, Morocco
| |
Collapse
|
34
|
Comparative Genomic Insights into Secondary Metabolism Biosynthetic Gene Cluster Distributions of Marine Streptomyces. Mar Drugs 2019; 17:md17090498. [PMID: 31454987 PMCID: PMC6780079 DOI: 10.3390/md17090498] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/19/2019] [Accepted: 08/21/2019] [Indexed: 12/21/2022] Open
Abstract
Bacterial secondary metabolites have huge application potential in multiple industries. Biosynthesis of bacterial secondary metabolites are commonly encoded in a set of genes that are organized in the secondary metabolism biosynthetic gene clusters (SMBGCs). The development of genome sequencing technology facilitates mining bacterial SMBGCs. Marine Streptomyces is a valuable resource of bacterial secondary metabolites. In this study, 87 marine Streptomyces genomes were obtained and carried out into comparative genomic analysis, which revealed their high genetic diversity due to pan-genomes owning 123,302 orthologous clusters. Phylogenomic analysis indicated that the majority of Marine Streptomyces were classified into three clades named Clade I, II, and III, containing 23, 38, and 22 strains, respectively. Genomic annotations revealed that SMBGCs in the genomes of marine Streptomyces ranged from 16 to 84. Statistical analysis pointed out that phylotypes and ecotypes were both associated with SMBGCs distribution patterns. The Clade I and marine sediment-derived Streptomyces harbored more specific SMBGCs, which consisted of several common ones; whereas the Clade II and marine invertebrate-derived Streptomyces have more SMBGCs, acting as more plentiful resources for mining secondary metabolites. This study is beneficial for broadening our knowledge about SMBGC distribution patterns in marine Streptomyces and developing their secondary metabolites in the future.
Collapse
|
35
|
Qi D, Zou L, Zhou D, Chen Y, Gao Z, Feng R, Zhang M, Li K, Xie J, Wang W. Taxonomy and Broad-Spectrum Antifungal Activity of Streptomyces sp. SCA3-4 Isolated From Rhizosphere Soil of Opuntia stricta. Front Microbiol 2019; 10:1390. [PMID: 31316480 PMCID: PMC6609889 DOI: 10.3389/fmicb.2019.01390] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 06/03/2019] [Indexed: 11/13/2022] Open
Abstract
Actinobacteria are important producers of bioactive compounds. Extreme ecosystems cause evolution of novel secondary metabolic pathways of Actinobacteria and increase the possible discovery of new biological functions of bioactive compounds. Here, we isolated 65 Actinobacteria from rhizosphere soil samples of Opuntia stricta. An Actinobacteria strain (named SCA3-4) was screened against Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4, ATCC 76255). The strain produced pink-white aerial mycelia and brown substrate mycelium on Gause No. 1 agar. Biverticillate chains of cylindrical spores were observed by scanning electron microscopy (SEM). Based on alignment of 16S rRNA sequences, a constructed phylogenetic tree showed that strain SCA3-4 shared a 99.54% similarity with Streptomyces lilacinus NRRL B-1968T. The morphological, biochemical, physiological, and molecular characteristics further indicated that strain SCA3-4 belongs to the Streptomyces sp. It can grow well on medium with the following antibiotics chloramphenicol, streptomycin, penicillin-G, gentamicin, erythromycin, nystatin or neomycin sulfate. The polymerase chain reaction (PCR) amplification of types I and II polyketide synthase genes (PKS-I and PKS-II) suggested its bioactive potential. Under treatment with 100 μg/ml of ethyl acetate extracts isolated from Streptomyces sp. SCA3-4, growth of Foc TR4 was inhibited and cell membrane was destroyed. Crude extracts also showed a broad-spectrum antifungal activity against 13 phytopathogenic fungi including Foc TR4 and displayed the lowest minimum inhibitory concentration (MIC) (0.781 μg/ml) against Colletotrichum fragariae (ATCC 58718). A total of 21 different compounds identified by gas chromatography-mass spectrometry (GC-MS) were composed of phenolic compound, pyrrolizidine, hydrocarbons, esters, and acids. Besides the known active compounds, Streptomyces sp. SCA3-4 possesses antimicrobial or other biological activities. Further attention will be paid on other compounds with no functional annotation, aiming at the discovery of new bioactive substances.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Jianghui Xie
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Wei Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| |
Collapse
|