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Ramesh C, Anwesh M, Alessia T, Giuffrida D, La Tella R, Chiaia V, Mondello L, Anil K, Le Loarer A, Gauvin-Bialecki A, Fouillaud M, Dufossé L. Genome and Compound Analysis of Sioxanthin-Producing Marine Actinobacterium Micromonospora sp. nov. Strain SH-82 Isolated from Sponge Scopalina hapalia. Curr Microbiol 2024; 81:298. [PMID: 39107520 DOI: 10.1007/s00284-024-03812-8] [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: 04/15/2024] [Accepted: 07/19/2024] [Indexed: 08/15/2024]
Abstract
Pigments and other secondary metabolites originating from marine microbes have been a promising natural colorants and drugs for multifaceted applications. However, marine actinobacteria producing such natural molecules are least investigated in terms of their taxonomy, chemical diversity and applications in biomedical, textile, and food industries. In this study, sioxanthin pigment-producing Gram-positive actinobacteria, Micromonospora sp. strain SH-82 was isolated from a marine sponge, Scopalina hapalia, and its whole genome was analyzed. Strain SH-82is a prolific producer of diverse chemical molecules as it produced more compounds on A1 medium with different culture conditions. The genome size of SH-82 is 6.24 Mb (6,246,890 bp) carrying 23 identified biosynthetic gene clusters. A total of 5415 CDS, 60 tRNA, 9 rRNA, and 1 tmRNA are identified from SH-82 genome. The GC content (%) of whole genome was 71.6%. Strain SH-82 harbors genes encoding type I, type II, and type III polyketide synthases. Based on the multi-locus sequence analysis and fatty acid methyl ester (FAME) composition, strain SH-82 is confirmed as a novel species. The genetic information of Micromonospora sp. SH-82 has been deposited to NCBI under the BioProject ID PRJNA1087320, with corresponding identifiers in the Sequence Read Archive (SRA) as SAMN40439676 and the Genome accession as CP148049.
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Affiliation(s)
- Chatragadda Ramesh
- Biological Oceanography Division (BOD), National Institute of Oceanography (CSIR-NIO), Dona Paula, Panaji, Goa, 403004, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
| | - Maile Anwesh
- DBT-Centre for Microbial Informatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, Telangana, 500046, India.
| | - Tropea Alessia
- Messina Institute of Technology c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Former Veterinary School, University of Messina, Viale G. Palatucci snc, 98168, Messina, Italy.
| | - Daniele Giuffrida
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences, University of Messina, Via Consolare Valeria, 98125, Messina, Italy
| | - Roberta La Tella
- Messina Institute of Technology c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Former Veterinary School, University of Messina, Viale G. Palatucci snc, 98168, Messina, Italy
| | - Valentina Chiaia
- Messina Institute of Technology c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Former Veterinary School, University of Messina, Viale G. Palatucci snc, 98168, Messina, Italy
| | - Luigi Mondello
- Messina Institute of Technology c/o Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Former Veterinary School, University of Messina, Viale G. Palatucci snc, 98168, Messina, Italy
- Chromaleont S.R.L., Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, Former Veterinary School, University of Messina, Viale G. Palatucci snc, 98168, Messina, Italy
| | - Kanakam Anil
- Biological Oceanography Division (BOD), National Institute of Oceanography (CSIR-NIO), Dona Paula, Panaji, Goa, 403004, India
| | - Alexandre Le Loarer
- Chemistry and Biotechnology of Natural Products, CHEMBIOPRO, Université de La Réunion, Faculté des Sciences et Technologies, 15 Avenue René Cassin, 97744, Saint-Denis CEDEX 9, France
| | - Anne Gauvin-Bialecki
- Chemistry and Biotechnology of Natural Products, CHEMBIOPRO, Université de La Réunion, Faculté des Sciences et Technologies, 15 Avenue René Cassin, 97744, Saint-Denis CEDEX 9, France
| | - Mireille Fouillaud
- Chemistry and Biotechnology of Natural Products, CHEMBIOPRO, Université de La Réunion, Faculté des Sciences et Technologies, 15 Avenue René Cassin, 97744, Saint-Denis CEDEX 9, France
| | - Laurent Dufossé
- Chemistry and Biotechnology of Natural Products, CHEMBIOPRO, Université de La Réunion, Faculté des Sciences et Technologies, 15 Avenue René Cassin, 97744, Saint-Denis CEDEX 9, France.
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Tuytschaevers S, Aden L, Greene Z, Nixon C, Shaw W, Hatch D, Kumar G, Miranda RR, Hudson AO. Isolation, whole-genome sequencing, and annotation of two antibiotic-producing and antibiotic-resistant bacteria, Pantoea rodasii RIT 836 and Pseudomonas endophytica RIT 838, collected from the environment. PLoS One 2024; 19:e0293943. [PMID: 38412159 PMCID: PMC10898753 DOI: 10.1371/journal.pone.0293943] [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: 06/21/2023] [Accepted: 10/22/2023] [Indexed: 02/29/2024] Open
Abstract
Antimicrobial resistance (AMR) is a global threat to human health since infections caused by antimicrobial-resistant bacteria are life-threatening conditions with minimal treatment options. Bacteria become resistant when they develop the ability to overcome the compounds that are meant to kill them, i.e., antibiotics. The increasing number of resistant pathogens worldwide is contrasted by the slow progress in the discovery and production of new antibiotics. About 700,000 global deaths per year are estimated as a result of drug-resistant infections, which could escalate to nearly 10 million by 2050 if we fail to address the AMR challenge. In this study, we collected and isolated bacteria from the environment to screen for antibiotic resistance. We identified several bacteria that showed resistance to multiple clinically relevant antibiotics when tested in antibiotic susceptibility disk assays. We also found that two strains, identified as Pantoea rodasii RIT 836 and Pseudomonas endophytica RIT 838 via whole genome sequencing and annotation, produce bactericidal compounds against both Gram-positive and Gram-negative bacteria in disc-diffusion inhibitory assays. We mined the two strains' whole-genome sequences to gain more information and insights into the antibiotic resistance and production by these bacteria. Subsequently, we aim to isolate, identify, and further characterize the novel antibiotic compounds detected in our assays and bioinformatics analysis.
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Affiliation(s)
- Serena Tuytschaevers
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, United States of America
| | - Leila Aden
- Rochester Prep High School, Rochester, New York, United States of America
| | - Zacchaeus Greene
- Rochester Prep High School, Rochester, New York, United States of America
| | - Chanei Nixon
- Rochester Prep High School, Rochester, New York, United States of America
| | - Wade Shaw
- Rochester Prep High School, Rochester, New York, United States of America
| | - Dillan Hatch
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, United States of America
| | - Girish Kumar
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, United States of America
| | - Renata Rezende Miranda
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York, United States of America
| | - André O. Hudson
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, United States of America
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Sun C, Ha Y, Liu X, Wang N, Lian XY, Zhang Z. Isolation and Structure Elucidation of New Metabolites from the Mariana-Trench-Associated Fungus Aspergillus sp. SY2601. Molecules 2024; 29:459. [PMID: 38257372 PMCID: PMC10819015 DOI: 10.3390/molecules29020459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/07/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
Fungi are important resource for the discovery of novel bioactive natural products. This study investigated the metabolites produced by Mariana-Trench-associated fungus Aspergillus sp. SY2601 in EY liquid and rice solid media, resulting in the isolation and structure determination of 28 metabolites, including five new compounds, asperindopiperazines A-C (1-3), 5-methoxy-8,9-dihydroxy-8,9-deoxyaspyrone (21), and 12S-aspertetranone D (26). Structures of the new compounds were elucidated based on extensive NMR spectral analyses, HRESIMS data, optical rotation, ECD, and 13C NMR calculations. The new compound 12S-aspertetranone D (26) exhibited antibacterial activity against both methicillin-resistant Staphylococcus aureus and Escherichia coli with MIC values of 3.75 and 5 μg/mL, respectively.
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Affiliation(s)
- Cangzhu Sun
- Ocean College, Zhoushan Campus, Zhejiang University, Zhoushan 316021, China; (C.S.); (Y.H.); (X.L.)
| | - Yura Ha
- Ocean College, Zhoushan Campus, Zhejiang University, Zhoushan 316021, China; (C.S.); (Y.H.); (X.L.)
| | - Xin Liu
- Ocean College, Zhoushan Campus, Zhejiang University, Zhoushan 316021, China; (C.S.); (Y.H.); (X.L.)
| | - Nan Wang
- Ocean College, Zhoushan Campus, Zhejiang University, Zhoushan 316021, China; (C.S.); (Y.H.); (X.L.)
- Hainan Institute of Zhejiang University, Sanya 572025, China
| | - Xiao-Yuan Lian
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China;
| | - Zhizhen Zhang
- Ocean College, Zhoushan Campus, Zhejiang University, Zhoushan 316021, China; (C.S.); (Y.H.); (X.L.)
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Huang R, Meng X, Tao K, Cao M, Nie L, Dong Y, Lyu Y, Wang S, Feng Z. Discovery and Biosynthesis of the Amodesmycins, Aromatic Polyketide-Siderophore Hybrid Conjugates. Org Lett 2022; 24:9408-9412. [PMID: 36534026 DOI: 10.1021/acs.orglett.2c03788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A type II polyketide synthase biosynthetic gene cluster (amd) containing three P450 genes was identified from a soil metagenomic library, and novel benz[h]isoquinoline-desferrioxamine B conjugated compound amodesmycins were isolated from Streptomyces albus J1074 harboring the amd gene cluster. Genetic evidence showed that the benz[h]isoquinoline part and desferrioxamine B part in amodesmycins were derived from the amd gene cluster and S. albus J1074, respectively, while P450 enzymes played critical roles in the conjunction of these two parts.
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Affiliation(s)
- Ruijie Huang
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Xiaolu Meng
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Kaixiang Tao
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Mingming Cao
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Lishuang Nie
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Yao Dong
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Yunbin Lyu
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Shaochen Wang
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
| | - Zhiyang Feng
- College of Food Science and Technology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China
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The Diversity of Deep-Sea Actinobacteria and Their Natural Products: An Epitome of Curiosity and Drug Discovery. DIVERSITY 2022. [DOI: 10.3390/d15010030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Bioprospecting of novel antibiotics has been the conventional norm of research fostered by researchers worldwide to combat drug resistance. With the exhaustion of incessant leads, the search for new chemical entities moves into uncharted territories such as the deep sea. The deep sea is a furthermost ecosystem with much untapped biodiversity thriving under extreme conditions. Accordingly, it also encompasses a vast pool of ancient natural products. Actinobacteria are frequently regarded as the bacteria of research interest due to their inherent antibiotic-producing capabilities. These interesting groups of bacteria occupy diverse ecological habitats including a multitude of different deep-sea habitats. In this review, we provide a recent update on the novel species and compounds of actinomycetes from the deep-sea environments within a period of 2016–2022. Within this period, a total of 24 new species of actinomycetes were discovered and characterized as well as 101 new compounds of various biological activities. The microbial communities of various deep-sea ecosystems are the emerging frontiers of bioprospecting.
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Carro L, Oren A. Descriptions of Micromonospora grosourdyae nom. nov., Micromonospora sonchi comb. nov. and Micromonospora thawaii sp. nov. to resolve problems with the taxonomy and nomenclature of strains named Micromonospora endophytica. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748590 DOI: 10.1099/ijsem.0.005628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The name Micromonospora endophytica has been used for three different organisms. The first organism with this name is the species represented by strain DCWR9-8-2T, a species published in 2015 but whose name was never validated. In 2019 the type species of the genus Jishengella was reclassified into the genus Micromonospora, while maintaining its original epithet, thus establishing the second group of organisms known as M. endophytica, but the first for which the name was validated. Additionally, in 2018 the reclassification of the genus Verrucosispora into the genus Micromonospora was proposed, but a new epithet has not been specified for the species named Verrucosispora endophytica, which remains an orphaned species. Therefore, it is necessary to propose new names that can unequivocally identify these taxa. We have analysed the taxonomic position of the strains, comparing them with the species with valid published names of the genus Micromonospora. We here propose Micromonospora thawaii sp. nov. for the species represented by strain DCWR9-8-2T, and Micromonospora grosourdyae nom. nov. and Micromonospora sonchi comb. nov. for the two orphaned species of Verrucosispora, V. endophytica and Verrucosispora sonchi, respectively. Genomic analysis also showed that M. trujilloniae is a later heterotypic synonym of M. andamanensis.
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Affiliation(s)
- Lorena Carro
- Departamento de Microbiología y Genética, Facultad de CC Agrarias y Ambientales, Universidad de Salamanca, Plaza Doctores de la Reina, Lab 230, 37007 Salamanca, Spain
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
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Wang F, Wan JJ, Zhang XY, Xin Y, Sun ML, Wang P, Zhang WP, Tian JW, Zhang YZ, Li CY, Fu HH. Halomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005210] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two novel Gram-stain-negative, facultative anaerobic, non-flagellated, rod-shaped bacterial strains, designated MT13T and MT32, were isolated from sediment samples collected from the Mariana Trench at a depth of 8300 m. The two strains grew at −2–30 °C (optimum, 25 °C), at pH 5.5–10.0 (optimum, pH 7.5–8.0) and with 0–15 % (w/v) NaCl (optimum, 3–6 %). They did not reduce nitrate to nitrite nor hydrolyse Tweens 40 and 80, aesculin, casein, starch and DNA. The genomic G+C contents of draft genomes of strain MT13T and MT32 were 52.2 and 54.1 m ol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains MT13T and MT32 were affiliated with the genus
Halomonas
, with the highest similarity to the type strain of
Halomonas olivaria
. The values of average nucleotide identity and in silico DNA–DNA hybridization between strain MT13T and MT32, and between strain MT13T and five closely related type strains of
Halomonas
species indicated that strains MT13T and MT32 belonged to the same species, but represented a novel species in the genus of
Halomonas
. The major cellular fatty acids of strains MT13T and MT32 were C16 : 0, summed feature 3(C16 : 1
ω7c/ω6c) and summed feature 8 (C18 : 1
ω7c/ω6c). Major polar lipids of strains MT13T and MT32 included phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Ubiquinone-9 was the predominant respiratory quinone. Based on data from the present polyphasic study, strains MT13T and MT32 represent a novel species of the genus
Halomonas
, for which the name Halomonas profundi sp. nov. is proposed. The type strain is MT13T (=MCCC 1K06389T=KCTC 82923T).
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Affiliation(s)
- Fan Wang
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, PR China
| | - Jin-Jian Wan
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, PR China
| | - Xi-Ying Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, PR China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Yu Xin
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, and Institute for Advanced Ocean Study, Ocean University of China, Qingdao, Shandong, PR China
| | - Mei-Ling Sun
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, PR China
| | - Peng Wang
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, PR China
| | - Wei-Peng Zhang
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, PR China
| | - Ji-Wei Tian
- MOE Key Laboratory of Physical Oceanography and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, PR China
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, PR China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, PR China
| | - Chun-Yang Li
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, PR China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
| | - Hui-Hui Fu
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, PR China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, PR China
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Arulprakasam KR, Dharumadurai D. Genome mining of biosynthetic gene clusters intended for secondary metabolites conservation in actinobacteria. Microb Pathog 2021; 161:105252. [PMID: 34662717 DOI: 10.1016/j.micpath.2021.105252] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/10/2021] [Accepted: 10/11/2021] [Indexed: 12/13/2022]
Abstract
Evolution of genome sequencing technology, on the one hand, and advancement of computational genome mining tools, on the other hand, paves way for improvement in predicting secondary metabolites. In past, numerous efforts were made concerning genome mining for recognizing secondary metabolites within the genus, but only a negligible quantity of comparative genomic reports had carried out among species of different genera. In this study, we explored potential of 24 actinobacteria species belonging to the genera, including Streptomyces, Nocardia, Micromonospora, and Saccharomonospora, to traverse diversity and distribution of Biosynthetic Gene Clusters (BGCs). Investigating results obtained from antiSMASH (Antibiotics and Secondary Metabolites Analysis Shell), NaPDoS (Natural Product Domain Seeker), and NP.searcher revealed conservation of genus-specific gene clusters among various species. E.g., NAGGN (n-acetyl glutaminyl glutamine amide) is present in Micromonospora, furan in Nocardia, melanin, and lassopeptide occur in Streptomyces. Bioactive compounds like alkyl-O-dihydro geranyl methoxy hydroquinone, SapB, desferrioxamine E, 2-Methylisoborneol, mayamycin, cyclodipeptide synthase, diisonitrile, salinichelin, hopene, ectoine and isorenieratene are highly conserved among diverse genera. Furthermore, pharmacological activity of actinobacterial derived metabolites against bacterial and fungal pathogens were illustrated. We need to accomplish large-scale analysis of natural products, including various genera of actinobacteria to deliver comprehensive intuition to overcome antibiotic resistance.
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Affiliation(s)
- Karthick Raja Arulprakasam
- Department of Microbiology, School of Life Sciences Bharathidasan University, Tiruchirappalli, Tamil Nadu, India
| | - Dhanasekaran Dharumadurai
- Department of Microbiology, School of Life Sciences Bharathidasan University, Tiruchirappalli, Tamil Nadu, India.
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