Pair your accounts.

Export articles to Mendeley

Get article recommendations from ACS based on references in your Mendeley library.

Pair your accounts.

Export articles to Mendeley

Get article recommendations from ACS based on references in your Mendeley library.

You’ve supercharged your research process with ACS and Mendeley!

STEP 1:
Click to create an ACS ID

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

Please note: If you switch to a different device, you may be asked to login again with only your ACS ID.

MENDELEY PAIRING EXPIRED
Your Mendeley pairing has expired. Please reconnect
ACS Publications. Most Trusted. Most Cited. Most Read
My Activity
CONTENT TYPES

Prioritizing Natural Product Diversity in a Collection of 146 Bacterial Strains Based on Growth and Extraction Protocols

View Author Information
† ‡ Center for Marine Biotechnology & Biomedicine, Scripps Institution of Oceanography, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
§ Research Support Center in Natural and Synthetic Products, Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences, University of São Paulo, Ribeirão Preto, 14040-903, Brazil
Cite this: J. Nat. Prod. 2017, 80, 3, 588–597
Publication Date (Web):November 11, 2016
https://doi.org/10.1021/acs.jnatprod.6b00722
Copyright © 2016 The American Chemical Society and American Society of Pharmacognosy

    Article Views

    3798

    Altmetric

    -

    Citations

    LEARN ABOUT THESE METRICS
    Other access options
    Supporting Info (1)»

    Abstract

    Abstract Image

    In order to expedite the rapid and efficient discovery and isolation of novel specialized metabolites, while minimizing the waste of resources on rediscovery of known compounds, it is crucial to develop efficient approaches for strain prioritization, rapid dereplication, and the assessment of favored cultivation and extraction conditions. Herein we interrogated bacterial strains by systematically evaluating cultivation and extraction parameters with LC-MS/MS analysis and subsequent dereplication through the Global Natural Product Social Molecular Networking (GNPS) platform. The developed method is fast, requiring minimal time and sample material, and is compatible with high-throughput extract analysis, thereby streamlining strain prioritization and evaluation of culturing parameters. With this approach, we analyzed 146 marine Salinispora and Streptomyces strains that were grown and extracted using multiple different protocols. In total, 603 samples were analyzed, generating approximately 1.8 million mass spectra. We constructed a comprehensive molecular network and identified 15 molecular families of diverse natural products and their analogues. The size and breadth of this network shows statistically supported trends in molecular diversity when comparing growth and extraction conditions. The network provides an extensive survey of the biosynthetic capacity of the strain collection and a method to compare strains based on the variety and novelty of their metabolites. This approach allows us to quickly identify patterns in metabolite production that can be linked to taxonomy, culture conditions, and extraction methods, as well as informing the most valuable growth and extraction conditions.

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.

    Recommended

    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. You can change your affiliated institution below.

    Supporting Information

    ARTICLE SECTIONS
    Jump To

    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jnatprod.6b00722.

    • Tables S1–S3, Figures S1–S9 (PDF)

    Terms & Conditions

    Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.

    Cited By

    This article is cited by 99 publications.

    1. Jinmei Xia, Hongkun Si, Xiaomei Huang, Xiangwei Chen, Xiaoteng Fu, Guangyu Li, Qiliang Lai, Fang Li, Weiyi Wang, Zongze Shao. Metabolomics and Molecular Networking-Guided Screening of Bacillus-Derived Bioactive Compounds Against a Highly Lethal Vibrio Species. Analytical Chemistry 2024, 96 (11) , 4359-4368. https://doi.org/10.1021/acs.analchem.3c02958
    2. Shuyuan Mo, Yaxin Zhang, Rui Jiang, Hanxiao Zeng, Zhihong Huang, Jie Yin, Sitian Zhang, Jun Yao, Jianping Wang, Zhengxi Hu, Yonghui Zhang. Dipeniroqueforins A–B and Peniroqueforin D: Eremophilane-Type Sesquiterpenoid Derivatives with Cytotoxic Activity from Penicillium roqueforti. The Journal of Organic Chemistry 2024, 89 (2) , 1209-1219. https://doi.org/10.1021/acs.joc.3c02360
    3. Yanduo Wang, Jian Yang, Ling Hu, Ruibin Bai, Tielin Wang, Xiaoke Xing, Lin Chen, Gang Ding. LC–MS/MS-Guided Molecular Networking for Targeted Discovery of Undescribed and Bioactive Ophiobolins from Bipolaris eleusines. Journal of Agricultural and Food Chemistry 2023, 71 (31) , 11982-11992. https://doi.org/10.1021/acs.jafc.3c03352
    4. Mitja M. Zdouc, Marianna Iorio, Sonia I. Maffioli, Max Crüsemann, Stefano Donadio, Margherita Sosio. Planomonospora: A Metabolomics Perspective on an Underexplored Actinobacteria Genus. Journal of Natural Products 2021, 84 (2) , 204-219. https://doi.org/10.1021/acs.jnatprod.0c00807
    5. Rong Chao, Xue-Mei Hou, Wei-Feng Xu, Yang Hai, Mei-Yan Wei, Chang-Yun Wang, Yu-Cheng Gu, Chang-Lun Shao. Targeted Isolation of Asperheptatides from a Coral-Derived Fungus Using LC-MS/MS-Based Molecular Networking and Antitubercular Activities of Modified Cinnamate Derivatives. Journal of Natural Products 2021, 84 (1) , 11-19. https://doi.org/10.1021/acs.jnatprod.0c00804
    6. José Rivera-Chávez, Celia Bustos-Brito, Enrique Aguilar-Ramírez, Diego Martínez-Otero, Luis D. Rosales-Vázquez, Alejandro Dorazco-González, Patricia Cano-Sánchez. Hydroxy-neo-Clerodanes and 5,10-seco-neo-Clerodanes from Salvia decora. Journal of Natural Products 2020, 83 (7) , 2212-2220. https://doi.org/10.1021/acs.jnatprod.0c00313
    7. Julie P. G. Rodríguez, Darlon I. Bernardi, Juliana R. Gubiani, Juliana Magalhães de Oliveira, Raquel P. Morais-Urano, Ariane F. Bertonha, Karin F. Bandeira, Jairo I. Q. Bulla, Lara D. Sette, Antonio G. Ferreira, João M. Batista, Jr., Thayná de Souza Silva, Raquel Alves dos Santos, Carlos H. G. Martins, Simone P. Lira, Marcos G. da Cunha, Daniela B. B. Trivella, Nathalia Grazzia, Natália E. S. Gomes, Fernanda Gadelha, Danilo C. Miguel, Ana Carolina G. Cauz, Marcelo Brocchi, Roberto G. S. Berlinck. Water-Soluble Glutamic Acid Derivatives Produced in Culture by Penicillium solitum IS1-A from King George Island, Maritime Antarctica. Journal of Natural Products 2020, 83 (1) , 55-65. https://doi.org/10.1021/acs.jnatprod.9b00635
    8. Maria S. Costa, Chase M. Clark, Sesselja Ómarsdóttir, Laura M. Sanchez, Brian T. Murphy. Minimizing Taxonomic and Natural Product Redundancy in Microbial Libraries Using MALDI-TOF MS and the Bioinformatics Pipeline IDBac. Journal of Natural Products 2019, 82 (8) , 2167-2173. https://doi.org/10.1021/acs.jnatprod.9b00168
    9. José Rivera-Chávez, Jade Zacatenco-Abarca, Jesús Morales-Jiménez, Blanca Martínez-Aviña, Simón Hernández-Ortega, Enrique Aguilar-Ramírez. Cuautepestalorin, a 7,8-Dihydrochromene–Oxoisochromane Adduct Bearing a Hexacyclic Scaffold from Pestalotiopsis sp. IQ-011. Organic Letters 2019, 21 (10) , 3558-3562. https://doi.org/10.1021/acs.orglett.9b00962
    10. Jean-Luc Wolfender, Jean-Marc Nuzillard, Justin J. J. van der Hooft, Jean-Hugues Renault, Samuel Bertrand. Accelerating Metabolite Identification in Natural Product Research: Toward an Ideal Combination of Liquid Chromatography–High-Resolution Tandem Mass Spectrometry and NMR Profiling, in Silico Databases, and Chemometrics. Analytical Chemistry 2019, 91 (1) , 704-742. https://doi.org/10.1021/acs.analchem.8b05112
    11. Raphael Reher, Markus Kuschak, Nina Heycke, Suvi Annala, Stefan Kehraus, Hao-Fu Dai, Christa E. Müller, Evi Kostenis, Gabriele M. König, Max Crüsemann. Applying Molecular Networking for the Detection of Natural Sources and Analogues of the Selective Gq Protein Inhibitor FR900359. Journal of Natural Products 2018, 81 (7) , 1628-1635. https://doi.org/10.1021/acs.jnatprod.8b00222
    12. Michael Hoffmann, David Auerbach, Fabian Panter, Thomas Hoffmann, Pieter C. Dorrestein, and Rolf Müller . Homospermidine Lipids: A Compound Class Specifically Formed during Fruiting Body Formation of Myxococcus xanthus DK1622. ACS Chemical Biology 2018, 13 (1) , 273-280. https://doi.org/10.1021/acschembio.7b00816
    13. Florent Olivon, Pierre-Marie Allard, Alexey Koval, Davide Righi, Gregory Genta-Jouve, Johan Neyts, Cécile Apel, Christophe Pannecouque, Louis-Félix Nothias, Xavier Cachet, Laurence Marcourt, Fanny Roussi, Vladimir L. Katanaev, David Touboul, Jean-Luc Wolfender, and Marc Litaudon . Bioactive Natural Products Prioritization Using Massive Multi-informational Molecular Networks. ACS Chemical Biology 2017, 12 (10) , 2644-2651. https://doi.org/10.1021/acschembio.7b00413
    14. Nicholas Lorig-Roach, Patrick C. Still, David Coppage, Jennifer E. Compton, Mitchell S. Crews, Gabriel Navarro, Karen Tenney, and Phillip Crews . Evaluating Nitrogen-Containing Biosynthetic Products Produced by Saltwater Culturing of Several California Littoral Zone Gram-Negative Bacteria. Journal of Natural Products 2017, 80 (8) , 2304-2310. https://doi.org/10.1021/acs.jnatprod.7b00302
    15. Naydja Moralles Maimone, Gladys Angélica Apaza-Castillo, Maria Carolina Quecine, Simone Possedente de Lira. Accessing the specialized metabolome of actinobacteria from the bulk soil of Paullinia cupana Mart. on the Brazilian Amazon: a promising source of bioactive compounds against soybean phytopathogens. Brazilian Journal of Microbiology 2024, 55 (2) , 1863-1882. https://doi.org/10.1007/s42770-024-01286-1
    16. Jingwan Wu, Dandan Chen, Qing Li, Ting Feng, Jing Xu. Metabolomics-Guided Discovery of New Dimeric Xanthones from Co-Cultures of Mangrove Endophytic Fungi Phomopsis asparagi DHS-48 and Phomopsis sp. DHS-11. Marine Drugs 2024, 22 (3) , 102. https://doi.org/10.3390/md22030102
    17. Alexandre Le Loarer, Laurent Dufossé, Jérôme Bignon, Michel Frédérich, Allison Ledoux, Mireille Fouillaud, Anne Gauvin-Bialecki. OSMAC Method to Assess Impact of Culture Parameters on Metabolomic Diversity and Biological Activity of Marine-Derived Actinobacteria. Marine Drugs 2024, 22 (1) , 23. https://doi.org/10.3390/md22010023
    18. Joris J. R. Louwen, Marnix H. Medema, Justin J. J. van der Hooft. Enhanced correlation-based linking of biosynthetic gene clusters to their metabolic products through chemical class matching. Microbiome 2023, 11 (1) https://doi.org/10.1186/s40168-022-01444-3
    19. Izzah Shahid, Salma Batool, Maleeha Hassan, Hammad Ismail, Samina Mehnaz, Farah Deeba, Muhammad Anwar, Faisal Zulfiqar, Rashid Iqbal, Hayssam M Ali. A Decade of Progress in Rhizoengineering to Exploit Plant Microbiome for Salinity Amelioration. Plant Stress 2023, 9 , 100325. https://doi.org/10.1016/j.stress.2023.100325
    20. Duc Dat Le, Soojung Yu, Thinhulinh Dang, Mina Lee. Molecular Networking and Bioassay-Guided Preparation and Separation of Active Extract and Constituents from Vicia tenuifolia Roth. Antioxidants 2023, 12 (10) , 1876. https://doi.org/10.3390/antiox12101876
    21. Arun Kumar Singh, Rishabha Malviya, Rishav Sharma. Prospects for New Antibiotics Discovered through Genome Analysis. Anti-Infective Agents 2023, 21 (5) https://doi.org/10.2174/2211352521666230717164854
    22. Shamsunnahar Khushi, Angela A. Salim, Robert J. Capon. Case Studies in Molecular Network-Guided Marine Biodiscovery. Marine Drugs 2023, 21 (7) , 413. https://doi.org/10.3390/md21070413
    23. Naydja Moralles Maimone, Mario Cezar Pozza Junior, Lucianne Ferreira Paes de Oliveira, Dorian Rojas-Villalta, Simone Possedente de Lira, Leticia Barrientos, Kattia Núñez-Montero. Metabologenomics analysis of Pseudomonas sp. So3.2b, an Antarctic strain with bioactivity against Rhizoctonia solani. Frontiers in Microbiology 2023, 14 https://doi.org/10.3389/fmicb.2023.1187321
    24. Susana P. Gaudêncio, Engin Bayram, Lada Lukić Bilela, Mercedes Cueto, Ana R. Díaz-Marrero, Berat Z. Haznedaroglu, Carlos Jimenez, Manolis Mandalakis, Florbela Pereira, Fernando Reyes, Deniz Tasdemir. Advanced Methods for Natural Products Discovery: Bioactivity Screening, Dereplication, Metabolomics Profiling, Genomic Sequencing, Databases and Informatic Tools, and Structure Elucidation. Marine Drugs 2023, 21 (5) , 308. https://doi.org/10.3390/md21050308
    25. Yanshen Li, Ying Shao, Ya'ning Zhu, Anqi Chen, Jingyao Qu, Yonglin Gao, Sunan Lu, Pengjie Luo, Xin Mao. Temperature-dependent mycotoxins production investigation in Alternaria infected cherry by ultra-high performance liquid chromatography and Orbitrap high resolution mass spectrometry. International Journal of Food Microbiology 2023, 388 , 110070. https://doi.org/10.1016/j.ijfoodmicro.2022.110070
    26. Alexandre Le Loarer, Rémy Marcellin-Gros, Laurent Dufossé, Jérôme Bignon, Michel Frédérich, Allison Ledoux, Emerson Ferreira Queiroz, Jean-Luc Wolfender, Anne Gauvin-Bialecki, Mireille Fouillaud. Prioritization of Microorganisms Isolated from the Indian Ocean Sponge Scopalina hapalia Based on Metabolomic Diversity and Biological Activity for the Discovery of Natural Products. Microorganisms 2023, 11 (3) , 697. https://doi.org/10.3390/microorganisms11030697
    27. Joris J. R. Louwen, Satria A. Kautsar, Sven van der Burg, Marnix H. Medema, Justin J. J. van der Hooft, . iPRESTO: Automated discovery of biosynthetic sub-clusters linked to specific natural product substructures. PLOS Computational Biology 2023, 19 (2) , e1010462. https://doi.org/10.1371/journal.pcbi.1010462
    28. Guo-Fei Qin, Xiao Zhang, Feng Zhu, Zong-Qing Huo, Qing-Qiang Yao, Qun Feng, Zhong Liu, Gui-Min Zhang, Jing-Chun Yao, Hong-Bao Liang. MS/MS-Based Molecular Networking: An Efficient Approach for Natural Products Dereplication. Molecules 2023, 28 (1) , 157. https://doi.org/10.3390/molecules28010157
    29. Paulo Wender P. Gomes, Talita Carla de Tralia Medeiros, Naydja Moralles Maimone, Tiago F. Leão, Luiz Alberto Beraldo de Moraes, Anelize Bauermeister. Microbial Metabolites Annotation by Mass Spectrometry-Based Metabolomics. 2023, 225-248. https://doi.org/10.1007/978-3-031-41741-2_9
    30. Yuya KAKUMU, Tohru MITSUNAGA. Approach of Natural Product Discovery by Molecular Networking. KAGAKU TO SEIBUTSU 2023, 61 (1) , 32-39. https://doi.org/10.1271/kagakutoseibutsu.61.32
    31. Niek F. de Jonge, Kevin Mildau, David Meijer, Joris J. R. Louwen, Christoph Bueschl, Florian Huber, Justin J. J. van der Hooft. Good practices and recommendations for using and benchmarking computational metabolomics metabolite annotation tools. Metabolomics 2022, 18 (12) https://doi.org/10.1007/s11306-022-01963-y
    32. Federica Fiorini, Felizitas Bajerski, Olga Jeske, Cendrella Lepleux, Jörg Overmann, Mark Brönstrup. A Metabolomics-Based Toolbox to Assess and Compare the Metabolic Potential of Unexplored, Difficult-to-Grow Bacteria. Marine Drugs 2022, 20 (11) , 713. https://doi.org/10.3390/md20110713
    33. Aniruddha Sarker, Debasis Mitra, Pradeep K. Das Mohapatra, Most. Waheda Rahman Ansary, Tofazzal Islam. Plant Growth-Promoting Rhizobacteria as Biostimulants in Sustainable Crop Production. 2022, 455-483. https://doi.org/10.1079/9781789248098.0028
    34. Shao-Wei Liu, Norovsuren Jadambaa, Arina A. Nikandrova, Ilya A. Osterman, Cheng-Hang Sun. Exploring the Diversity and Antibacterial Potentiality of Cultivable Actinobacteria from the Soil of the Saxaul Forest in Southern Gobi Desert in Mongolia. Microorganisms 2022, 10 (5) , 989. https://doi.org/10.3390/microorganisms10050989
    35. Helena Mannochio-Russo, Rafael F. de Almeida, Wilhan D. G. Nunes, Paula C. P. Bueno, Andrés M. Caraballo-Rodríguez, Anelize Bauermeister, Pieter C. Dorrestein, Vanderlan S. Bolzani. Untargeted Metabolomics Sheds Light on the Diversity of Major Classes of Secondary Metabolites in the Malpighiaceae Botanical Family. Frontiers in Plant Science 2022, 13 https://doi.org/10.3389/fpls.2022.854842
    36. Roberto G. S. Berlinck, Camila M. Crnkovic, Juliana R. Gubiani, Darlon I. Bernardi, Laura P. Ióca, Jairo I. Quintana-Bulla. The isolation of water-soluble natural products – challenges, strategies and perspectives. Natural Product Reports 2022, 39 (3) , 596-669. https://doi.org/10.1039/D1NP00037C
    37. Dibya Jyoti Hazarika, Merilin Kakoti, Ashok Bhattacharyya, Robin Chandra Boro. Biocontrol applications of microbial metabolites. 2022, 181-216. https://doi.org/10.1016/B978-0-323-88478-5.00010-9
    38. Qin-Pei Lu, Yong-Mei Huang, Shao-Wei Liu, Gang Wu, Qin Yang, Li-Fang Liu, Hai-Tao Zhang, Yi Qi, Ting Wang, Zhong-Ke Jiang, Jun-Jie Li, Hao Cai, Xiu-Jun Liu, Hui Luo, Cheng-Hang Sun. Metabolomics Tools Assisting Classic Screening Methods in Discovering New Antibiotics from Mangrove Actinomycetia in Leizhou Peninsula. Marine Drugs 2021, 19 (12) , 688. https://doi.org/10.3390/md19120688
    39. Scott A. Jarmusch, Justin J. J. van der Hooft, Pieter C. Dorrestein, Alan K. Jarmusch. Advancements in capturing and mining mass spectrometry data are transforming natural products research. Natural Product Reports 2021, 38 (11) , 2066-2082. https://doi.org/10.1039/D1NP00040C
    40. Nico Ortlieb, Elke Klenk, Andreas Kulik, Timo Horst Johannes Niedermeyer, . Development of an agar-plug cultivation system for bioactivity assays of actinomycete strain collections. PLOS ONE 2021, 16 (11) , e0258934. https://doi.org/10.1371/journal.pone.0258934
    41. Yan Bai, Ping Yi, Yun Zhang, Jiangchun Hu, Ying Wang, Jianhua Ju, Huaqi Pan. Structure-based molecular networking for the target discovery of novel germicidin derivatives from the sponge-associated streptomyces sp. 18A01. The Journal of Antibiotics 2021, 74 (11) , 799-806. https://doi.org/10.1038/s41429-021-00447-w
    42. Naydja Moralles Maimone, Lucianne Ferreira Paes de Oliveira, Suikinai Nobre Santos, Simone Possedente de Lira. Elicitation of Streptomyces lunalinharesii secondary metabolism through co-cultivation with Rhizoctonia solani. Microbiological Research 2021, 251 , 126836. https://doi.org/10.1016/j.micres.2021.126836
    43. Agustina Undabarrena, Camila F. Pereira, Worarat Kruasuwan, Jonathan Parra, Nelly Sélem-Mojica, Kristiina Vind, Jana K. Schniete. Integrating perspectives in actinomycete research: an ActinoBase review of 2020–21. Microbiology 2021, 167 (9) https://doi.org/10.1099/mic.0.001084
    44. Xinhui Wang, Karolina Subko, Sara Kildgaard, Jens C. Frisvad, Thomas O. Larsen. Mass Spectrometry-Based Network Analysis Reveals New Insights Into the Chemodiversity of 28 Species in Aspergillus section Flavi. Frontiers in Fungal Biology 2021, 2 https://doi.org/10.3389/ffunb.2021.719420
    45. Yang Yu, Changliang Yao, De-an Guo. Insight into chemical basis of traditional Chinese medicine based on the state-of-the-art techniques of liquid chromatography−mass spectrometry. Acta Pharmaceutica Sinica B 2021, 11 (6) , 1469-1492. https://doi.org/10.1016/j.apsb.2021.02.017
    46. Grímur Hjörleifsson Eldjárn, Andrew Ramsay, Justin J. J. van der Hooft, Katherine R. Duncan, Sylvia Soldatou, Juho Rousu, Rónán Daly, Joe Wandy, Simon Rogers, . Ranking microbial metabolomic and genomic links in the NPLinker framework using complementary scoring functions. PLOS Computational Biology 2021, 17 (5) , e1008920. https://doi.org/10.1371/journal.pcbi.1008920
    47. Nathan Carriot, Benoît Paix, Stéphane Greff, Bruno Viguier, Jean-François Briand, Gérald Culioli. Integration of LC/MS-based molecular networking and classical phytochemical approach allows in-depth annotation of the metabolome of non-model organisms - The case study of the brown seaweed Taonia atomaria. Talanta 2021, 225 , 121925. https://doi.org/10.1016/j.talanta.2020.121925
    48. Antonio Hernandez, Linh T. Nguyen, Radhika Dhakal, Brian T. Murphy. The need to innovate sample collection and library generation in microbial drug discovery: a focus on academia. Natural Product Reports 2021, 38 (2) , 292-300. https://doi.org/10.1039/D0NP00029A
    49. Max Crüsemann. Coupling Mass Spectral and Genomic Information to Improve Bacterial Natural Product Discovery Workflows. Marine Drugs 2021, 19 (3) , 142. https://doi.org/10.3390/md19030142
    50. Peter J. Blanco Carcache, Ermias Mekuria Addo, A. Douglas Kinghorn. Higher Plant Sources of Cancer Chemotherapeutic Agents and the Potential Role of Biotechnological Approaches for Their Supply. 2021, 545-581. https://doi.org/10.1007/978-3-030-74779-4_17
    51. Keshab Bhattarai, Keshab Bhattarai, Md Ehsanul Kabir, Rina Bastola, Bikash Baral. Fungal natural products galaxy: Biochemistry and molecular genetics toward blockbuster drugs discovery. 2021, 193-284. https://doi.org/10.1016/bs.adgen.2020.11.006
    52. Caroline Utermann, Vivien A. Echelmeyer, Ernest Oppong-Danquah, Martina Blümel, Deniz Tasdemir. Diversity, Bioactivity Profiling and Untargeted Metabolomics of the Cultivable Gut Microbiota of Ciona intestinalis. Marine Drugs 2021, 19 (1) , 6. https://doi.org/10.3390/md19010006
    53. Marcelo M. P. Tangerina, Luciana Costa Furtado, Vida M. B. Leite, Anelize Bauermeister, Karen Velasco-Alzate, Paula C. Jimenez, Leandro M. Garrido, Gabriel Padilla, Norberto P. Lopes, Leticia V. Costa-Lotufo, Marcelo J. Pena Ferreira, . Metabolomic study of marine Streptomyces sp.: Secondary metabolites and the production of potential anticancer compounds. PLOS ONE 2020, 15 (12) , e0244385. https://doi.org/10.1371/journal.pone.0244385
    54. Ling-Li Liu, Zhi-Fan Chen, Yao Liu, Dan Tang, Hua-Hua Gao, Qiang Zhang, Jin-Ming Gao. Molecular networking-based for the target discovery of potent antiproliferative polycyclic macrolactam ansamycins from Streptomyces cacaoi subsp. asoensis. Organic Chemistry Frontiers 2020, 7 (24) , 4008-4018. https://doi.org/10.1039/D0QO00557F
    55. Hyun Woo Kim, Soo Sung Kim, Kyo Bin Kang, Byeol Ryu, Eunjin Park, Jungmoo Huh, Won Kyung Jeon, Hee-Sung Chae, Won Keun Oh, Jinwoong Kim, Sang Hyun Sung, Young-Won Chin. Combined MS/MS-NMR Annotation Guided Discovery of Iris lactea var. chinensis Seed as a Source of Viral Neuraminidase Inhibitory Polyphenols. Molecules 2020, 25 (15) , 3383. https://doi.org/10.3390/molecules25153383
    56. Allegra T. Aron, Emily C. Gentry, Kerry L. McPhail, Louis-Félix Nothias, Mélissa Nothias-Esposito, Amina Bouslimani, Daniel Petras, Julia M. Gauglitz, Nicole Sikora, Fernando Vargas, Justin J. J. van der Hooft, Madeleine Ernst, Kyo Bin Kang, Christine M. Aceves, Andrés Mauricio Caraballo-Rodríguez, Irina Koester, Kelly C. Weldon, Samuel Bertrand, Catherine Roullier, Kunyang Sun, Richard M. Tehan, Cristopher A. Boya P., Martin H. Christian, Marcelino Gutiérrez, Aldo Moreno Ulloa, Javier Andres Tejeda Mora, Randy Mojica-Flores, Johant Lakey-Beitia, Victor Vásquez-Chaves, Yilue Zhang, Angela I. Calderón, Nicole Tayler, Robert A. Keyzers, Fidele Tugizimana, Nombuso Ndlovu, Alexander A. Aksenov, Alan K. Jarmusch, Robin Schmid, Andrew W. Truman, Nuno Bandeira, Mingxun Wang, Pieter C. Dorrestein. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nature Protocols 2020, 15 (6) , 1954-1991. https://doi.org/10.1038/s41596-020-0317-5
    57. Fidele Ntie-Kang, Daniel Svozil. An enumeration of natural products from microbial, marine and terrestrial sources. Physical Sciences Reviews 2020, 5 (8) https://doi.org/10.1515/psr-2018-0121
    58. Marija Mojicevic, Paul M. D'Agostino, Aleksandar Pavic, Sandra Vojnovic, Ramsankar Senthamaraikannan, Branka Vasiljevic, Tobias A. M. Gulder, Jasmina Nikodinovic‐Runic. Streptomyces sp. BV410 isolate from chamomile rhizosphere soil efficiently produces staurosporine with antifungal and antiangiogenic properties. MicrobiologyOpen 2020, 9 (3) https://doi.org/10.1002/mbo3.986
    59. Qing Fang, Fleurdeliz Maglangit, Linrui Wu, Rainer Ebel, Kwaku Kyeremeh, Jeanette H. Andersen, Frederick Annang, Guiomar Pérez-Moreno, Fernando Reyes, Hai Deng. Signalling and Bioactive Metabolites from Streptomyces sp. RK44. Molecules 2020, 25 (3) , 460. https://doi.org/10.3390/molecules25030460
    60. Sara P. Puckett, Robert M. Samples, Patrick D. Schloss, Marcy J. Balunas. Metabolomics and the Microbiome: Characterizing Molecular Diversity in Complex Microbial Communities. 2020, 502-518. https://doi.org/10.1016/B978-0-12-409547-2.14802-4
    61. Ryo Nakabayashi, Kazuki Saito. Top-Down Metabolomics Approaches: Nitrogen- and Sulfur-Omics by Ultrahigh-Resolution Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry. 2020, 138-155. https://doi.org/10.1016/B978-0-12-409547-2.14823-1
    62. Ellis O’Neill. Using new techniques to study old favorites: A case study of Euglena. 2020, 161-170. https://doi.org/10.1016/B978-0-12-818305-2.00010-3
    63. Garima Agarwal, Peter J. Blanco Carcache, Ermias Mekuria Addo, A. Douglas Kinghorn. Current status and contemporary approaches to the discovery of antitumor agents from higher plants. Biotechnology Advances 2020, 38 , 107337. https://doi.org/10.1016/j.biotechadv.2019.01.004
    64. Andrey Stavrianidi. A classification of liquid chromatography mass spectrometry techniques for evaluation of chemical composition and quality control of traditional medicines. Journal of Chromatography A 2020, 1609 , 460501. https://doi.org/10.1016/j.chroma.2019.460501
    65. Joshua Kellogg, Seogchan Kang. Metabolomics, an Essential Tool in Exploring and Harnessing Microbial Chemical Ecology. Phytobiomes Journal 2020, 4 (3) , 195-210. https://doi.org/10.1094/PBIOMES-04-20-0032-RVW
    66. . Full Issue PDF. Phytobiomes Journal 2020, 195-289. https://doi.org/10.1094/PBIOMES-4-3
    67. Phuong-Y Mai, Marceau Levasseur, Didier Buisson, David Touboul, Véronique Eparvier. Identification of Antimicrobial Compounds from Sandwithia guyanensis-Associated Endophyte Using Molecular Network Approach. Plants 2020, 9 (1) , 47. https://doi.org/10.3390/plants9010047
    68. Marilia Valli, Helena Mannochio Russo, Alan Cesar Pilon, Meri Emili Ferreira Pinto, Nathalia B. Dias, Rafael Teixeira Freire, Ian Castro-Gamboa, Vanderlan da Silva Bolzani. Computational methods for NMR and MS for structure elucidation II: database resources and advanced methods. Physical Sciences Reviews 2019, 4 (11) https://doi.org/10.1515/psr-2018-0167
    69. Guoqing Niu, Wenli Li. Next-Generation Drug Discovery to Combat Antimicrobial Resistance. Trends in Biochemical Sciences 2019, 44 (11) , 961-972. https://doi.org/10.1016/j.tibs.2019.05.005
    70. Lucy Foulston. Genome mining and prospects for antibiotic discovery. Current Opinion in Microbiology 2019, 51 , 1-8. https://doi.org/10.1016/j.mib.2019.01.001
    71. Marija Mojicevic, Paul M. D’Agostino, Jasmina Nikodinovic-Runic, Branka Vasiljevic, Tobias A.M. Gulder, Sandra Vojnovic. Antifungal potential of bacterial rhizosphere isolates associated with three ethno-medicinal plants (poppy, chamomile, and nettle). International Microbiology 2019, 22 (3) , 343-353. https://doi.org/10.1007/s10123-019-00054-8
    72. Maglangit, Fang, Leman, Soldatou, Ebel, Kyeremeh, Deng. Accramycin A, a New Aromatic Polyketide, from the Soil Bacterium, Streptomyces sp. MA37. Molecules 2019, 24 (18) , 3384. https://doi.org/10.3390/molecules24183384
    73. Alexander E. Fox Ramos, Laurent Evanno, Erwan Poupon, Pierre Champy, Mehdi A. Beniddir. Natural products targeting strategies involving molecular networking: different manners, one goal. Natural Product Reports 2019, 36 (7) , 960-980. https://doi.org/10.1039/C9NP00006B
    74. Sylvia Soldatou, Grimur Hjorleifsson Eldjarn, Alejandro Huerta-Uribe, Simon Rogers, Katherine R Duncan. Linking biosynthetic and chemical space to accelerate microbial secondary metabolite discovery. FEMS Microbiology Letters 2019, 366 (13) https://doi.org/10.1093/femsle/fnz142
    75. Madeleine Ernst, Kyo Bin Kang, Andrés Mauricio Caraballo-Rodríguez, Louis-Felix Nothias, Joe Wandy, Christopher Chen, Mingxun Wang, Simon Rogers, Marnix H. Medema, Pieter C. Dorrestein, Justin J.J. van der Hooft. MolNetEnhancer: Enhanced Molecular Networks by Integrating Metabolome Mining and Annotation Tools. Metabolites 2019, 9 (7) , 144. https://doi.org/10.3390/metabo9070144
    76. Jean-Luc Wolfender, Marc Litaudon, David Touboul, Emerson Ferreira Queiroz. Innovative omics-based approaches for prioritisation and targeted isolation of natural products – new strategies for drug discovery. Natural Product Reports 2019, 36 (6) , 855-868. https://doi.org/10.1039/C9NP00004F
    77. Cynthia M Grim, Gordon T Luu, Laura M Sanchez. Staring into the void: demystifying microbial metabolomics. FEMS Microbiology Letters 2019, 366 (11) https://doi.org/10.1093/femsle/fnz135
    78. Yessica Parera-Valadez, Alejandro Yam-Puc, Lluvia Korynthia López-Aguiar, Rocío Borges-Argáez, Mario Alberto Figueroa-Saldivar, Mirbella Cáceres-Farfán, Norma Angélica Márquez-Velázquez, Alejandra Prieto-Davó. Ecological Strategies Behind the Selection of Cultivable Actinomycete Strains from the Yucatan Peninsula for the Discovery of Secondary Metabolites with Antibiotic Activity. Microbial Ecology 2019, 77 (4) , 839-851. https://doi.org/10.1007/s00248-019-01329-3
    79. Asih Triastuti, Marieke Vansteelandt, Fatima Barakat, Manon Trinel, Patricia Jargeat, Nicolas Fabre, Carlos A. Amasifuen Guerra, Kember Mejia, Alexis Valentin, Mohamed Haddad. How Histone Deacetylase Inhibitors Alter the Secondary Metabolites of Botryosphaeria mamane , an Endophytic Fungus Isolated from Bixa orellana. Chemistry & Biodiversity 2019, 16 (4) https://doi.org/10.1002/cbdv.201800485
    80. F P Jake Haeckl, João L Baldim, Dasha Iskakova, Kenji L Kurita, Marisi G Soares, Roger G Linington. A selective genome-guided method for environmental Burkholderia isolation. Journal of Industrial Microbiology and Biotechnology 2019, 46 (3-4) , 345-362. https://doi.org/10.1007/s10295-018-02121-x
    81. Christophe Junot, François Fenaille. Metabolomics using Fourier transform mass spectrometry. 2019, 325-356. https://doi.org/10.1016/B978-0-12-814013-0.00011-9
    82. Ram Krishna, Waquar Akhter Ansari, Jay Prakash Verma, Major Singh. Modern molecular and omics tools for understanding the plant growth-promoting rhizobacteria. 2019, 39-53. https://doi.org/10.1016/B978-0-12-817004-5.00003-8
    83. Yutong Shi, Chengqian Pan, Suoyu Cen, Leilei Fu, Xun Cao, Hong Wang, Kuiwu Wang, Bin Wu. Comparative metabolomics reveals defence‐related modification of citrinin by Penicillium citrinum within a synthetic Penicillium – Pseudomonas community. Environmental Microbiology 2019, 21 (1) , 496-510. https://doi.org/10.1111/1462-2920.14482
    84. Bicheng Fan, Delphine Parrot, Martina Blümel, Antje Labes, Deniz Tasdemir. Influence of OSMAC-Based Cultivation in Metabolome and Anticancer Activity of Fungi Associated with the Brown Alga Fucus vesiculosus. Marine Drugs 2019, 17 (1) , 67. https://doi.org/10.3390/md17010067
    85. Liang-Yu Chen, Hao-Tian Cui, Chun Su, Feng-Wu Bai, Xin-Qing Zhao. Analysis of the complete genome sequence of a marine-derived strain Streptomyces sp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides. PeerJ 2019, 7 , e6122. https://doi.org/10.7717/peerj.6122
    86. Anelize Bauermeister, Karen Velasco-Alzate, Tiago Dias, Helena Macedo, Elthon G. Ferreira, Paula C. Jimenez, Tito M. C. Lotufo, Norberto P. Lopes, Susana P. Gaudêncio, Letícia V. Costa-Lotufo. Metabolomic Fingerprinting of Salinispora From Atlantic Oceanic Islands. Frontiers in Microbiology 2018, 9 https://doi.org/10.3389/fmicb.2018.03021
    87. Katherine A Hollywood, Kamila Schmidt, Eriko Takano, Rainer Breitling. Metabolomics tools for the synthetic biology of natural products. Current Opinion in Biotechnology 2018, 54 , 114-120. https://doi.org/10.1016/j.copbio.2018.02.015
    88. Keqiang Fan, Qian Zhang. The functional differentiation of the post-PKS tailoring oxygenases contributed to the chemical diversities of atypical angucyclines. Synthetic and Systems Biotechnology 2018, 3 (4) , 275-282. https://doi.org/10.1016/j.synbio.2018.11.001
    89. Jamshid Amiri Moghaddam, Max Crüsemann, Mohammad Alanjary, Henrik Harms, Antonio Dávila-Céspedes, Jochen Blom, Anja Poehlein, Nadine Ziemert, Gabriele M. König, Till F. Schäberle. Analysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites. Scientific Reports 2018, 8 (1) https://doi.org/10.1038/s41598-018-34954-y
    90. Emilia Palazzotto, Tilmann Weber. Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms. Current Opinion in Microbiology 2018, 45 , 109-116. https://doi.org/10.1016/j.mib.2018.03.004
    91. Florbela Pereira, Joao Aires-de-Sousa. Computational Methodologies in the Exploration of Marine Natural Product Leads. Marine Drugs 2018, 16 (7) , 236. https://doi.org/10.3390/md16070236
    92. Joachim J. Hug, Chantal D. Bader, Maja Remškar, Katarina Cirnski, Rolf Müller. Concepts and Methods to Access Novel Antibiotics from Actinomycetes. Antibiotics 2018, 7 (2) , 44. https://doi.org/10.3390/antibiotics7020044
    93. Daniela B. B. Trivella, Rafael de Felicio. The Tripod for Bacterial Natural Product Discovery: Genome Mining, Silent Pathway Induction, and Mass Spectrometry-Based Molecular Networking. mSystems 2018, 3 (2) https://doi.org/10.1128/mSystems.00160-17
    94. Jose G. Maciá‐Vicente, Yan‐Ni Shi, Zakaria Cheikh‐Ali, Peter Grün, Kyriaki Glynou, Sevda Haghi Kia, Meike Piepenbring, Helge B. Bode. Metabolomics‐based chemotaxonomy of root endophytic fungi for natural products discovery. Environmental Microbiology 2018, 20 (3) , 1253-1270. https://doi.org/10.1111/1462-2920.14072
    95. F. Olivon, C. Apel, P. Retailleau, P. M. Allard, J. L. Wolfender, D. Touboul, F. Roussi, M. Litaudon, S. Desrat. Searching for original natural products by molecular networking: detection, isolation and total synthesis of chloroaustralasines. Organic Chemistry Frontiers 2018, 5 (14) , 2171-2178. https://doi.org/10.1039/C8QO00429C
    96. Lara Rajeev. Antibiotic Discovery. Materials and Methods 2018, 8 https://doi.org/10.13070/mm.en.8.2671
    97. Gregory C. A. Amos, Takayoshi Awakawa, Robert N. Tuttle, Anne-Catrin Letzel, Min Cheol Kim, Yuta Kudo, William Fenical, Bradley S. Moore, Paul R. Jensen. Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality. Proceedings of the National Academy of Sciences 2017, 114 (52) https://doi.org/10.1073/pnas.1714381115
    98. Henrique Machado, Robert N Tuttle, Paul R Jensen. Omics-based natural product discovery and the lexicon of genome mining. Current Opinion in Microbiology 2017, 39 , 136-142. https://doi.org/10.1016/j.mib.2017.10.025
    99. David Newman. Screening and identification of novel biologically active natural compounds. F1000Research 2017, 6 , 783. https://doi.org/10.12688/f1000research.11221.1