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Tata A, Massaro A, Miano B, Petrin S, Antonelli P, Peruzzo A, Pezzuto A, Favretti M, Bragolusi M, Zacometti C, Losasso C, Piro R. A Snapshot, Using a Multi-Omic Approach, of the Metabolic Cross-Talk and the Dynamics of the Resident Microbiota in Ripening Cheese Inoculated with Listeria innocua. Foods 2024; 13:1912. [PMID: 38928853 PMCID: PMC11203185 DOI: 10.3390/foods13121912] [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: 05/23/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Raw milk cheeses harbor complex microbial communities. Some of these microorganisms are technologically essential, but undesirable microorganisms can also be present. While most of the microbial dynamics and cross-talking studies involving interaction between food-derived bacteria have been carried out on agar plates in laboratory-controlled conditions, the present study evaluated the modulation of the resident microbiota and the changes of metabolite production directly in ripening raw milk cheese inoculated with Listeria innocua strains. Using a proxy of the pathogenic Listeria monocytogenes, we aimed to establish the key microbiota players and chemical signals that characterize Latteria raw milk cheese over 60 days of ripening time. The microbiota of both the control and Listeria-inoculated cheeses was analyzed using 16S rRNA targeted amplicon sequencing, while direct analysis in real time mass spectrometry (DART-HRMS) was applied to investigate the differences in the metabolic profiles of the cheeses. The diversity analysis showed the same microbial diversity trend in both the control cheese and the inoculated cheese, while the taxonomic analysis highlighted the most representative genera of bacteria in both the control and inoculated cheese: Lactobacillus and Streptococcus. On the other hand, the metabolic fingerprints revealed that the complex interactions between resident microbiota and L. innocua were governed by continuously changing chemical signals. Changes in the amounts of small organic acids, hydroxyl fatty acids, and antimicrobial compounds, including pyroglutamic acid, hydroxy-isocaproic acid, malic acid, phenyllactic acid, and lactic acid, were observed over time in the L. innocua-inoculated cheese. In cheese that was inoculated with L. innocua, Streptococcus was significantly correlated with the volatile compounds carboxylbenzaldheyde and cyclohexanecarboxylic acid, while Lactobacillus was positively correlated with some volatile and flavor compounds (cyclohexanecarboxylic acid, pyroxidal acid, aminobenzoic acid, and vanillic acid). Therefore, we determined the metabolic markers that characterize a raw milk cheese inoculated with L. innocua, the changes in these markers with the ripening time, and the positive correlation of flavor and volatile compounds with the resident microbiota. This multi-omics approach could suggest innovative food safety strategies based on the enhanced management of undesirable microorganisms by means of strain selection in raw matrices and the addition of specific antimicrobial metabolites to prevent the growth of undesirable microorganisms.
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Affiliation(s)
- Alessandra Tata
- Laboratorio di Chimica Sperimentale, Istituto Zooprofilattico Sperimentale delle Venezie, Viale Fiume 78, 36100 Vicenza, Italy; (A.M.); (B.M.); (M.B.); (C.Z.); (R.P.)
| | - Andrea Massaro
- Laboratorio di Chimica Sperimentale, Istituto Zooprofilattico Sperimentale delle Venezie, Viale Fiume 78, 36100 Vicenza, Italy; (A.M.); (B.M.); (M.B.); (C.Z.); (R.P.)
| | - Brunella Miano
- Laboratorio di Chimica Sperimentale, Istituto Zooprofilattico Sperimentale delle Venezie, Viale Fiume 78, 36100 Vicenza, Italy; (A.M.); (B.M.); (M.B.); (C.Z.); (R.P.)
| | - Sara Petrin
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, 35020 Legnaro, Italy; (S.P.); (P.A.); (A.P.); (C.L.)
| | - Pietro Antonelli
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, 35020 Legnaro, Italy; (S.P.); (P.A.); (A.P.); (C.L.)
| | - Arianna Peruzzo
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, 35020 Legnaro, Italy; (S.P.); (P.A.); (A.P.); (C.L.)
- PhD National Programme in One Health Approaches to Infectious Diseases and Life Science Research, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy
| | - Alessandra Pezzuto
- Laboratory of Hygiene and Safety of the Food Chain, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, 35020 Legnaro, Italy; (A.P.); (M.F.)
| | - Michela Favretti
- Laboratory of Hygiene and Safety of the Food Chain, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, 35020 Legnaro, Italy; (A.P.); (M.F.)
| | - Marco Bragolusi
- Laboratorio di Chimica Sperimentale, Istituto Zooprofilattico Sperimentale delle Venezie, Viale Fiume 78, 36100 Vicenza, Italy; (A.M.); (B.M.); (M.B.); (C.Z.); (R.P.)
| | - Carmela Zacometti
- Laboratorio di Chimica Sperimentale, Istituto Zooprofilattico Sperimentale delle Venezie, Viale Fiume 78, 36100 Vicenza, Italy; (A.M.); (B.M.); (M.B.); (C.Z.); (R.P.)
| | - Carmen Losasso
- Laboratory of Microbial Ecology and Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell’Università, 35020 Legnaro, Italy; (S.P.); (P.A.); (A.P.); (C.L.)
| | - Roberto Piro
- Laboratorio di Chimica Sperimentale, Istituto Zooprofilattico Sperimentale delle Venezie, Viale Fiume 78, 36100 Vicenza, Italy; (A.M.); (B.M.); (M.B.); (C.Z.); (R.P.)
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Liang Q, Liu S, Xu W, Zhai Y. Capillary-in-Capillary Electrospray Ionization (CC-ESI) Source Enabling Convenient Sampling and Quantitative Analysis for Point-of-Care Testing. Anal Chem 2023; 95:2420-2427. [PMID: 36642870 DOI: 10.1021/acs.analchem.2c04524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
With outstanding analytical performances, mass spectrometry (MS) has shown great potential for clinical applications. To facilitate the sampling process and quantitative analysis, a capillary-in-capillary electrospray ionization (CC-ESI) source was developed in this study. Utilizing two nested capillaries as a sampler and an ESI emitter, the source enabled spontaneous liquid sampling based on the capillary phenomenon and electrospray ionization mass spectrometry (ESI-MS) analysis. Apart from the cheap price, high portability, and disposability, the CC-ESI had merits of quantitation capability as well as adequate sensitivity. By coupling CC-ESI to a miniature mass spectrometer (mini-MS), a limit of detection (LOD) of 1 ng/mL was achieved for standard imatinib at collision-induced dissociation (CID) tandem MS mode, and a LOQ of 1 ng/mL was obtained for atenolol and imatinib (with isotopic internal standard) at multiple ion reaction monitoring (MRM) modes. As two demonstrations for analysis of practical samples, rapid analysis of abused drugs on surface and quantitative analysis of therapeutic drugs in whole blood were also performed with a CC-ESI mini-MS.
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Affiliation(s)
- Qiong Liang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Siyu Liu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China.,Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, China
| | - Yanbing Zhai
- Institute of Engineering Medicine, Beijing Institute of Technology, Beijing 100081, China.,School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
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Lima NM, Dos Santos GF, da Silva Lima G, Vaz BG. Advances in Mass Spectrometry-Metabolomics Based Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1439:101-122. [PMID: 37843807 DOI: 10.1007/978-3-031-41741-2_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Highly selective and sensitive analytical techniques are necessary for microbial metabolomics due to the complexity of the microbial sample matrix. Hence, mass spectrometry (MS) has been successfully applied in microbial metabolomics due to its high precision, versatility, sensitivity, and wide dynamic range. The different analytical tools using MS have been employed in microbial metabolomics investigations and can contribute to the discovery or accelerate the search for bioactive substances. The coupling with chromatographic and electrophoretic separation techniques has resulted in more efficient technologies for the analysis of microbial compounds occurring in trace levels. This book chapter describes the current advances in the application of mass spectrometry-based metabolomics in the search for new biologically active agents from microbial sources; the development of new approaches for in silico annotation of natural products; the different technologies employing mass spectrometry imaging to deliver more comprehensive analysis and elucidate the metabolome involved in ecological interactions as they enable visualization of the spatial dispersion of small molecules. We also describe other ambient ionization techniques applied to the fingerprint of microbial natural products and modern techniques such as ion mobility mass spectrometry used to microbial metabolomic analyses and the dereplication of natural microbial products through MS.
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Tsai SH, Chen YT, Yang YL, Lee BY, Huang CJ, Chen CY. The Potential Biocontrol Agent Paenibacillus polymyxa TP3 Produces Fusaricidin-Type Compounds Involved in the Antagonism Against Gray Mold Pathogen Botrytis cinerea. PHYTOPATHOLOGY 2022; 112:775-783. [PMID: 34587815 DOI: 10.1094/phyto-04-21-0178-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Paenibacillus polymyxa is a beneficial bacterium for plant health. P. polymyxa TP3 exhibits antagonistic activity toward Botrytis cinerea and alleviates gray mold symptoms on the leaves of strawberry plants. Moreover, suppression of gray mold on the flowers and fruits of strawberry plants in field trials, including vegetative cells and endospores, was demonstrated, indicating the potential of strain TP3 as a biological control agent. To examine the anti-B. cinerea compounds produced by P. polymyxa TP3, we performed matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, and fusaricidin-corresponding mass spectra were detected. Moreover, fusaricidin-related signals appeared in imaging mass spectrometry of TP3 when confronted with B. cinerea. By using liquid chromatography mass spectrometry-based molecular networking approach, we identified several fusaricidins including a new variant of mass/charge ratio 917.5455 with serine in the first position of the hexapeptide. Via advanced mass spectrometry and network analysis, fusaricidin-type compounds produced by P. polymyxa TP3 were efficiently disclosed and were presumed to play roles in the antagonism against gray mold pathogen B. cinerea.
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Affiliation(s)
- Shuen-Huang Tsai
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 10617, Taiwan, Republic of China
| | - Yu-Ting Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 10617, Taiwan, Republic of China
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan, Republic of China
| | - Bo-Yi Lee
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 10617, Taiwan, Republic of China
| | - Chien-Jui Huang
- Department of Plant Medicine, National Chiayi University, Chiayi 60004, Taiwan, Republic of China
| | - Chao-Ying Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei 10617, Taiwan, Republic of China
- Master Program for Plant Medicine, National Taiwan University, Taipei 10617, Taiwan, Republic of China
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Naureen Z, Gilani SA, Benny BK, Sadia H, Hafeez FY, Khanum A. Metabolomic Profiling of Plant Growth-Promoting Rhizobacteria for Biological Control of Phytopathogens. Fungal Biol 2022. [DOI: 10.1007/978-3-031-04805-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Gupta P, Verma A, Rai N, Singh AK, Singh SK, Kumar B, Kumar R, Gautam V. Mass Spectrometry-Based Technology and Workflows for Studying the Chemistry of Fungal Endophyte Derived Bioactive Compounds. ACS Chem Biol 2021; 16:2068-2086. [PMID: 34724607 DOI: 10.1021/acschembio.1c00581] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Bioactive compounds have gained substantial attention in research and have conferred great advancements in the industrial and pharmacological fields. Highly diverse fungi and their metabolome serve as a big platform to be explored for their diverse bioactive compounds. Omics tools coupled with bioinformatics, statistical, and well-developed algorithm tools have elucidated immense knowledge about fungal endophyte derived bioactive compounds. Further, these compounds are subjected to chromatography-gas chromatography and liquid chromatography (LC), spectroscopy-nuclear magnetic resonance (NMR), and "soft ionization" technique-matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) based analytical techniques for structural characterization. The mass spectrometry (MS)-based approach, being highly sensitive, reproducible, and reliable, produces quick and high-profile identification. Coupling these techniques with MS has resulted in a descriptive account of the identification and quantification of fungal endophyte derived bioactive compounds. This paper emphasizes the workflows of the above-mentioned techniques, their advancement, and future directions to study the unraveled area of chemistry of fungal endophyte-derived bioactive compounds.
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Affiliation(s)
- Priyamvada Gupta
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
| | - Ashish Verma
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
| | - Nilesh Rai
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
| | - Anurag Kumar Singh
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
| | - Santosh Kumar Singh
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
| | - Brijesh Kumar
- Department of Pharmacology, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
| | - Rajiv Kumar
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
| | - Vibhav Gautam
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, India
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Tata A, Marzoli F, Massaro A, Passabì E, Bragolusi M, Negro A, Cristaudo I, Piro R, Belluco S. Assessing direct analysis in real-time mass spectrometry for the identification and serotyping of Legionella pneumophila. J Appl Microbiol 2021; 132:1479-1488. [PMID: 34543502 DOI: 10.1111/jam.15301] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/01/2021] [Accepted: 09/05/2021] [Indexed: 12/11/2022]
Abstract
AIMS The efficacy of ambient mass spectrometry to identify and serotype Legionella pneumophila was assessed. To this aim, isolated waterborne colonies were submitted to a rapid extraction method and analysed by direct analysis in real-time mass spectrometry (DART-HRMS). METHODS AND RESULTS The DART-HRMS profiles, coupled with partial least squares discriminant analysis (PLS-DA), were first evaluated for their ability to differentiate Legionella spp. from other bacteria. The resultant classification model achieved an accuracy of 98.1% on validation. Capitalising on these encouraging results, DART-HRMS profiling was explored as an alternative approach for the identification of L. pneumophila sg. 1, L. pneumophila sg. 2-15 and L. non-pneumophila; therefore, a different PLS-DA classifier was built. When tested on a validation set, this second classifier reached an overall accuracy of 95.93%. It identified the harmful L. pneumophila sg. 1 with an impressive specificity (100%) and slightly lower sensitivity (91.7%), and similar performances were reached in the classification of L. pneumophila sg. 2-15 and L. non-pneumophila. CONCLUSIONS The results of this study show the DART-HMRS method has good accuracy, and it is an effective method for Legionella serogroup profiling. SIGNIFICANCE AND IMPACT OF THE STUDY These preliminary findings could open a new avenue for the rapid identification and quick epidemiologic tracing of L. pneumophila, with a consequent improvement to risk assessment.
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Affiliation(s)
- Alessandra Tata
- Istituto Zooprofilattico Sperimentale delle Venezie, Laboratorio di Chimica Sperimentale, Vicenza, Italy
| | - Filippo Marzoli
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Andrea Massaro
- Istituto Zooprofilattico Sperimentale delle Venezie, Laboratorio di Chimica Sperimentale, Vicenza, Italy
| | - Eleonora Passabì
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Marco Bragolusi
- Istituto Zooprofilattico Sperimentale delle Venezie, Laboratorio di Chimica Sperimentale, Vicenza, Italy
| | - Alessandro Negro
- Istituto Zooprofilattico Sperimentale delle Venezie, Laboratorio di Chimica Sperimentale, Vicenza, Italy
| | - Ilaria Cristaudo
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Roberto Piro
- Istituto Zooprofilattico Sperimentale delle Venezie, Laboratorio di Chimica Sperimentale, Vicenza, Italy
| | - Simone Belluco
- Department of Food Safety, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
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Ding L, Bar-Shalom R, Aharonovich D, Kurisawa N, Patial G, Li S, He S, Yan X, Iwasaki A, Suenaga K, Zhu C, Luo H, Tian F, Fares F, Naman CB, Luzzatto-Knaan T. Metabolomic Characterization of a cf. Neolyngbya Cyanobacterium from the South China Sea Reveals Wenchangamide A, a Lipopeptide with In Vitro Apoptotic Potential in Colon Cancer Cells. Mar Drugs 2021; 19:md19070397. [PMID: 34356822 PMCID: PMC8307421 DOI: 10.3390/md19070397] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/17/2022] Open
Abstract
Metabolomics can be used to study complex mixtures of natural products, or secondary metabolites, for many different purposes. One productive application of metabolomics that has emerged in recent years is the guiding direction for isolating molecules with structural novelty through analysis of untargeted LC-MS/MS data. The metabolomics-driven investigation and bioassay-guided fractionation of a biomass assemblage from the South China Sea dominated by a marine filamentous cyanobacteria, cf. Neolyngbya sp., has led to the discovery of a natural product in this study, wenchangamide A (1). Wenchangamide A was found to concentration-dependently cause fast-onset apoptosis in HCT116 human colon cancer cells in vitro (24 h IC50 = 38 μM). Untargeted metabolomics, by way of MS/MS molecular networking, was used further to generate a structural proposal for a new natural product analogue of 1, here coined wenchangamide B, which was present in the organic extract and bioactive sub-fractions of the biomass examined. The wenchangamides are of interest for anticancer drug discovery, and the characterization of these molecules will facilitate the future discovery of related natural products and development of synthetic analogues.
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Affiliation(s)
- Lijian Ding
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 31905, Israel;
| | - Rinat Bar-Shalom
- Department of Human Biology, Faculty of Life Sciences, University of Haifa, Haifa 31905, Israel; (R.B.-S.); (F.F.)
| | - Dikla Aharonovich
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 31905, Israel;
| | - Naoaki Kurisawa
- Department of Chemistry, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan; (N.K.); (A.I.); (K.S.)
| | - Gaurav Patial
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
| | - Shuang Li
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
| | - Shan He
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
| | - Xiaojun Yan
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
| | - Arihiro Iwasaki
- Department of Chemistry, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan; (N.K.); (A.I.); (K.S.)
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
| | - Kiyotake Suenaga
- Department of Chemistry, Keio University, 3-14-1, Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan; (N.K.); (A.I.); (K.S.)
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
| | - Chengcong Zhu
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
| | - Haixi Luo
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
| | - Fuli Tian
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
| | - Fuad Fares
- Department of Human Biology, Faculty of Life Sciences, University of Haifa, Haifa 31905, Israel; (R.B.-S.); (F.F.)
| | - C. Benjamin Naman
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, Department of Marine Pharmacy, College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo 315800, China; (L.D.); (G.P.); (S.L.); (S.H.); (X.Y.)
- Key Laboratory of Medicinal and Edible Plant Resources of Hainan Province, Hainan Vocational University of Science and Technology, Haikou 571126, China; (C.Z.); (H.L.); (F.T.)
- Correspondence: (C.B.N.); (T.L.-K.)
| | - Tal Luzzatto-Knaan
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa 31905, Israel;
- Correspondence: (C.B.N.); (T.L.-K.)
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Ayhan K, Coşansu S, Orhan-Yanıkan E, Gülseren G. Advance methods for the qualitative and quantitative determination of microorganisms. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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AlMasoud N, Muhamadali H, Chisanga M, AlRabiah H, Lima CA, Goodacre R. Discrimination of bacteria using whole organism fingerprinting: the utility of modern physicochemical techniques for bacterial typing. Analyst 2021; 146:770-788. [DOI: 10.1039/d0an01482f] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review compares and contrasts MALDI-MS, FT-IR spectroscopy and Raman spectroscopy for whole organism fingerprinting and bacterial typing.
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Affiliation(s)
- Najla AlMasoud
- Department of Chemistry
- College of Science
- Princess Nourah bint Abdulrahman University
- Riyadh 11671
- Saudi Arabia
| | - Howbeer Muhamadali
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
| | - Malama Chisanga
- School of Chemistry and Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Haitham AlRabiah
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh
- Saudi Arabia
| | - Cassio A. Lima
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
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Pailliè-Jiménez ME, Stincone P, Brandelli A. Natural Pigments of Microbial Origin. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.590439] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Newman DJ, Cragg GM. Plant Endophytes and Epiphytes: Burgeoning Sources of Known and "Unknown" Cytotoxic and Antibiotic Agents? PLANTA MEDICA 2020; 86:891-905. [PMID: 32023633 DOI: 10.1055/a-1095-1111] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
In the last 20 or so years, the influence of endophytes and, quite recently, epiphytes of plants upon the compounds found in those plants, which were usually assumed to be phytochemicals produced by the plant for a variety of reasons, often as a defense against predators, is becoming more evident, in particular in the case of antitumor agents originally isolated from plant sources, though antibiotic agents might also be found, particularly from epiphytes. In this review, we started with the first report in 1993 of a taxol-producing endophyte and then expanded the compounds discussed to include camptothecin, the vinca alkaloids, podophyllotoxin, and homoharringtonine from endophytic microbes and then the realization that maytansine is not a plant secondary metabolite at all, and that even such a well-studied plant such as Arabidopsis thaliana has a vast repertoire of potential bioactive agents in its leaf epiphytic bacteria. We have taken data from a variety of sources, including a reasonable history of these discoveries that were not given in recent papers by us, nor in other papers covering this topic. The sources included the Scopus database, but we also performed other searches using bibliographic tools, thus, the majority of the papers referenced are the originals, though we note some very recent papers that have built on previous results. We concluded with a discussion of the more modern techniques that can be utilized to "persuade" endophytes and epiphytes to switch on silent biosynthetic pathways and how current analytical techniques may aid in evaluating such programs. We also comment at times on some findings, particularly in the case of homoharringtonine, where there are repetitious data reports differing by a few years claiming the same endophyte as the producer.
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Affiliation(s)
- David J Newman
- NIH Special Volunteer, NCI Natural Products Branch, Wayne, PA, USA
| | - Gordon M Cragg
- NIH Special Volunteer, NCI Natural Products Branch, Gaithersburg, MD, USA
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13
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Calla-Quispe E, Fuentes-Rivera HL, Ramírez P, Martel C, Ibañez AJ. Mass Spectrometry: A Rosetta Stone to Learn How Fungi Interact and Talk. Life (Basel) 2020; 10:E89. [PMID: 32575729 PMCID: PMC7345136 DOI: 10.3390/life10060089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 01/08/2023] Open
Abstract
Fungi are a highly diverse group of heterotrophic organisms that play an important role in diverse ecological interactions, many of which are chemically mediated. Fungi have a very versatile metabolism, which allows them to synthesize a large number of still little-known chemical compounds, such as soluble compounds that are secreted into the medium and volatile compounds that are chemical mediators over short and long distances. Mass spectrometry (MS) is currently playing a dominant role in mycological studies, mainly due to its inherent sensitivity and rapid identification capabilities of different metabolites. Furthermore, MS has also been used as a reliable and accurate tool for fungi identification (i.e., biotyping). Here, we introduce the readers about fungal specialized metabolites, their role in ecological interactions and provide an overview on the MS-based techniques used in fungal studies. We particularly present the importance of sampling techniques, strategies to reduce false-positive identification and new MS-based analytical strategies that can be used in mycological studies, further expanding the use of MS in broader applications. Therefore, we foresee a bright future for mass spectrometry-based research in the field of mycology.
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Affiliation(s)
- Erika Calla-Quispe
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Perú (PUCP), Av. Universitaria 1801, San Miguel 15088, Lima, Peru; (E.C.-Q.); (H.L.F.-R.); (C.M.)
| | - Hammerly Lino Fuentes-Rivera
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Perú (PUCP), Av. Universitaria 1801, San Miguel 15088, Lima, Peru; (E.C.-Q.); (H.L.F.-R.); (C.M.)
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos (UNMSM), Av. Germán Amézaga 375, Lima 15081, Peru;
| | - Pablo Ramírez
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos (UNMSM), Av. Germán Amézaga 375, Lima 15081, Peru;
| | - Carlos Martel
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Perú (PUCP), Av. Universitaria 1801, San Miguel 15088, Lima, Peru; (E.C.-Q.); (H.L.F.-R.); (C.M.)
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos (UNMSM), Av. Arenales 1256, Jesús María 15072, Lima, Peru
| | - Alfredo J. Ibañez
- Instituto de Ciencias Ómicas y Biotecnología Aplicada (ICOBA), Pontificia Universidad Católica del Perú (PUCP), Av. Universitaria 1801, San Miguel 15088, Lima, Peru; (E.C.-Q.); (H.L.F.-R.); (C.M.)
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14
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Grim CM, Luu GT, Sanchez LM. Staring into the void: demystifying microbial metabolomics. FEMS Microbiol Lett 2020; 366:5519856. [PMID: 31210257 DOI: 10.1093/femsle/fnz135] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/14/2019] [Indexed: 12/18/2022] Open
Abstract
Metabolites give us a window into the chemistry of microbes and are split into two subclasses: primary and secondary. Primary metabolites are required for life whereas secondary metabolites have historically been classified as those appearing after exponential growth and are not necessarily needed for survival. Many microbial species are estimated to produce hundreds of metabolites and can be affected by differing nutrients. Using various analytical techniques, metabolites can be directly detected in order to elucidate their biological significance. Currently, a single experiment can produce anywhere from megabytes to terabytes of data. This big data has motivated scientists to develop informatics tools to help target specific metabolites or sets of metabolites. Broadly, it is imperative to identify clear biological questions before embarking on a study of metabolites (metabolomics). For instance, studying the effect of a transposon insertion on phenazine biosynthesis in Pseudomonas is a very different from asking what molecules are present in a specific banana-derived strain of Pseudomonas. This review is meant to serve as a primer for a 'choose your own adventure' approach for microbiologists with limited mass spectrometry expertise, with a strong focus on liquid chromatography mass spectrometry based workflows developed or optimized within the past five years.
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Affiliation(s)
- Cynthia M Grim
- Department of Pharmaceutical Sciences, University of Ilinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA
| | - Gordon T Luu
- Department of Pharmaceutical Sciences, University of Ilinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA
| | - Laura M Sanchez
- Department of Pharmaceutical Sciences, University of Ilinois at Chicago, 833 S Wood St, Chicago, IL 60612, USA
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15
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Pishchany G. Applying microbial ecology to antimicrobial discovery. Curr Opin Microbiol 2020; 57:7-12. [PMID: 32339893 DOI: 10.1016/j.mib.2020.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/24/2020] [Accepted: 03/30/2020] [Indexed: 01/27/2023]
Abstract
Introduction of antibiotics into clinical use has contributed to some of the greatest improvements to public health in the 20th century. Most antibiotics are based on antimicrobials that were isolated from environmental microorganisms over 50 years ago, but emerging resistance requires discovery of new molecules and development of these molecules into therapeutics. Bioinformatic analyses of microbial genomes indicate that many more microbial bioactive molecules remain undiscovered. Understanding when, where, and why these molecules are produced informs efforts to tap into the hidden unexplored chemical diversity. Expanding the search to undersampled ecological niches and improving culturing techniques will ensure discovery of new antibiotics.
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Affiliation(s)
- Gleb Pishchany
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
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16
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Götze S, Stallforth P. Structure, properties, and biological functions of nonribosomal lipopeptides from pseudomonads. Nat Prod Rep 2020; 37:29-54. [DOI: 10.1039/c9np00022d] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Bacteria of the genusPseudomonasdisplay a fascinating metabolic diversity. In this review, we focus our attention on the natural product class of nonribosomal lipopeptides, which help pseudomonads to colonize a wide range of ecological niches.
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Affiliation(s)
- Sebastian Götze
- Faculty 7: Natural and Environmental Sciences
- Institute for Environmental Sciences
- University Koblenz Landau
- 76829 Landau
- Germany
| | - Pierre Stallforth
- Junior Research Group Chemistry of Microbial Communication
- Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute (HKI)
- 07745 Jena
- Germany
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17
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Kjærbølling I, Mortensen UH, Vesth T, Andersen MR. Strategies to establish the link between biosynthetic gene clusters and secondary metabolites. Fungal Genet Biol 2019; 130:107-121. [DOI: 10.1016/j.fgb.2019.06.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/26/2019] [Accepted: 06/02/2019] [Indexed: 01/01/2023]
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18
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Park HG, Jang KS, Park HM, Song WS, Jeong YY, Ahn DH, Kim SM, Yang YH, Kim YG. MALDI-TOF MS-based total serum protein fingerprinting for liver cancer diagnosis. Analyst 2019; 144:2231-2238. [PMID: 30849133 DOI: 10.1039/c8an02241k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Serum is one of the most commonly used samples in many studies to identify protein biomarkers to diagnose cancer. Although conventional enzyme-linked immunosorbent assay (ELISA) or liquid chromatography-mass spectrometry (LC-MS)-based methods have been applied as clinical tools for diagnosing cancer, there have been troublesome problems, such as inferior multiplexing capabilities, high development costs and long turnaround times, which are inappropriate for high-throughput analytical platforms. Here, we developed a simple and robust cancer diagnostic method using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based total serum protein fingerprinting. First, serum samples were simply diluted with distilled water and subsequently spotted onto a MALDI plate without prior chromatographic purification or separation. The sample preparation method was enough to collect reproducible total serum protein fingerprints and would be highly advantageous for high-throughput assay. Each of the integrated main spectrum profiles (MSPs), which are representative of liver cancer patients (n = 40) or healthy controls (n = 80), was automatically generated by the MALDI Biotyper 3 software. The reliability of the integrated MSPs was successfully evaluated in comparison with a blind test set (n = 31), which consisted of 13 liver cancer patients and 18 healthy controls. Additionally, our partial least squares discriminant analysis (PLS-DA) demonstrated a statistically significant difference in MALDI-TOF MS-based total serum protein fingerprints between liver cancer patients and healthy controls. Taken together, this work suggests that this method may be an effective high-throughput platform technology for various cancer diagnoses and disease evaluations.
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Affiliation(s)
- Han-Gyu Park
- Department of Chemical Engineering, Soongsil University, Seoul 06978, Korea.
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19
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Luzzatto-Knaan T, Melnik AV, Dorrestein PC. Mass Spectrometry Uncovers the Role of Surfactin as an Interspecies Recruitment Factor. ACS Chem Biol 2019; 14:459-467. [PMID: 30763059 DOI: 10.1021/acschembio.8b01120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Microbes use metabolic exchange to sense and respond to their changing environment. Surfactins, produced by Bacillus subtilis, have been extensively studied for their role in biofilm formation, biosurfactant properties, and antimicrobial activity, affecting the surrounding microbial consortia. Using mass spectrometry, we reveal that Paenibacillus dendritiformis, originally isolated with B. subtilis, is not antagonized by the presence of surfactins and is actually attracted to them. We demonstrate here for the first time that P. dendritiformis is also actively degrading surfactins produced by B. subtilis and accumulating the degradation products that serve as territorial markers. This new attribute as an attractant of selected microbes and the conversion into a deterrent highlight the diverse role natural products have in shaping the environment and establishing mixed communities.
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Affiliation(s)
- Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Alexey V. Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
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20
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Liu S, Zuo J, Lu Y, Gao L, Zhai Y, Xu W. Direct bacteria analysis using laserspray ionization miniature mass spectrometry. Anal Bioanal Chem 2018; 411:4031-4040. [DOI: 10.1007/s00216-018-1385-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/15/2018] [Accepted: 09/17/2018] [Indexed: 01/29/2023]
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21
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Khan RA. Natural products chemistry: The emerging trends and prospective goals. Saudi Pharm J 2018; 26:739-753. [PMID: 29991919 PMCID: PMC6036106 DOI: 10.1016/j.jsps.2018.02.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 02/05/2018] [Indexed: 01/01/2023] Open
Abstract
The role and contributions of natural products chemistry in advancements of the physical and biological sciences, its interdisciplinary domains, and emerging of new avenues by providing novel applications, constructive inputs, thrust, comprehensive understanding, broad perspective, and a new vision for future is outlined. The developmental prospects in bio-medical, health, nutrition, and other interrelated sciences along with some of the emerging trends in the subject area are also discussed as part of the current review of the basic and core developments, innovation in techniques, advances in methodology, and possible applications with their effects on the sciences in general and natural products chemistry in particular. The overview of the progress and ongoing developments in broader areas of the natural products chemistry discipline, its role and concurrent economic and scientific implications, contemporary objectives, future prospects as well as impending goals are also outlined. A look at the natural products chemistry in providing scientific progress in various disciplines is deliberated upon.
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Affiliation(s)
- Riaz A. Khan
- Department of Medicinal Chemistry, Qassim University, Qassim 51452, Saudi Arabia
- Manav Rachna International University, National Capital Region, Faridabad, HR 121 004, India
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22
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Kind T, Tsugawa H, Cajka T, Ma Y, Lai Z, Mehta SS, Wohlgemuth G, Barupal DK, Showalter MR, Arita M, Fiehn O. Identification of small molecules using accurate mass MS/MS search. MASS SPECTROMETRY REVIEWS 2018; 37:513-532. [PMID: 28436590 PMCID: PMC8106966 DOI: 10.1002/mas.21535] [Citation(s) in RCA: 265] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 03/17/2017] [Accepted: 03/18/2017] [Indexed: 05/03/2023]
Abstract
Tandem mass spectral library search (MS/MS) is the fastest way to correctly annotate MS/MS spectra from screening small molecules in fields such as environmental analysis, drug screening, lipid analysis, and metabolomics. The confidence in MS/MS-based annotation of chemical structures is impacted by instrumental settings and requirements, data acquisition modes including data-dependent and data-independent methods, library scoring algorithms, as well as post-curation steps. We critically discuss parameters that influence search results, such as mass accuracy, precursor ion isolation width, intensity thresholds, centroiding algorithms, and acquisition speed. A range of publicly and commercially available MS/MS databases such as NIST, MassBank, MoNA, LipidBlast, Wiley MSforID, and METLIN are surveyed. In addition, software tools including NIST MS Search, MS-DIAL, Mass Frontier, SmileMS, Mass++, and XCMS2 to perform fast MS/MS search are discussed. MS/MS scoring algorithms and challenges during compound annotation are reviewed. Advanced methods such as the in silico generation of tandem mass spectra using quantum chemistry and machine learning methods are covered. Community efforts for curation and sharing of tandem mass spectra that will allow for faster distribution of scientific discoveries are discussed.
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Affiliation(s)
- Tobias Kind
- Genome Center, Metabolomics, UC Davis, Davis, California
| | - Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Tomas Cajka
- Genome Center, Metabolomics, UC Davis, Davis, California
| | - Yan Ma
- National Institute of Biological Sciences, Beijing, People’s Republic of China
| | - Zijuan Lai
- Genome Center, Metabolomics, UC Davis, Davis, California
| | | | | | | | | | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Oliver Fiehn
- Genome Center, Metabolomics, UC Davis, Davis, California
- Faculty of Sciences, Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
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23
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Sandrin TR, Demirev PA. Characterization of microbial mixtures by mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:321-349. [PMID: 28509357 DOI: 10.1002/mas.21534] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/09/2017] [Accepted: 03/09/2017] [Indexed: 05/27/2023]
Abstract
MS applications in microbiology have increased significantly in the past 10 years, due in part to the proliferation of regulator-approved commercial MALDI MS platforms for rapid identification of clinical infections. In parallel, with the expansion of MS technologies in the "omics" fields, novel MS-based research efforts to characterize organismal as well as environmental microbiomes have emerged. Successful characterization of microorganisms found in complex mixtures of other organisms remains a major challenge for researchers and clinicians alike. Here, we review recent MS advances toward addressing that challenge. These include sample preparation methods and protocols, and established, for example, MALDI, as well as newer, for example, atmospheric pressure ionization (API) techniques. MALDI mass spectra of intact cells contain predominantly information on the highly expressed house-keeping proteins used as biomarkers. The API methods are applicable for small biomolecule analysis, for example, phospholipids and lipopeptides, and facilitate species differentiation. MS hardware and techniques, for example, tandem MS, including diverse ion source/mass analyzer combinations are discussed. Relevant examples for microbial mixture characterization utilizing these combinations are provided. Chemometrics and bioinformatics methods and algorithms, including those applied to large scale MS data acquisition in microbial metaproteomics and MS imaging of biofilms, are highlighted. Select MS applications for polymicrobial culture analysis in environmental and clinical microbiology are reviewed as well.
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Affiliation(s)
- Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona
| | - Plamen A Demirev
- Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland
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24
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Hoffmann M, Auerbach D, Panter F, Hoffmann T, Dorrestein PC, Müller R. Homospermidine Lipids: A Compound Class Specifically Formed during Fruiting Body Formation of Myxococcus xanthus DK1622. ACS Chem Biol 2018; 13:273-280. [PMID: 29185703 DOI: 10.1021/acschembio.7b00816] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The fascinating ability of myxobacteria to form multicellular spore filled fruiting bodies under starvation conditions was widely studied as a model for cooperative microbial behavior. The potential of a life cycle induced change of secondary metabolism, as a means to discover novel natural products, remains largely underexplored. We therefore studied the model organism Myxococcus xanthus DK1622 under submersed and solid cultivation conditions to find putatively life-cycle related compounds by applying statistical analysis on analytical data. Utilizing the advantageous characteristics of LC-MS, LC-MS/MS, and MALDI-MSI allowed the identification of compounds unambiguously associated with myxobacterial fruiting bodies. Our screening effort resulted in the purification and structure elucidation of a novel compound, the homospermidine lipid, from cultures that had undergone the fruiting process. A combination of molecular networking and targeted LC-MS/MS in conjunction with our in-house metabolomics database subsequently revealed alternative producers of the respective compound as well as a number of compounds belonging to the same structural class. Three further members of this compound class were isolated from an alternative producer and structurally elucidated by NMR. Insights into the biosynthesis of this novel compound class was gained by feeding of isotopically labeled substrates and in silico analysis.
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Affiliation(s)
- Michael Hoffmann
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - David Auerbach
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Panter
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Thomas Hoffmann
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
- Collaborative Mass Spectrometry Innovation Center, Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San
Diego, California 92093, United States
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California, San
Diego, California 92093, United States
| | - Rolf Müller
- Department
of Microbial Natural Products (MINS), Department of Microbial Natural Products (MINS), Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI) and Institute for Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
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25
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Shu LJ, Yang YL. Bacillus Classification Based on Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry-Effects of Culture Conditions. Sci Rep 2017; 7:15546. [PMID: 29138467 PMCID: PMC5686160 DOI: 10.1038/s41598-017-15808-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 11/02/2017] [Indexed: 12/15/2022] Open
Abstract
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a reliable and rapid technique applied widely in the identification and classification of microbes. MALDI-TOF MS has been used to identify many endospore-forming Bacillus species; however, endospores affect the identification accuracy when using MALDI-TOF MS because they change the protein composition of samples. Since culture conditions directly influence endospore formation and Bacillus growth, in this study we clarified how culture conditions influence the classification of Bacillus species by using MALDI-TOF MS. We analyzed members of the Bacillus subtilis group and Bacillus cereus group using different incubation periods, temperatures and media. Incubation period was found to affect mass spectra due to endospores which were observed mixing with vegetative cells after 24 hours. Culture temperature also resulted in different mass spectra profiles depending on the temperature best suited growth and sporulation. Conversely, the four common media for Bacillus incubation, Luria-Bertani agar, nutrient agar, plate count agar and brain-heart infusion agar did not result in any significant differences in mass spectra profiles. Profiles in the range m/z 1000-3000 were found to provide additional data to the standard ribosomal peptide/protein region m/z 3000-15000 profiles to enable easier differentiation of some highly similar species and the identification of new strains under fresh culture conditions. In summary, control of culture conditions is vital for Bacillus identification and classification by MALDI-TOF MS.
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Affiliation(s)
- Lin-Jie Shu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan.
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26
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Luzzatto-Knaan T, Garg N, Wang M, Glukhov E, Peng Y, Ackermann G, Amir A, Duggan BM, Ryazanov S, Gerwick L, Knight R, Alexandrov T, Bandeira N, Gerwick WH, Dorrestein PC. Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae. eLife 2017; 6. [PMID: 28492366 PMCID: PMC5441867 DOI: 10.7554/elife.24214] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 04/29/2017] [Indexed: 12/13/2022] Open
Abstract
Natural product screening programs have uncovered molecules from diverse natural sources with various biological activities and unique structures. However, much is yet underexplored and additional information is hidden in these exceptional collections. We applied untargeted mass spectrometry approaches to capture the chemical space and dispersal patterns of metabolites from an in-house library of marine cyanobacterial and algal collections. Remarkably, 86% of the metabolomics signals detected were not found in other available datasets of similar nature, supporting the hypothesis that marine cyanobacteria and algae possess distinctive metabolomes. The data were plotted onto a world map representing eight major sampling sites, and revealed potential geographic locations with high chemical diversity. We demonstrate the use of these inventories as a tool to explore the diversity and distribution of natural products. Finally, we utilized this tool to guide the isolation of a new cyclic lipopeptide, yuvalamide A, from a marine cyanobacterium. DOI:http://dx.doi.org/10.7554/eLife.24214.001 Cyanobacteria and algae are found in all oceans around the globe. Like plants, they can use sunlight as a source of energy in a process called photosynthesis. As a result, these organisms are important sources of oxygen and another vital nutrient called nitrogen for other marine organisms. Many of these organisms also produce a variety of other chemicals known as “natural products” to help them to survive in their environments. Some of these natural products have shown potential as medicinal drugs. The search for new chemicals with useful medicinal properties has led researchers to collect samples of algae and cyanobacteria from various locations around the world. An approach called mass spectrometry is often used to identify new chemicals because it can provide information about the structure of a molecule based on how much its fragments weigh. Luzzatto-Knaan et al. used mass spectrometry to search for new chemicals in samples of algae and cyanobacteria that had been collected by diving and snorkeling in a wide variety of tropical marine environments over several decades. The experiments reveal that the organisms in these samples produce a diverse range of chemicals, most of which were previously unknown and have not been found in other similar environmental collections. The data were grouped together into eight major collection areas covering different parts of the tropics. The samples from some areas contained a wider variety of chemicals than others. Within each collection area, some molecules were found to be very common whereas others were only present at specific locations. To highlight the distribution of these natural products, Luzzatto-Knaan et al. display the data on a world map. Further experiments used this approach as a guide to extract a previously unknown chemical called yuvalamide A from a marine cyanobacterium. The next challenge would be to associate the geographical patterns of chemicals to their potential ecological roles. This approach offers a new way to explore large-scale collections of environmental samples to discover and study new natural products. DOI:http://dx.doi.org/10.7554/eLife.24214.002
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Affiliation(s)
- Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States
| | - Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States
| | - Mingxun Wang
- Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - Evgenia Glukhov
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Yao Peng
- Department of Chemistry and Biochemistry, University of California San Diego, San Diego, United States
| | - Gail Ackermann
- Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - Amnon Amir
- Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - Brendan M Duggan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States
| | | | - Lena Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Rob Knight
- Departments of Pediatrics and Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - Theodore Alexandrov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States.,European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nuno Bandeira
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States.,Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, University of California San Diego, San Diego, United States
| | - William H Gerwick
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, United States.,Center for Computational Mass Spectrometry and Department of Computer Science and Engineering, University of California San Diego, San Diego, United States.,Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, San Diego, United States
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27
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Ho YN, Shu LJ, Yang YL. Imaging mass spectrometry for metabolites: technical progress, multimodal imaging, and biological interactions. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 9. [PMID: 28488813 DOI: 10.1002/wsbm.1387] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 01/24/2017] [Accepted: 02/28/2017] [Indexed: 12/19/2022]
Abstract
Imaging mass spectrometry (IMS) allows the study of the spatial distribution of small molecules in biological samples. IMS is able to identify and quantify chemicals in situ from whole tissue sections to single cells. Both vacuum mass spectrometry (MS) and ambient MS systems have advanced considerably over the last decade; however, some limitations are still hard to surmount. Sample pretreatment, matrix or solvent choices, and instrument improvement are the key factors that determine the successful application of IMS to different samples and analytes. IMS with innovative MS analyzers, powerful MS spectrum databases, and analysis tools can efficiently dereplicate, identify, and quantify natural products. Moreover, multimodal imaging systems and multiple MS-based systems provide additional structural, chemical, and morphological information and are applied as complementary tools to explore new fields. IMS has been applied to reveal interactions between living organisms at molecular level. Recently, IMS has helped solve many previously unidentifiable relations between bacteria, fungi, plants, animals, and insects. Other significant interactions on the chemical level can also be resolved using expanding IMS techniques. WIREs Syst Biol Med 2017, 9:e1387. doi: 10.1002/wsbm.1387 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Ying-Ning Ho
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Lin-Jie Shu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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28
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The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria. Trends Microbiol 2017; 25:280-292. [DOI: 10.1016/j.tim.2016.12.002] [Citation(s) in RCA: 240] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 11/15/2016] [Accepted: 12/05/2016] [Indexed: 01/11/2023]
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29
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Pulliam CJ, Wei P, Snyder DT, Wang X, Ouyang Z, Pielak RM, Graham Cooks R. Rapid discrimination of bacteria using a miniature mass spectrometer. Analyst 2017; 141:1633-6. [PMID: 26844973 DOI: 10.1039/c5an02575c] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Bacteria colonies were analyzed using paper spray ionization coupled with a portable mass spectrometer. The spectra were averaged and processed using multivariate analysis to discriminate between different species of bacteria based on their unique phospholipid profiles. Full scan mass spectra and product ion MS/MS data were compared to those recorded using a benchtop linear ion trap mass spectrometer.
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Affiliation(s)
| | - Pu Wei
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
| | - Dalton T Snyder
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
| | - Xiao Wang
- Department of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Zheng Ouyang
- Department of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Rafal M Pielak
- L'Oreal California Research Center, San Francisco, CA, USA
| | - R Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.
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30
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Kumaran S, Abdelhamid HN, Wu HF. Quantification analysis of protein and mycelium contents upon inhibition of melanin for Aspergillus niger: a study of matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS). RSC Adv 2017. [DOI: 10.1039/c7ra03741d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Mass spectrometry (MS) provides a simple discrimination method for microorganisms.
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Affiliation(s)
- Sekar Kumaran
- Department of Chemistry and Center for Nanoscience and Nanotechnology
- National Sun Yat-Sen University
- Kaohsiung
- Taiwan
- School of Pharmacy
| | - Hani Nasser Abdelhamid
- Department of Chemistry and Center for Nanoscience and Nanotechnology
- National Sun Yat-Sen University
- Kaohsiung
- Taiwan
- School of Pharmacy
| | - Hui-Fen Wu
- Department of Chemistry and Center for Nanoscience and Nanotechnology
- National Sun Yat-Sen University
- Kaohsiung
- Taiwan
- School of Pharmacy
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31
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New antibiotics from Nature’s chemical inventory. Bioorg Med Chem 2016; 24:6227-6252. [DOI: 10.1016/j.bmc.2016.09.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/07/2016] [Indexed: 01/07/2023]
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32
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Newman DJ. Predominately Uncultured Microbes as Sources of Bioactive Agents. Front Microbiol 2016; 7:1832. [PMID: 27917159 PMCID: PMC5114300 DOI: 10.3389/fmicb.2016.01832] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 11/01/2016] [Indexed: 12/15/2022] Open
Abstract
In this short review, I am discussing the relatively recent awareness of the role of symbionts in plant, marine-invertebrates and fungal areas. It is now quite obvious that in marine-invertebrates, a majority of compounds found are from either as yet unculturable or poorly culturable microbes, and techniques involving “state of the art” genomic analyses and subsequent computerized analyses are required to investigate these interactions. In the plant kingdom evidence is amassing that endophytes (mainly fungal in nature) are heavily involved in secondary metabolite production and that mimicking the microbial interactions of fermentable microbes leads to involvement of previously unrecognized gene clusters (cryptic clusters is one name used), that when activated, produce previously unknown bioactive molecules.
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33
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Abstract
Polyketides are a diverse group of natural products that form the basis of many important drugs. The engineering of the polyketide synthase (PKS) enzymes responsible for the formation of these compounds has long been considered to have great potential for producing new bioactive molecules. Recent advances in this field have contributed to the understanding of this powerful and complex enzymatic machinery, particularly with regard to domain activity and engineering, unique building block formation and incorporation, and programming rules and limitations. New developments in tools for
in vitro biochemical analysis, full-length megasynthase structural studies, and
in vivo heterologous expression will continue to improve our fundamental understanding of polyketide synthesis as well as our ability to engineer the production of polyketides.
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Affiliation(s)
- Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
| | - Joyce Liu
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
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34
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Beemelmanns C, Guo H, Rischer M, Poulsen M. Natural products from microbes associated with insects. Beilstein J Org Chem 2016; 12:314-27. [PMID: 26977191 PMCID: PMC4778507 DOI: 10.3762/bjoc.12.34] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/02/2016] [Indexed: 12/11/2022] Open
Abstract
Here we review discoveries of secondary metabolites from microbes associated with insects. We mainly focus on natural products, where the ecological role has been at least partially elucidated, and/or the pharmaceutical properties evaluated, and on compounds with unique structural features. We demonstrate that the exploration of specific microbial–host interactions, in combination with multidisciplinary dereplication processes, has emerged as a successful strategy to identify novel chemical entities and to shed light on the ecology and evolution of defensive associations.
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Affiliation(s)
- Christine Beemelmanns
- Leibniz Institute for Natural Product Research and Infection Biology e.V., Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Huijuan Guo
- Leibniz Institute for Natural Product Research and Infection Biology e.V., Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Maja Rischer
- Leibniz Institute for Natural Product Research and Infection Biology e.V., Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Michael Poulsen
- Centre for Social Evolution, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, Building 3, 1st floor, 2100 Copenhagen East, Denmark
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