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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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Maximo HJ, Araújo FDDS, Pagotto CC, Boava LP, Dalio RJD, Duarte GHB, Eberlin MN, Machado MA. Influence of Citrus sunki and Poncirus trifoliata Root Extracts on Metabolome of Phytophthora parasitica. Metabolites 2024; 14:206. [PMID: 38668334 PMCID: PMC11052222 DOI: 10.3390/metabo14040206] [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: 11/09/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 04/28/2024] Open
Abstract
Phytophthora parasitica is an oomycete pathogen that infects a broad range of crops of worldwide economic interest; among them are citrus species. In general, some Citrus and the rootstocks of related genera offer considerable resistance against P. parasitica; therefore, understanding the mechanisms involved in the virulence of this pathogen is crucial. In this work, P. parasitica secondary metabolite production was studied using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and ultrahigh-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight tandem mass spectrometry (UHPLC/ESI-Q-TOF-MS) combined with chemometric tools, and its metabolic profile was evaluated under the influence of Citrus sunki (a highly susceptible host) and Poncirus trifoliata (a resistant genotype) extracts. The root extracts of Citrus sunki had an influence on the growth and hyphae morphology, and the root extracts of P. trifoliata had an influence on the zoospore behavior. In parallel, the spatial distribution of several metabolites was revealed in P. parasitica colonies using MALDI-MSI, and the metabolite ion of m/z 246 was identified as the protonated molecule of Arg-Ala. The MALDI-MSI showed variations in the surface metabolite profile of P. parasitica under the influence of the P. trifoliata extract. The P. parasitica metabolome analysis using UHPLC-ESI-Q-TOF-MS resulted in the detection of Arg-Gln (m/z 303.1775), as well as L-arginine (m/z 175.1191) and other unidentified metabolites. Significant variations in this metabolome were detected under the influence of the plant extracts when evaluated using UHPLC-ESI-Q-TOF-MS. Both techniques proved to be complementary, offering valuable insights at the molecular level when used to assess the impact of the plant extracts on microbial physiology in vitro. The metabolites identified in this study may play significant roles in the interaction or virulence of P. parasitica, but their functional characterization remains to be analyzed. Overall, these data confirm our initial hypotheses, demonstrating that P. parasitica has the capabilities of (i) recognizing host signals and altering its reproductive programing and (ii) distinguishing between hosts with varying responses in terms of reproduction and the production of secondary metabolites.
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Affiliation(s)
- Héros José Maximo
- Biotechnology Laboratory, Centro de Citricultura Sylvio Moreira, Agronomic Institute, Cordeirópolis 13490-970, SP, Brazil; (L.P.B.); (R.J.D.D.)
- BioXyz Biotecnologia Microbiana e Bioprocessos e Industriais Ltda., Piracicaba 13414-224, SP, Brazil
| | - Francisca Diana da Silva Araújo
- ThoMSon Mass Spectrometry Laboratory, Chemistry Institute, University of Campinas, UNICAMP, Campinas 13083-970, SP, Brazil; (F.D.d.S.A.); (C.C.P.); (G.H.B.D.); (M.N.E.)
- Campus Professora Cinobelina Elvas, Federal University of Piauí, Bom Jesus 64900-000, PI, Brazil
| | - Carolina Clepf Pagotto
- ThoMSon Mass Spectrometry Laboratory, Chemistry Institute, University of Campinas, UNICAMP, Campinas 13083-970, SP, Brazil; (F.D.d.S.A.); (C.C.P.); (G.H.B.D.); (M.N.E.)
| | - Leonardo Pires Boava
- Biotechnology Laboratory, Centro de Citricultura Sylvio Moreira, Agronomic Institute, Cordeirópolis 13490-970, SP, Brazil; (L.P.B.); (R.J.D.D.)
- Centro Universitário ‘Dr. Edmundo Ulson’—UNAR, Araras 13603-112, SP, Brazil
| | - Ronaldo José Durigan Dalio
- Biotechnology Laboratory, Centro de Citricultura Sylvio Moreira, Agronomic Institute, Cordeirópolis 13490-970, SP, Brazil; (L.P.B.); (R.J.D.D.)
| | - Gustavo Henrique Bueno Duarte
- ThoMSon Mass Spectrometry Laboratory, Chemistry Institute, University of Campinas, UNICAMP, Campinas 13083-970, SP, Brazil; (F.D.d.S.A.); (C.C.P.); (G.H.B.D.); (M.N.E.)
| | - Marcos Nogueira Eberlin
- ThoMSon Mass Spectrometry Laboratory, Chemistry Institute, University of Campinas, UNICAMP, Campinas 13083-970, SP, Brazil; (F.D.d.S.A.); (C.C.P.); (G.H.B.D.); (M.N.E.)
- School of Material Engineering and Nanotechnology, MackMass Laboratory, Mackenzie Presbyterian University, São Paulo 01302-907, SP, Brazil
| | - Marcos Antonio Machado
- Biotechnology Laboratory, Centro de Citricultura Sylvio Moreira, Agronomic Institute, Cordeirópolis 13490-970, SP, Brazil; (L.P.B.); (R.J.D.D.)
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3
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Yu J, Hermann M, Smith R, Tomm H, Metwally H, Kolwich J, Liu C, Le Blanc JCY, Covey TR, Ross AC, Oleschuk R. Hyperspectral Visualization-Based Mass Spectrometry Imaging by LMJ-SSP: A Novel Strategy for Rapid Natural Product Profiling in Bacteria. Anal Chem 2023; 95:2020-2028. [PMID: 36634199 DOI: 10.1021/acs.analchem.2c04550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Mass spectrometry imaging (MSI) has been widely used to discover natural products (NPs) from underexplored microbiological sources. However, the technique is limited by incompatibility with complicated/uneven surface topography and labor-intensive sample preparation, as well as lengthy compound profiling procedures. Here, liquid micro-junction surface sampling probe (LMJ-SSP)-based MSI is used for rapid profiling of natural products from Gram-negative marine bacteria Pseudoalteromonas on nutrient agar media without any sample preparation. A conductance-based autosampling platform with 1 mm spatial resolution and an innovative multivariant analysis-driven method was used to create one hyperspectral image for the sampling area. NP discovery requires general spatial correlation between m/z and colony location but not highly precise spatial resolution. The hyperspectral image was used to annotate different m/z by straightforward color differences without the need to directly interrogate the spectra. To demonstrate the utility of our approach, the rapid analysis of Pseudoalteromonas rubra DSM6842, Pseudoalteromonas tunicata DSM14096, Pseudoalteromonas piscicida JCM20779, and Pseudoalteromonas elyakovii ATCC700519 cultures was directly performed on Agar. Various natural products, including prodiginine and tambjamine analogues, were quickly identified from the hyperspectral image, and the dynamic extracellular environment was shown with compound heatmaps. Hyperspectral visualization-based MSI is an efficient and sensitive strategy for direct and rapid natural product profiling from different Pseudoalteromonas strains.
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Affiliation(s)
- Jian Yu
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Matthias Hermann
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Rachael Smith
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Hailey Tomm
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Haidy Metwally
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Jennifer Kolwich
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Chang Liu
- SCIEX, Concord, Ontario L4K 4 V8, Canada
| | | | | | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Richard Oleschuk
- Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
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Feucherolles M, Frache G. MALDI Mass Spectrometry Imaging: A Potential Game-Changer in a Modern Microbiology. Cells 2022; 11:cells11233900. [PMID: 36497158 PMCID: PMC9738593 DOI: 10.3390/cells11233900] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/11/2022] Open
Abstract
Nowadays, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is routinely implemented as the reference method for the swift and straightforward identification of microorganisms. However, this method is not flawless and there is a need to upgrade the current methodology in order to free the routine lab from incubation time and shift from a culture-dependent to an even faster independent culture system. Over the last two decades, mass spectrometry imaging (MSI) gained tremendous popularity in life sciences, including microbiology, due to its ability to simultaneously detect biomolecules, as well as their spatial distribution, in complex samples. Through this literature review, we summarize the latest applications of MALDI-MSI in microbiology. In addition, we discuss the challenges and avenues of exploration for applying MSI to solve current MALDI-TOF MS limits in routine and research laboratories.
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Li H, Li Z. The Exploration of Microbial Natural Products and Metabolic Interaction Guided by Mass Spectrometry Imaging. Bioengineering (Basel) 2022; 9:707. [PMID: 36421108 PMCID: PMC9687252 DOI: 10.3390/bioengineering9110707] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/02/2022] [Accepted: 11/12/2022] [Indexed: 10/17/2023] Open
Abstract
As an impressive mass spectrometry technology, mass spectrometric imaging (MSI) can provide mass spectra data and spatial distribution of analytes simultaneously. MSI has been widely used in diverse fields such as clinical diagnosis, the pharmaceutical industry and environmental study due to its accuracy, high resolution and developing reproducibility. Natural products (NPs) have been a critical source of leading drugs; almost half of marketed drugs are derived from NPs or their derivatives. The continuous search for bioactive NPs from microorganisms or microbiomes has always been attractive. MSI allows us to analyze and characterize NPs directly in monocultured microorganisms or a microbial community. In this review, we briefly introduce current mainstream ionization technologies for microbial samples and the key issue of sample preparation, and then summarize some applications of MSI in the exploration of microbial NPs and metabolic interaction, especially NPs from marine microbes. Additionally, remaining challenges and future prospects are discussed.
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Affiliation(s)
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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6
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Michán C, Blasco J, Alhama J. High-throughput molecular analyses of microbiomes as a tool to monitor the wellbeing of aquatic environments. Microb Biotechnol 2021; 14:870-885. [PMID: 33559398 PMCID: PMC8085945 DOI: 10.1111/1751-7915.13763] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/12/2021] [Accepted: 01/19/2021] [Indexed: 12/15/2022] Open
Abstract
Aquatic environments are the recipients of many sources of environmental stress that trigger both local and global changes. To evaluate the associated risks to organisms and ecosystems more sensitive and accurate strategies are required. The analysis of the microbiome is one of the most promising candidates for environmental diagnosis of aquatic systems. Culture-independent interconnected meta-omic approaches are being increasing used to fill the gaps that classical microbial approaches cannot resolve. Here, we provide a prospective view of the increasing application of these high-throughput molecular technologies to evaluate the structure and functional activity of microbial communities in response to changes and disturbances in the environment, mostly of anthropogenic origin. Some relevant topics are reviewed, such as: (i) the use of microorganisms for water quality assessment, highlighting the incidence of antimicrobial resistance as an increasingly serious threat to global public health; (ii) the crucial role of microorganisms and their complex relationships with the ongoing climate change, and other stress threats; (iii) the responses of the environmental microbiome to extreme pollution conditions, such as acid mine drainage or oil spills. Moreover, protists and viruses, due to their huge impacts on the structure of microbial communities, are emerging candidates for the assessment of aquatic environmental health.
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Affiliation(s)
- Carmen Michán
- Departamento de Bioquímica y Biología MolecularCampus de Excelencia Internacional Agroalimentario CeiA3Universidad de CórdobaCampus de Rabanales, Edificio Severo OchoaCórdobaE‐14071Spain
| | - Julián Blasco
- Department of Ecology and Coastal ManagementICMAN‐CSICCampus Rio San PedroPuerto Real (Cádiz)E‐11510Spain
| | - José Alhama
- Departamento de Bioquímica y Biología MolecularCampus de Excelencia Internacional Agroalimentario CeiA3Universidad de CórdobaCampus de Rabanales, Edificio Severo OchoaCórdobaE‐14071Spain
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Santos T, Théron L, Chambon C, Viala D, Centeno D, Esbelin J, Hébraud M. MALDI mass spectrometry imaging and in situ microproteomics of Listeria monocytogenes biofilms. J Proteomics 2018; 187:152-160. [PMID: 30071319 DOI: 10.1016/j.jprot.2018.07.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/16/2018] [Accepted: 07/16/2018] [Indexed: 02/08/2023]
Abstract
MALDI-TOF Mass spectrometry Imaging (MSI) is a surface-sampling technology that can determine spatial information and relative abundance of analytes directly from biological samples. Human listeriosis cases are due to the ingestion of contaminated foods with the pathogenic bacteria Listeria monocytogenes. The reduction of water availability in food workshops by decreasing the air relative humidity (RH) is one strategy to improve the control of bacterial contamination. This study aims to develop and implement an MSI approach on L. monocytogenes biofilms and proof of concept using a dehumidified stress condition. MSI allowed examining the distribution of low molecular weight proteins within the biofilms subjected to a dehumidification environment, mimicking the one present in a food workshop (10 °C, 75% RH). Furthermore, a LC-MS/MS approach was made to link the dots between MSI and protein identification. Five identified proteins were assigned to registered MSI m/z, including two cold-shock proteins and a ligase involved in cell wall biogenesis. These data demonstrate how imaging can be used to dissect the proteome of an intact bacterial biofilm giving new insights into protein expression relating to a dehumidification stress adaptation. Data are available via ProteomeXchange with identifier PXD010444. BIOLOGICAL SIGNIFICANCE The ready-to-eat food processing industry has the daily challenge of controlling the contamination of surfaces and machines with spoilage and pathogenic microorganisms. In some cases, it is a lost cause due to these microorganisms' capacity to withstand the cleaning treatments, like desiccation procedures. Such a case is the ubiquitous Gram-positive Bacterium Listeria monocytogenes. Its surface proteins have particular importance for the interaction with its environment, being important factors contributing to adaptation to stress conditions. There are few reproducibly techniques to obtain the surface proteins of Gram-positive cells. Here, we developed a workflow that enables the use of MALDI imaging on Gram-positive bacterium biofilms to study the impact of dehumidification on sessile cells. It will be of the most interest to test this workflow with different environmental conditions and potentially apply it to other biofilm-forming bacteria.
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Affiliation(s)
- Tiago Santos
- Université Clermont Auvergne, INRA, UMR MEDiS, F-63122 Saint-Genès Champanelle, France
| | - Laëtitia Théron
- INRA, Plateforme d'Exploration du Métabolisme, composante protéomique (PFEMcp), F-63122 Saint-Genès Champanelle, France
| | - Christophe Chambon
- INRA, Plateforme d'Exploration du Métabolisme, composante protéomique (PFEMcp), F-63122 Saint-Genès Champanelle, France
| | - Didier Viala
- INRA, Plateforme d'Exploration du Métabolisme, composante protéomique (PFEMcp), F-63122 Saint-Genès Champanelle, France
| | - Delphine Centeno
- INRA, Plateforme d'Exploration du Métabolisme, composante protéomique (PFEMcp), F-63122 Saint-Genès Champanelle, France
| | - Julia Esbelin
- Université Clermont Auvergne, INRA, UMR MEDiS, F-63122 Saint-Genès Champanelle, France
| | - Michel Hébraud
- Université Clermont Auvergne, INRA, UMR MEDiS, F-63122 Saint-Genès Champanelle, France; INRA, Plateforme d'Exploration du Métabolisme, composante protéomique (PFEMcp), F-63122 Saint-Genès Champanelle, France.
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Imaging mass spectrometry-guided fast identification of antifungal secondary metabolites from Penicillium polonicum. Appl Microbiol Biotechnol 2018; 102:8493-8500. [DOI: 10.1007/s00253-018-9218-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/29/2018] [Accepted: 07/03/2018] [Indexed: 01/27/2023]
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9
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Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function. Proc Natl Acad Sci U S A 2018; 115:4981-4986. [PMID: 29686101 PMCID: PMC5949002 DOI: 10.1073/pnas.1801247115] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mass spectrometry is a powerful technique that has been used to identify bacteria by their protein content and to assess bacterial functional traits through analysis of their specialized metabolites. However, until now these analyses have operated independently, which has resulted in the inability to rapidly connect bacterial phylogenetic identity with potential environmental function. To bridge this gap, we designed a MALDI-TOF mass spectrometry data acquisition and bioinformatics pipeline (IDBac) to integrate data from both intact protein and specialized metabolite spectra directly from bacterial cells grown on agar. This technique organizes bacteria into highly similar phylogenetic groups and allows for comparison of metabolic differences of hundreds of isolates in just a few hours. For decades, researchers have lacked the ability to rapidly correlate microbial identity with bacterial metabolism. Since specialized metabolites are critical to bacterial function and survival in the environment, we designed a data acquisition and bioinformatics technique (IDBac) that utilizes in situ matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to analyze protein and specialized metabolite spectra recorded from single bacterial colonies picked from agar plates. We demonstrated the power of our approach by discriminating between two Bacillus subtilis strains in <30 min solely on the basis of their differential ability to produce cyclic peptide antibiotics surfactin and plipastatin, caused by a single frameshift mutation. Next, we used IDBac to detect subtle intraspecies differences in the production of metal scavenging acyl-desferrioxamines in a group of eight freshwater Micromonospora isolates that share >99% sequence similarity in the 16S rRNA gene. Finally, we used IDBac to simultaneously extract protein and specialized metabolite MS profiles from unidentified Lake Michigan sponge-associated bacteria isolated from an agar plate. In just 3 h, we created hierarchical protein MS groupings of 11 environmental isolates (10 MS replicates each, for a total of 110 spectra) that accurately mirrored phylogenetic groupings. We further distinguished isolates within these groupings, which share nearly identical 16S rRNA gene sequence identity, based on interspecies and intraspecies differences in specialized metabolite production. IDBac is an attempt to couple in situ MS analyses of protein content and specialized metabolite production to allow for facile discrimination of closely related bacterial colonies.
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10
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Stasulli NM, Shank EA. Profiling the metabolic signals involved in chemical communication between microbes using imaging mass spectrometry. FEMS Microbiol Rev 2018; 40:807-813. [PMID: 28204504 DOI: 10.1093/femsre/fuw032] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/11/2016] [Accepted: 07/22/2016] [Indexed: 02/07/2023] Open
Abstract
The ability of microbes to secrete bioactive chemical signals into their environment has been known for over a century. However, it is only in the last decade that imaging mass spectrometry has provided us with the ability to directly visualize the spatial distributions of these microbial metabolites. This technology involves collecting mass spectra from multiple discrete locations across a biological sample, yielding chemical ‘maps’ that simultaneously reveal the distributions of hundreds of metabolites in two dimensions. Advances in microbial imaging mass spectrometry summarized here have included the identification of novel strain- or coculture-specific compounds, the visualization of biotransformation events (where one metabolite is converted into another by a neighboring microbe), and the implementation of a method to reconstruct the 3D subsurface distributions of metabolites, among others. Here we review the recent literature and discuss how imaging mass spectrometry has spurred novel insights regarding the chemical consequences of microbial interactions.
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Affiliation(s)
- Nikolas M Stasulli
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA
| | - Elizabeth A Shank
- Department of Biology, University of North Carolina at Chapel Hill, NC, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, NC, USA.,Curriculum of Genetics and Molecular Biology, University of North Carolina at Chapel Hill, NC, USA
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11
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Vallet M, Vanbellingen QP, Fu T, Le Caer JP, Della-Negra S, Touboul D, Duncan KR, Nay B, Brunelle A, Prado S. An Integrative Approach to Decipher the Chemical Antagonism between the Competing Endophytes Paraconiothyrium variabile and Bacillus subtilis. JOURNAL OF NATURAL PRODUCTS 2017; 80:2863-2873. [PMID: 29139291 DOI: 10.1021/acs.jnatprod.6b01185] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
An integrative approach combining traditional natural products chemistry, molecular networking, and mass spectrometry imaging has been undertaken to decipher the molecular dialogue between the fungus Paraconiothyrium variabile and the bacterium Bacillus subtilis, which were isolated as endophytes from the conifer Cephalotaxus harringtonia and are characterized by a strong and mutual antibiosis. From this study, we highlight that bacterial surfactins and a fungal tetronic acid are involved in such competition and that the fungus is able to hydrolyze surfactins to fight against the bacterial partner.
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Affiliation(s)
- Marine Vallet
- Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS , CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Quentin P Vanbellingen
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Tingting Fu
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Jean-Pierre Le Caer
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Serge Della-Negra
- Institut de Physique Nucléaire, UMR8608, IN2P3-CNRS, Université Paris-Sud, Université Paris-Saclay , 91406, Orsay, France
| | - David Touboul
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Katherine R Duncan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, HW608, University of Strathclyde , 161 Cathedral Street, Glasgow G4 ORE, U.K
| | - Bastien Nay
- Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS , CP 54, 57 rue Cuvier, 75005 Paris, France
| | - Alain Brunelle
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Sud, Université Paris-Saclay , Avenue de la Terrasse, 91198 Gif-sur-Yvette, France
| | - Soizic Prado
- Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS , CP 54, 57 rue Cuvier, 75005 Paris, France
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12
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Antony-Babu S, Stien D, Eparvier V, Parrot D, Tomasi S, Suzuki MT. Multiple Streptomyces species with distinct secondary metabolomes have identical 16S rRNA gene sequences. Sci Rep 2017; 7:11089. [PMID: 28894255 PMCID: PMC5593946 DOI: 10.1038/s41598-017-11363-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 08/23/2017] [Indexed: 11/19/2022] Open
Abstract
Microbial diversity studies using small subunit (SSU) rRNA gene sequences continue to advance our understanding of biological and ecological systems. Although a good predictor of overall diversity, using this gene to infer the presence of a species in a sample is more controversial. Here, we present a detailed polyphasic analysis of 10 bacterial strains isolated from three coastal lichens Lichina confinis, Lichina pygmaea and Roccella fuciformis with SSU rRNA gene sequences identical to the type strain of Streptomyces cyaneofuscatus. This analysis included phenotypic, microscopic, genetic and genomic comparisons and showed that despite their identical SSU rRNA sequences the strains had markedly different properties, and could be distinguished as 5 different species. Significantly, secondary metabolites profiles from these strains were also found to be different. It is thus clear that SSU rRNA based operational taxonomy units, even at the most stringent cut-off can represent multiple bacterial species, and that at least for the case of Streptomyces, strain de-replication based on SSU gene sequences prior to screening for bioactive molecules can miss potentially interesting novel molecules produced by this group that is notorious for the production of drug-leads.
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Affiliation(s)
- Sanjay Antony-Babu
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, F-66650 Banyuls/Mer, France CNRS, USR 3579, LBBM, Observatoire Océanologique, 66650, Banyuls-sur-Mer, France
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States of America
| | - Didier Stien
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, F-66650 Banyuls/Mer, France CNRS, USR 3579, LBBM, Observatoire Océanologique, 66650, Banyuls-sur-Mer, France
| | - Véronique Eparvier
- CNRS, Institut de Chimie des Substances Naturelles, 91198, Gif-sur-Yvette cedex, France
| | - Delphine Parrot
- UMR CNRS 6226, Institut des Sciences Chimiques de Rennes, Equipe CORINT "Chimie Organique et Interface", UFR Sciences Pharmaceutiques et Biologiques, Univ. Rennes 1, Université Bretagne Loire, 2 Avenue du Pr. Léon Bernard, F-35043, Rennes, France
| | - Sophie Tomasi
- UMR CNRS 6226, Institut des Sciences Chimiques de Rennes, Equipe CORINT "Chimie Organique et Interface", UFR Sciences Pharmaceutiques et Biologiques, Univ. Rennes 1, Université Bretagne Loire, 2 Avenue du Pr. Léon Bernard, F-35043, Rennes, France
| | - Marcelino T Suzuki
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, F-66650 Banyuls/Mer, France CNRS, USR 3579, LBBM, Observatoire Océanologique, 66650, Banyuls-sur-Mer, France.
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13
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Araújo FDDS, Araújo WL, Eberlin MN. Potential of Burkholderia seminalis TC3.4.2R3 as Biocontrol Agent Against Fusarium oxysporum Evaluated by Mass Spectrometry Imaging. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:901-907. [PMID: 28194740 DOI: 10.1007/s13361-017-1610-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/18/2017] [Accepted: 01/19/2017] [Indexed: 06/06/2023]
Abstract
Species of genus Burkholderia display different interaction profiles in the environment, causing either several diseases in plants and animals or being beneficial to some plants, promoting their growth, and suppressing phytopathogens. Burkholderia spp. also produce many types of biomolecules with antimicrobial activity, which may be commercially used to protect crops of economic interest, mainly against fungal diseases. Herein we have applied matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) to investigate secondary metabolites produced by B. seminalis TC3.4.2R3 in monoculture and coculture with plant pathogen Fusarium oxysporum. The siderophore pyochelin and the rhamnolipid Rha-Rha-C15-C14 were detected in wild-type B. seminalis strain, and their productions were found to vary in mutant strains carrying disruptions in gene clusters associated with antimicrobial compounds. Two mycotoxins were detected in F. oxysporum. During coculture with B. seminalis, metabolites probably related to defense mechanisms of these microorganisms were observed in the interspecies interaction zone. Our findings demonstrate the effective application of MALDI-MSI in the detection of bioactive molecules involved in the defense mechanism of B. seminalis, and these findings suggest the potential use of this bacterium in the biocontrol of plant diseases caused by F. oxysporum. Graphical Abstract ᅟ.
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Affiliation(s)
- Francisca Diana da Silva Araújo
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, UNICAMP, 13083-970, Campinas, SP, Brazil.
| | - Welington Luiz Araújo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, USP, São Paulo, 05508-900, SP, Brazil
| | - Marcos Nogueira Eberlin
- ThoMSon Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, UNICAMP, 13083-970, Campinas, SP, Brazil
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14
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Liao JH, Chen PY, Yang YL, Kan SC, Hsieh FC, Liu YC. Clarification of the Antagonistic Effect of the Lipopeptides Produced by Bacillus amyloliquefaciens BPD1 against Pyricularia oryzae via In Situ MALDI-TOF IMS Analysis. Molecules 2016; 21:molecules21121670. [PMID: 27918491 PMCID: PMC6273258 DOI: 10.3390/molecules21121670] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 11/23/2022] Open
Abstract
This study tried to clarify the antagonistic effect of the lipopeptides secreted by Bacillus amyloliquefaciens strain BPD1 (Ba-BPD1) against Pyricularia oryzae Cavara (PO). To determine the major antifungal lipopeptides effective against PO, single and dual cultures were carried out in solid-state media. The matrix-assisted laser desorption/ionization–time of flight imaging mass spectrometry (MALDI-TOF IMS) was used to identify the most effective lipopeptide in situ. Meanwhile, the morphology of pathogen fungi treated with lipopeptides was observed via the SEM. Of the three lipopeptide families, surfactin, iturin, and fengycin, the last was identified as the most effective for inhibiting mycelium growth and conidial germination of PO. The conidia and hyphae of fengycin-treated PO were shown to become deformed and tumorous under exposure. This study provides insights into the antagonistic effect of Ba-BPD1 against fungal phytopathogens. Such insights are helpful in the development of reagents for biological control applications.
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Affiliation(s)
- Jen-Hung Liao
- Department of Chemical Engineering, National Chung Hsing University, Taichung 40227, Taiwan.
- Biopesticides Division, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Council of Agriculture, Taichung 41358, Taiwan.
| | - Pi-Yu Chen
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan.
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan.
| | - Shu-Chen Kan
- Department of Chemical Engineering, National Chung Hsing University, Taichung 40227, Taiwan.
| | - Feng-Chia Hsieh
- Biopesticides Division, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Council of Agriculture, Taichung 41358, Taiwan.
| | - Yung-Chang Liu
- Department of Chemical Engineering, National Chung Hsing University, Taichung 40227, Taiwan.
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15
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Vanbellingen QP, Castellanos A, Rodriguez-Silva M, Paudel I, Chambers JW, Fernandez-Lima FA. Analysis of Chemotherapeutic Drug Delivery at the Single Cell Level Using 3D-MSI-TOF-SIMS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:2033-2040. [PMID: 27582118 PMCID: PMC5088064 DOI: 10.1007/s13361-016-1485-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/08/2016] [Accepted: 08/13/2016] [Indexed: 05/18/2023]
Abstract
In this work, we show the advantages of label-free, tridimensional mass spectrometry imaging using dual beam analysis (25 keV Bi3+) and depth profiling (20 keV with a distribution centered at Ar1500+) coupled to time of flight secondary ion mass spectrometry (3D-MSI-TOF-SIMS) for the study of A-172 human glioblastoma cell line treated with B-cell lymphoma 2 (Bcl-2) inhibitor ABT-737. The high spatial (~250 nm) and high mass resolution (m/Δm ~10,000) of TOF-SIMS permitted the localization and identification of the intact, unlabeled drug molecular ion (m/z 811.26 C42H44ClN6O5S2- [M - H]-) as well as characteristic fragment ions. We propose a novel approach based on the inspection of the drug secondary ion yield, which showed a good correlation with the drug concentration during cell treatment at therapeutic dosages (0-200 μM with 4 h incubation). Chemical maps using endogenous molecular markers showed that the ABT-737 is mainly localized in subsurface regions and absent in the nucleus. A semiquantitative workflow is proposed to account for the biological cell diversity based on the spatial distribution of endogenous molecular markers (e.g., nuclei and cytoplasm) and secondary ion confirmation based on the ratio of drug-specific fragments to molecular ion as a function of the therapeutic dosage. Graphical Abstract ᅟ.
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Affiliation(s)
- Quentin P Vanbellingen
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Anthony Castellanos
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA
| | - Monica Rodriguez-Silva
- Department of Cellular Biology and Pharmacology, Department of Neuroscience, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Iru Paudel
- Department of Cellular Biology and Pharmacology, Department of Neuroscience, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Jeremy W Chambers
- Department of Cellular Biology and Pharmacology, Department of Neuroscience, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Biomolecular Science Institute, Florida International University, Miami, FL, USA
| | - Francisco A Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL, USA.
- Biomolecular Science Institute, Florida International University, Miami, FL, USA.
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16
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Abstract
Chemical signaling between cells is an effective way to coordinate behavior within a community. Although cell-to-cell signaling has mostly been studied in single species, it is now appreciated that the sensing of chemical signals across kingdoms can be an important regulator of nutrient acquisition, virulence, and host defense. In this review, we focus on the role of interkingdom signaling in the interactions that occur between bacterial pathogens and their mammalian hosts. We discuss the quorum-sensing (QS) systems and other mechanisms used by these bacteria to sense, respond to, and modulate host signals that include hormones, immune factors, and nutrients. We also describe cross talk between these signaling pathways and strategies used by the host to interfere with bacterial signaling, highlighting the complex bidirectional signaling networks that are established across kingdoms.
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17
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Jeanson S, Floury J, Gagnaire V, Lortal S, Thierry A. Bacterial Colonies in Solid Media and Foods: A Review on Their Growth and Interactions with the Micro-Environment. Front Microbiol 2015; 6:1284. [PMID: 26648910 PMCID: PMC4664638 DOI: 10.3389/fmicb.2015.01284] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/31/2015] [Indexed: 01/26/2023] Open
Abstract
Bacteria, either indigenous or added, are immobilized in solid foods where they grow as colonies. Since the 80's, relatively few research groups have explored the implications of bacteria growing as colonies and mostly focused on pathogens in large colonies on agar/gelatine media. It is only recently that high resolution imaging techniques and biophysical characterization techniques increased the understanding of the growth of bacterial colonies, for different sizes of colonies, at the microscopic level and even down to the molecular level. This review covers the studies on bacterial colony growth in agar or gelatine media mimicking the food environment and in model cheese. The following conclusions have been brought to light. Firstly, under unfavorable conditions, mimicking food conditions, the immobilization of bacteria always constrains their growth in comparison with planktonic growth and increases the sensibility of bacteria to environmental stresses. Secondly, the spatial distribution describes both the distance between colonies and the size of the colonies as a function of the initial level of population. By studying the literature, we concluded that there systematically exists a threshold that distinguishes micro-colonies (radius < 100-200 μm) from macro-colonies (radius >200 μm). Micro-colonies growth resembles planktonic growth and no pH microgradients could be observed. Macro-colonies growth is slower than planktonic growth and pH microgradients could be observed in and around them due to diffusion limitations which occur around, but also inside the macro-colonies. Diffusion limitations of milk proteins have been demonstrated in a model cheese around and in the bacterial colonies. In conclusion, the impact of immobilization is predominant for macro-colonies in comparison with micro-colonies. However, the interaction between the colonies and the food matrix itself remains to be further investigated at the microscopic scale.
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Affiliation(s)
- Sophie Jeanson
- INRA, UMR1253, Science and Technology of Milk and EggsRennes, France
- AGROCAMPUS OUEST, UMR1253, Science and Technology of Milk and EggsRennes, France
| | - Juliane Floury
- INRA, UMR1253, Science and Technology of Milk and EggsRennes, France
- AGROCAMPUS OUEST, UMR1253, Science and Technology of Milk and EggsRennes, France
| | - Valérie Gagnaire
- INRA, UMR1253, Science and Technology of Milk and EggsRennes, France
- AGROCAMPUS OUEST, UMR1253, Science and Technology of Milk and EggsRennes, France
| | - Sylvie Lortal
- INRA, UMR1253, Science and Technology of Milk and EggsRennes, France
- AGROCAMPUS OUEST, UMR1253, Science and Technology of Milk and EggsRennes, France
| | - Anne Thierry
- INRA, UMR1253, Science and Technology of Milk and EggsRennes, France
- AGROCAMPUS OUEST, UMR1253, Science and Technology of Milk and EggsRennes, France
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18
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Luzzatto-Knaan T, Melnik AV, Dorrestein PC. Mass spectrometry tools and workflows for revealing microbial chemistry. Analyst 2015; 140:4949-66. [PMID: 25996313 PMCID: PMC5444374 DOI: 10.1039/c5an00171d] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Since the time Van Leeuwenhoek was able to observe microbes through a microscope, an innovation that led to the birth of the field of microbiology, we have aimed to understand how microorganisms function, interact and communicate. The exciting progress in the development of analytical technologies and workflows has demonstrated that mass spectrometry is a very powerful technique for the interrogation of microbiology at the molecular level. In this review, we aim to highlight the available and emerging tools in mass spectrometry for microbial analysis by overviewing the methods and workflow advances for taxonomic identification, microbial interaction, dereplication and drug discovery. We emphasize their potential for future development and point out unsolved problems and future directions that would aid in the analysis of the chemistry produced by microbes.
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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, USA.
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19
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Vitroprocines, new antibiotics against Acinetobacter baumannii, discovered from marine Vibrio sp. QWI-06 using mass-spectrometry-based metabolomics approach. Sci Rep 2015; 5:12856. [PMID: 26238555 PMCID: PMC4523872 DOI: 10.1038/srep12856] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 07/08/2015] [Indexed: 01/09/2023] Open
Abstract
A robust and convenient research strategy integrating state-of-the-art analytical techniques is needed to efficiently discover novel compounds from marine microbial resources. In this study, we identified a series of amino-polyketide derivatives, vitroprocines A-J, from the marine bacterium Vibrio sp. QWI-06 by an integrated approach using imaging mass spectroscopy and molecular networking, as well as conventional bioactivity-guided fractionation and isolation. The structure-activity relationship of vitroprocines against Acinetobacter baumannii is proposed. In addition, feeding experiments with 13C-labeled precursors indicated that a pyridoxal 5′-phosphate-dependent mechanism is involved in the biosynthesis of vitroprocines. Elucidation of amino-polyketide derivatives from a species of marine bacteria for the first time demonstrates the potential of this integrated metabolomics approach to uncover marine bacterial biodiversity.
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20
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Lobete MM, Fernandez EN, Van Impe JFM. Recent trends in non-invasive in situ techniques to monitor bacterial colonies in solid (model) food. Front Microbiol 2015; 6:148. [PMID: 25798133 PMCID: PMC4351626 DOI: 10.3389/fmicb.2015.00148] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 02/09/2015] [Indexed: 12/29/2022] Open
Abstract
Planktonic cells typically found in liquid systems, are routinely used for building predictive models or assessing the efficacy of food preserving technologies. However, freely suspended cells often show different susceptibility to environmental hurdles than colony cells in solid matrices. Limited oxygen, water and nutrient availability, metabolite accumulation and physical constraints due to cell immobilization in the matrix, are main factors affecting cell growth. Moreover, intra- and inter-colony interactions, as a consequence of the initial microbial load in solid systems, may affect microbial physiology. Predictive food microbiology approaches are moving toward a more realistic resemblance to food products, performing studies in structured solid systems instead of liquids. Since structured systems promote microbial cells to become immobilized and grow as colonies, it is essential to study the colony behavior, not only for food safety assurance systems, but also for understanding cell physiology and optimizing food production processes in solid matrices. Traditionally, microbial dynamics in solid systems have been assessed with a macroscopic approach by applying invasive analytical techniques; for instance, viable plate counting, which yield information about overall population. In the last years, this approach is being substituted by more mechanistically inspired ones at mesoscopic (colony) and microscopic (cell) levels. Therefore, non-invasive and in situ monitoring is mandatory for a deeper insight into bacterial colony dynamics. Several methodologies that enable high-throughput data collection have been developed, such as microscopy-based techniques coupled with image analysis and OD-based measurements in microplate readers. This research paper provides an overview of non-invasive in situ techniques to monitor bacterial colonies in solid (model) food and emphasizes their advantages and inconveniences in terms of accuracy, performance and output information.
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Affiliation(s)
- María M. Lobete
- Flemish Cluster Predictive Microbiology in Foods, Leuven, Belgium
- Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Estefania Noriega Fernandez
- Flemish Cluster Predictive Microbiology in Foods, Leuven, Belgium
- Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jan F. M. Van Impe
- Flemish Cluster Predictive Microbiology in Foods, Leuven, Belgium
- Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
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21
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Affiliation(s)
- Bernhard Spengler
- Justus Liebig University Giessen, Institute of Inorganic and Analytical
Chemistry, Schubertstrasse
60, Building 16, 35392 Giessen, Germany
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22
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Vergeiner S, Schafferer L, Haas H, Müller T. Improved MALDI-TOF microbial mass spectrometry imaging by application of a dispersed solid matrix. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1498-1501. [PMID: 24894842 DOI: 10.1007/s13361-014-0923-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 03/28/2014] [Accepted: 05/03/2014] [Indexed: 06/03/2023]
Abstract
The key step in high quality microbial matrix-assisted laser desorption/ionization mass spectrometry imaging (microbial MALDI MSI) is the fabrication of a homogeneous matrix coating showing a fine-grained morphology. This application note addresses a novel method to apply solid MALDI matrices onto microbial cultures grown on thin agar media. A suspension of a mixture of 2,5-DHB and α-CHCA is sprayed onto the agar sample surface to form highly homogeneous matrix coatings. As a result, the signal intensities of metabolites secreted by the fungus Aspergillus fumigatus were found to be clearly enhanced.
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Affiliation(s)
- Stefan Vergeiner
- Institute of Organic Chemistry, University of Innsbruck, 6020, Innsbruck, Austria
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23
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Gonzalez DJ, Vuong L, Gonzalez IS, Keller N, McGrosso D, Hwang JH, Hung J, Zinkernagel A, Dixon JE, Dorrestein PC, Nizet V. Phenol soluble modulin (PSM) variants of community-associated methicillin-resistant Staphylococcus aureus (MRSA) captured using mass spectrometry-based molecular networking. Mol Cell Proteomics 2014; 13:1262-72. [PMID: 24567418 DOI: 10.1074/mcp.m113.031336] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Molecular genetic analysis indicates that the problematic human bacterial pathogen methicillin-resistant Staphylococcus aureus possesses more than 2000 open reading frames in its genome. This number of potential gene products, coupled with intrinsic mechanisms of posttranslational modification, endows methicillin-resistant Staphylococcus aureus with a highly complex biochemical repertoire. Recent proteomic and metabolomic advances have provided methodologies to better understand and characterize the biosynthetic factors released by microbial organisms. Here, the emerging tool of mass spectrometry-based molecular networking was used to visualize and map the repertoire of biosynthetic factors produced by a community-associated methicillin-resistant Staphylococcus aureus strain representative of the epidemic USA300 clone. In particular, the study focused on elucidating the complexity of the recently discovered phenol soluble modulin family of peptides when placed under various antibiotic treatment stresses. Novel PSM truncated variant peptides were captured, and the type of variants that were clustered by the molecular networks platform changed in response to the different antibiotic treatment conditions. After discovery, a group of the peptides were selected for functional analysis in vitro. The peptides displayed bioactive properties including the ability to induce proinflammatory responses in human THP-1 monocytes. Additionally, the tested peptides did not display antimicrobial activity as previously reported for other phenol soluble modulin truncated variants. Our findings reveal that the PSM family of peptides are quite structurally diverse, and suggest a single phenol soluble modulin parent peptide can functionally spawn differential bioactivities in response to various external stimuli.
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24
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Shih CJ, Chen PY, Liaw CC, Lai YM, Yang YL. Bringing microbial interactions to light using imaging mass spectrometry. Nat Prod Rep 2014; 31:739-55. [DOI: 10.1039/c3np70091g] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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25
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Morosi L, Spinelli P, Zucchetti M, Pretto F, Carrà A, D’Incalci M, Giavazzi R, Davoli E. Determination of paclitaxel distribution in solid tumors by nano-particle assisted laser desorption ionization mass spectrometry imaging. PLoS One 2013; 8:e72532. [PMID: 23991120 PMCID: PMC3753243 DOI: 10.1371/journal.pone.0072532] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 07/10/2013] [Indexed: 11/19/2022] Open
Abstract
A sensitive, simple and reproducible protocol for nanoparticle-assisted laser desorption/ionization mass spectrometry imaging technique is described. The use of commercially available TiO2 nanoparticles abolishes heterogeneous crystallization, matrix background interferences and enhances signal detection, especially in the low mass range. Molecular image normalization was based on internal standard deposition on tissues, allowing direct comparison of drug penetration and distribution between different organs and tissues. The method was applied to analyze the distribution of the anticancer drug paclitaxel, inside normal and neoplastic mouse tissue sections. Spatial resolution was good, with a linear response between different in vivo treatments and molecular imaging intensity using therapeutic drug doses. This technique distinguishes the different intensity of paclitaxel distribution in control organs of mice, such as liver and kidney, in relation to the dose. Animals treated with 30 mg/kg of paclitaxel had half of the concentration of those treated with 60 mg/kg. We investigated the spatial distribution of paclitaxel in human melanoma mouse xenografts, following different dosage schedules and found a more homogeneous drug distribution in tumors of mice given repeated doses (5×8 mg/kg) plus a 60 mg/kg dose than in those assigned only a single 60 mg/kg dose. The protocol can be readily applied to investigate anticancer drug distribution in neoplastic lesions and to develop strategies to optimize and enhance drug penetration through different tumor tissues.
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Affiliation(s)
- Lavinia Morosi
- IRCCS Istituto di Ricerche Farmacologiche “Mario Negri”, Department of Oncology, Milano, Italy
| | - Pietro Spinelli
- IRCCS Istituto di Ricerche Farmacologiche “Mario Negri”, Department of Oncology, Milano, Italy
| | - Massimo Zucchetti
- IRCCS Istituto di Ricerche Farmacologiche “Mario Negri”, Department of Oncology, Milano, Italy
| | - Francesca Pretto
- IRCCS Istituto di Ricerche Farmacologiche “Mario Negri”, Department of Oncology, Milano, Italy
| | - Andrea Carrà
- IRCCS Istituto di Ricerche Farmacologiche “Mario Negri”, Department of Environmental Health Sciences, Mass Spectrometry Laboratory, Milano, Italy
| | - Maurizio D’Incalci
- IRCCS Istituto di Ricerche Farmacologiche “Mario Negri”, Department of Oncology, Milano, Italy
| | - Raffaella Giavazzi
- IRCCS Istituto di Ricerche Farmacologiche “Mario Negri”, Department of Oncology, Milano, Italy
| | - Enrico Davoli
- IRCCS Istituto di Ricerche Farmacologiche “Mario Negri”, Department of Environmental Health Sciences, Mass Spectrometry Laboratory, Milano, Italy
- * E-mail:
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Lanekoff I, Geydebrekht O, Pinchuk GE, Konopka AE, Laskin J. Spatially resolved analysis of glycolipids and metabolites in living Synechococcus sp. PCC 7002 using nanospray desorption electrospray ionization. Analyst 2013; 138:1971-8. [PMID: 23392077 DOI: 10.1039/c3an36716a] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microorganisms release a diversity of organic compounds that couple interspecies metabolism, enable communication, or provide benefits to other microbes. Increased knowledge of microbial metabolite production will contribute to understanding of the dynamic microbial world and can potentially lead to new developments in drug discovery, biofuel production, and clinical research. Nanospray desorption electrospray ionization (nano-DESI) is an ambient ionization technique that enables detailed chemical characterization of molecules from a specific location on a surface without special sample pretreatment. Due to its ambient nature, living bacterial colonies growing on agar plates can be rapidly analyzed without affecting the viability of the colony. In this study we demonstrate for the first time the utility of nano-DESI for spatial profiling of chemical gradients generated by microbial communities on agar plates. We found that despite the high salt content of the agar used in this study (~350 mM), nano-DESI analysis enables detailed characterization of metabolites produced by the Synechococcus sp. PCC 7002 colonies. High resolution mass spectrometry and MS/MS analysis of the living Synechococcus sp. PCC 7002 colonies allowed us to detect metabolites and lipids on the colony and on the surrounding agar, and confirm their identities. High sensitivity of nano-DESI enabled identification of several glycolipids that have not been previously reported by extracting the cells using conventional methods. Spatial profiling demonstrated that a majority of lipids and metabolites were localized on the colony while sucrose and glucosylglycerol, an osmoprotective compound produced by cyanobacteria, were secreted onto agar. Furthermore, we demonstrated that the chemical gradients of sucrose and glucosylglycerol on agar depend on the age of the colony. The methodology presented in this study will facilitate future studies focused on molecular-level characterization of interactions between bacterial colonies.
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Affiliation(s)
- Ingela Lanekoff
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, PO Box 999, K8-88 Richland, WA 99352, USA.
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Havlicek V, Lemr K, Schug KA. Current Trends in Microbial Diagnostics Based on Mass Spectrometry. Anal Chem 2012; 85:790-7. [DOI: 10.1021/ac3031866] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Vladimir Havlicek
- Institute of Microbiology, v.v.i., Videnska
1083, CZ 142 20 Prague 4, Czech Republic
- Palacky University, Faculty
of Science, Department of Analytical Chemistry, RCPTM, 17. listopadu
12, 771 46 Olomouc, Czech Republic
| | - Karel Lemr
- Institute of Microbiology, v.v.i., Videnska
1083, CZ 142 20 Prague 4, Czech Republic
- Palacky University, Faculty
of Science, Department of Analytical Chemistry, RCPTM, 17. listopadu
12, 771 46 Olomouc, Czech Republic
| | - Kevin A. Schug
- The University of Texas at Arlington,
Department of Chemistry and Biochemistry, Arlington, Texas 76019-0065,
United States
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