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Mazzella V, Dell'Anno A, Etxebarría N, González-Gaya B, Nuzzo G, Fontana A, Núñez-Pons L. High microbiome and metabolome diversification in coexisting sponges with different bio-ecological traits. Commun Biol 2024; 7:422. [PMID: 38589605 PMCID: PMC11001883 DOI: 10.1038/s42003-024-06109-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Marine Porifera host diverse microbial communities, which influence host metabolism and fitness. However, functional relationships between sponge microbiomes and metabolic signatures are poorly understood. We integrate microbiome characterization, metabolomics and microbial predicted functions of four coexisting Mediterranean sponges -Petrosia ficiformis, Chondrosia reniformis, Crambe crambe and Chondrilla nucula. Microscopy observations reveal anatomical differences in microbial densities. Microbiomes exhibit strong species-specific trends. C. crambe shares many rare amplicon sequence variants (ASV) with the surrounding seawater. This suggests important inputs of microbial diversity acquired by selective horizontal acquisition. Phylum Cyanobacteria is mainly represented in C. nucula and C. crambe. According to putative functions, the microbiome of P. ficiformis and C. reniformis are functionally heterotrophic, while C. crambe and C. nucula are autotrophic. The four species display distinct metabolic profiles at single compound level. However, at molecular class level they share a "core metabolome". Concurrently, we find global microbiome-metabolome association when considering all four sponge species. Within each species still, sets of microbe/metabolites are identified driving multi-omics congruence. Our findings suggest that diverse microbial players and metabolic profiles may promote niche diversification, but also, analogous phenotypic patterns of "symbiont evolutionary convergence" in sponge assemblages where holobionts co-exist in the same area.
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Affiliation(s)
- Valerio Mazzella
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Ischia Marine Centre, 80077, Ischia, Naples, Italy
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy
| | - Antonio Dell'Anno
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy.
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
| | - Néstor Etxebarría
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Belén González-Gaya
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Genoveffa Nuzzo
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
| | - Angelo Fontana
- Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, 80078, Pozzuoli, Italy
- Department of Biology, University of Naples Federico II, Via Cinthia-Bld. 7, 80126, Napoli, Italy
| | - Laura Núñez-Pons
- NBFC, National Biodiversity Future Center, Piazza Marina 61, Palermo, 90133, Italy.
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
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Wu Y, Li Z, Zhu H, Zi R, Xue F, Yu Y. Identification of Tartary Buckwheat ( Fagopyrum tataricum (L.) Gaertn) and Common Buckwheat ( Fagopyrum esculentum Moench) Using Gas Chromatography-Mass Spectroscopy-Based Untargeted Metabolomics. Foods 2023; 12:2578. [PMID: 37444316 DOI: 10.3390/foods12132578] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Tartary buckwheat has attracted more attention than common buckwheat due to its unique chemical composition and higher efficacy in the prevention of various diseases. The content of flavonoids in Tartary buckwheat (Fagopyrum tataricum (L.) Gaertn) is higher than that in common buckwheat (Fagopyrum esculentum Moench). However, the processing process of Tartary buckwheat is complex, and the cost is high, which leads to the frequent phenomenon of common buckwheat counterfeiting and adulteration in Tartary buckwheat, which seriously damages the interests of consumers and disrupts the market order. In order to explore a new and simple identification method for Tartary buckwheat and common buckwheat, this article uses metabolomics technology based on GC-MS to identify Tartary buckwheat and common buckwheat. The results show that the PLS-DA model can identify Tartary buckwheat and common buckwheat, as well as Tartary buckwheat from different regions, without an over-fitting phenomenon. It was also found that ascorbate and aldarate metabolism was the main differential metabolic pathway between Tartary buckwheat and common buckwheat, as well as the amino acids biosynthesis pathway. This study provides a new attempt for the identification of Tartary buckwheat and common buckwheat for the quality control of related agricultural products.
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Affiliation(s)
- Yuling Wu
- School of Grain Science and Technology, Jiangsu University of Food Science and Technology, Zhenjiang 212100, China
| | - Zhanming Li
- School of Grain Science and Technology, Jiangsu University of Food Science and Technology, Zhenjiang 212100, China
- National University of Singapore Suzhou Research Institute, Suzhou 215127, China
| | - Hui Zhu
- School of Grain Science and Technology, Jiangsu University of Food Science and Technology, Zhenjiang 212100, China
| | - Run Zi
- National University of Singapore Suzhou Research Institute, Suzhou 215127, China
| | - Fang Xue
- School of Grain Science and Technology, Jiangsu University of Food Science and Technology, Zhenjiang 212100, China
| | - Yue Yu
- School of Grain Science and Technology, Jiangsu University of Food Science and Technology, Zhenjiang 212100, China
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Hoffmann N, Mayer G, Has C, Kopczynski D, Al Machot F, Schwudke D, Ahrends R, Marcus K, Eisenacher M, Turewicz M. A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics. Metabolites 2022; 12:metabo12070584. [PMID: 35888710 PMCID: PMC9319858 DOI: 10.3390/metabo12070584] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 12/13/2022] Open
Abstract
Mass spectrometry is a widely used technology to identify and quantify biomolecules such as lipids, metabolites and proteins necessary for biomedical research. In this study, we catalogued freely available software tools, libraries, databases, repositories and resources that support lipidomics data analysis and determined the scope of currently used analytical technologies. Because of the tremendous importance of data interoperability, we assessed the support of standardized data formats in mass spectrometric (MS)-based lipidomics workflows. We included tools in our comparison that support targeted as well as untargeted analysis using direct infusion/shotgun (DI-MS), liquid chromatography−mass spectrometry, ion mobility or MS imaging approaches on MS1 and potentially higher MS levels. As a result, we determined that the Human Proteome Organization-Proteomics Standards Initiative standard data formats, mzML and mzTab-M, are already supported by a substantial number of recent software tools. We further discuss how mzTab-M can serve as a bridge between data acquisition and lipid bioinformatics tools for interpretation, capturing their output and transmitting rich annotated data for downstream processing. However, we identified several challenges of currently available tools and standards. Potential areas for improvement were: adaptation of common nomenclature and standardized reporting to enable high throughput lipidomics and improve its data handling. Finally, we suggest specific areas where tools and repositories need to improve to become FAIRer.
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Affiliation(s)
- Nils Hoffmann
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences (IBG-5), 52425 Jülich, Germany
- Correspondence: (N.H.); (M.T.); Tel.: +49-(0)521-106-86780 (N.H.)
| | - Gerhard Mayer
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany;
| | - Canan Has
- Biological Mass Spectrometry, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany;
- University Hospital Carl Gustav Carus, 01307 Dresden, Germany
- CENTOGENE GmbH, 18055 Rostock, Germany
| | - Dominik Kopczynski
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (D.K.); (R.A.)
| | - Fadi Al Machot
- Faculty of Science and Technology, Norwegian University for Life Science (NMBU), 1433 Ås, Norway;
| | - Dominik Schwudke
- Bioanalytical Chemistry, Forschungszentrum Borstel, Leibniz Lung Center, 23845 Borstel, Germany;
- Airway Research Center North, German Center for Lung Research (DZL), 23845 Borstel, Germany
- German Center for Infection Research (DZIF), TTU Tuberculosis, 23845 Borstel, Germany
| | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (D.K.); (R.A.)
| | - Katrin Marcus
- Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany; (K.M.); (M.E.)
| | - Martin Eisenacher
- Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany; (K.M.); (M.E.)
- Faculty of Medicine, Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
| | - Michael Turewicz
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Düsseldorf, 85764 Neuherberg, Germany
- Correspondence: (N.H.); (M.T.); Tel.: +49-(0)521-106-86780 (N.H.)
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Flight RM, Mitchell JM, Moseley HNB. Scan-Centric, Frequency-Based Method for Characterizing Peaks from Direct Injection Fourier Transform Mass Spectrometry Experiments. Metabolites 2022; 12:metabo12060515. [PMID: 35736448 PMCID: PMC9228344 DOI: 10.3390/metabo12060515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/20/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022] Open
Abstract
We present a novel, scan-centric method for characterizing peaks from direct injection multi-scan Fourier transform mass spectra of complex samples that utilizes frequency values derived directly from the spacing of raw m/z points in spectral scans. Our peak characterization method utilizes intensity-independent noise removal and normalization of scan-level data to provide a much better fit of relative intensity to natural abundance probabilities for low abundance isotopologues that are not present in all of the acquired scans. Moreover, our method calculates both peak- and scan-specific statistics incorporated within a series of quality control steps that are designed to robustly derive peak centers, intensities, and intensity ratios with their scan-level variances. These cross-scan characterized peaks are suitable for use in our previously published peak assignment methodology, Small Molecule Isotope Resolved Formula Enumeration (SMIRFE).
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Affiliation(s)
- Robert M. Flight
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; (R.M.F.); (J.M.M.)
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
- Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY 40536, USA
| | - Joshua M. Mitchell
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; (R.M.F.); (J.M.M.)
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
- Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY 40536, USA
| | - Hunter N. B. Moseley
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA; (R.M.F.); (J.M.M.)
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
- Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY 40536, USA
- Institute for Biomedical Informatics, University of Kentucky, Lexington, KY 40536, USA
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
- Correspondence:
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Mitchell JM, Flight RM, Moseley HNB. Untargeted Lipidomics of Non-Small Cell Lung Carcinoma Demonstrates Differentially Abundant Lipid Classes in Cancer vs. Non-Cancer Tissue. Metabolites 2021; 11:740. [PMID: 34822397 PMCID: PMC8622625 DOI: 10.3390/metabo11110740] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 01/25/2023] Open
Abstract
Lung cancer remains the leading cause of cancer death worldwide and non-small cell lung carcinoma (NSCLC) represents 85% of newly diagnosed lung cancers. In this study, we utilized our untargeted assignment tool Small Molecule Isotope Resolved Formula Enumerator (SMIRFE) and ultra-high-resolution Fourier transform mass spectrometry to examine lipid profile differences between paired cancerous and non-cancerous lung tissue samples from 86 patients with suspected stage I or IIA primary NSCLC. Correlation and co-occurrence analysis revealed significant lipid profile differences between cancer and non-cancer samples. Further analysis of machine-learned lipid categories for the differentially abundant molecular formulas identified a high abundance sterol, high abundance and high m/z sphingolipid, and low abundance glycerophospholipid metabolic phenotype across the NSCLC samples. At the class level, higher abundances of sterol esters and lower abundances of cardiolipins were observed suggesting altered stearoyl-CoA desaturase 1 (SCD1) or acetyl-CoA acetyltransferase (ACAT1) activity and altered human cardiolipin synthase 1 or lysocardiolipin acyltransferase activity respectively, the latter of which is known to confer apoptotic resistance. The presence of a shared metabolic phenotype across a variety of genetically distinct NSCLC subtypes suggests that this phenotype is necessary for NSCLC development and may result from multiple distinct genetic lesions. Thus, targeting the shared affected pathways may be beneficial for a variety of genetically distinct NSCLC subtypes.
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Affiliation(s)
- Joshua M. Mitchell
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA;
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA;
- Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY 40536, USA
| | - Robert M. Flight
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA;
- Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY 40536, USA
| | - Hunter N. B. Moseley
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA;
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA;
- Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY 40536, USA
- Institute for Biomedical Informatics, University of Kentucky, Lexington, KY 40536, USA
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA
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6
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Colonia BSO, de Melo Pereira GV, Mendonça Rodrigues F, de Souza Miranda Muynarsk E, da Silva Vale A, Cesar de Carvalho J, Thomaz Soccol V, de Oliveira Penha R, Ricardo Soccol C. Integrating metagenetics and high-throughput screening for bioprospecting marine thraustochytrids producers of long-chain polyunsaturated fatty acids. BIORESOURCE TECHNOLOGY 2021; 333:125176. [PMID: 33894449 DOI: 10.1016/j.biortech.2021.125176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
Omega-3 produced by marine thraustochytrids has appeared as an alternative to fish oil and an eco-friendly solution to overfishing. Herein, an integrative analysis of metagenetics and high-throughput screening was used for bioprospecting marine thraustochytrids from southern Brazil mangrove and coastal seawater. All sampled environments showed biodiversity and abundance of SAR clade. Environmental samples detected with potential lipid-accumulating labyrinthulomycetes were further processed for direct plating and pollen baiting isolation. Microtiter plate system and fluorescence spectroscopy were combined for high-throughput screening of 319 isolates to accumulate lipids. Twenty isolates were selected for submerged cultivation and lipid characterization. Among them, B36 isolate, identified as Aurantiochytrium sp. by 18s rRNA sequencing, achieved the highest biomass (25.60 g/l CDW) and lipids (17.12 g/l CDW). This lipid content had a high biological value with 44.37% LC-PUFAs and 34.6% DHA, which can be used as a sustainable source in vegan, seafood-free and animal feed diets.
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Affiliation(s)
| | | | - Felipe Mendonça Rodrigues
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 81531-970 Curitiba, PR, Brazil
| | | | - Alexander da Silva Vale
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 81531-970 Curitiba, PR, Brazil
| | - Júlio Cesar de Carvalho
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 81531-970 Curitiba, PR, Brazil
| | - Vanete Thomaz Soccol
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 81531-970 Curitiba, PR, Brazil
| | - Rafaela de Oliveira Penha
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 81531-970 Curitiba, PR, Brazil
| | - Carlos Ricardo Soccol
- Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná (UFPR), 81531-970 Curitiba, PR, Brazil.
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Alves MA, Lamichhane S, Dickens A, McGlinchey A, Ribeiro HC, Sen P, Wei F, Hyötyläinen T, Orešič M. Systems biology approaches to study lipidomes in health and disease. Biochim Biophys Acta Mol Cell Biol Lipids 2020; 1866:158857. [PMID: 33278596 DOI: 10.1016/j.bbalip.2020.158857] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/13/2020] [Accepted: 11/27/2020] [Indexed: 12/15/2022]
Abstract
Lipids have many important biological roles, such as energy storage sources, structural components of plasma membranes and as intermediates in metabolic and signaling pathways. Lipid metabolism is under tight homeostatic control, exhibiting spatial and dynamic complexity at multiple levels. Consequently, lipid-related disturbances play important roles in the pathogenesis of most of the common diseases. Lipidomics, defined as the study of lipidomes in biological systems, has emerged as a rapidly-growing field. Due to the chemical and functional diversity of lipids, the application of a systems biology approach is essential if one is to address lipid functionality at different physiological levels. In parallel with analytical advances to measure lipids in biological matrices, the field of computational lipidomics has been rapidly advancing, enabling modeling of lipidomes in their pathway, spatial and dynamic contexts. This review focuses on recent progress in systems biology approaches to study lipids in health and disease, with specific emphasis on methodological advances and biomedical applications.
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Affiliation(s)
- Marina Amaral Alves
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Santosh Lamichhane
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Alex Dickens
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland
| | - Aidan McGlinchey
- School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden
| | | | - Partho Sen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden
| | - Fang Wei
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, PR China
| | | | - Matej Orešič
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku 20520, Finland; School of Medical Sciences, Örebro University, 702 81 Örebro, Sweden.
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