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Krause JL, Haange SB, Schäpe SS, Engelmann B, Rolle-Kampczyk U, Fritz-Wallace K, Wang Z, Jehmlich N, Türkowsky D, Schubert K, Pöppe J, Bote K, Rösler U, Herberth G, von Bergen M. The glyphosate formulation Roundup® LB plus influences the global metabolome of pig gut microbiota in vitro. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 745:140932. [PMID: 32731069 DOI: 10.1016/j.scitotenv.2020.140932] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/06/2020] [Accepted: 07/11/2020] [Indexed: 05/20/2023]
Abstract
Glyphosate is the world's most widely used herbicide, and its potential side effects on the intestinal microbiota of various animals, from honeybees to livestock and humans, are currently under discussion. Pigs are among the most abundant livestock animals worldwide and an impact of glyphosate on their intestinal microbiota function can have serious consequences on their health, not to mention the economic effects. Recent studies that addressed microbiota-disrupting effects focused on microbial taxonomy but lacked functional information. Therefore, we chose an experimental design with a short incubation time in which effects on the community structure are not expected, but functional effects can be detected. We cultivated intestinal microbiota derived from pig colon in chemostats and investigated the acute effect of 228 mg/d glyphosate acid equivalents from Roundup® LB plus, a frequently applied glyphosate formulation. The applied glyphosate concentration resembles a worst-case scenario for an 8-9 week-old pig and relates to the maximum residue levels of glyphosate on animal fodder. The effects were determined on the functional level by metaproteomics, targeted and untargeted meta-metabolomics, while variations in community structure were analyzed by 16S rRNA gene profiling and on the single cell level by microbiota flow cytometry. Roundup® LB plus did not affect the community taxonomy or the enzymatic repertoire of the cultivated microbiota in general or on the expression of the glyphosate target enzyme 5-enolpyruvylshikimate-3-phosphate synthase in detail. On the functional level, targeted metabolite analysis of short chain fatty acids (SCFAs), free amino acids and bile acids did not reveal significant changes, whereas untargeted meta-metabolomics did identify some effects on the functional level. This multi-omics approach provides evidence for subtle metabolic effects of Roundup® LB plus under the conditions applied.
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Affiliation(s)
- Jannike L Krause
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany.
| | - Sven-Bastiaan Haange
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany
| | - Stephanie S Schäpe
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany
| | - Beatrice Engelmann
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany
| | - Katarina Fritz-Wallace
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany; National Center for Tumor Diseases - NCT, Dresden, Germany
| | - Zhipeng Wang
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany
| | - Dominique Türkowsky
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany
| | - Kristin Schubert
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany
| | - Judith Pöppe
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Katrin Bote
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Uwe Rösler
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Gunda Herberth
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany
| | - Martin von Bergen
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany; Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Germany.
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Lohmann P, Schäpe SS, Haange SB, Oliphant K, Allen-Vercoe E, Jehmlich N, Von Bergen M. Function is what counts: how microbial community complexity affects species, proteome and pathway coverage in metaproteomics. Expert Rev Proteomics 2020; 17:163-173. [PMID: 32174200 DOI: 10.1080/14789450.2020.1738931] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Introduction: Metaproteomics is an established method to obtain a comprehensive taxonomic and functional view of microbial communities. After more than a decade, we are now able to describe the promise, reality, and perspectives of metaproteomics and provide useful information about the choice of method, applications, and potential improvement strategies.Areas covered: In this article, we will discuss current challenges of species and proteome coverage, and also highlight functional aspects of metaproteomics analysis of microbial communities with different levels of complexity. To do this, we re-analyzed data from microbial communities with low to high complexity (8, 72, 200 and >300 species). High species diversity leads to a reduced number of protein group identifications in a complex community, and thus the number of species resolved is underestimated. Ultimately, low abundance species remain undiscovered in complex communities. However, we observed that the main functional categories were better represented within complex microbiomes when compared to species coverage.Expert opinion: Our findings showed that even with low species coverage, metaproteomics has the potential to reveal habitat-specific functional features. Finally, we exploit this information to highlight future research avenues that are urgently needed to enhance our understanding of taxonomic composition and functions of complex microbiomes.
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Affiliation(s)
- Patrick Lohmann
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Stephanie Serena Schäpe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Sven-Bastiaan Haange
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Kaitlyn Oliphant
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Martin Von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.,Institute of Biochemistry, University of Leipzig, Leipzig, Germany
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Castro-Moretti FR, Gentzel IN, Mackey D, Alonso AP. Metabolomics as an Emerging Tool for the Study of Plant-Pathogen Interactions. Metabolites 2020; 10:E52. [PMID: 32013104 PMCID: PMC7074241 DOI: 10.3390/metabo10020052] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/16/2020] [Accepted: 01/27/2020] [Indexed: 12/19/2022] Open
Abstract
Plants defend themselves from most microbial attacks via mechanisms including cell wall fortification, production of antimicrobial compounds, and generation of reactive oxygen species. Successful pathogens overcome these host defenses, as well as obtain nutrients from the host. Perturbations of plant metabolism play a central role in determining the outcome of attempted infections. Metabolomic analyses, for example between healthy, newly infected and diseased or resistant plants, have the potential to reveal perturbations to signaling or output pathways with key roles in determining the outcome of a plant-microbe interaction. However, application of this -omic and its tools in plant pathology studies is lagging relative to genomic and transcriptomic methods. Thus, it is imperative to bring the power of metabolomics to bear on the study of plant resistance/susceptibility. This review discusses metabolomics studies that link changes in primary or specialized metabolism to the defense responses of plants against bacterial, fungal, nematode, and viral pathogens. Also examined are cases where metabolomics unveils virulence mechanisms used by pathogens. Finally, how integrating metabolomics with other -omics can advance plant pathology research is discussed.
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Affiliation(s)
- Fernanda R. Castro-Moretti
- BioDiscovery Institute, University of North Texas, TX 76201, USA;
- Department of Biological Sciences, University of North Texas, TX 76201, USA
| | - Irene N. Gentzel
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA;
| | - David Mackey
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, OH 43210, USA;
| | - Ana P. Alonso
- BioDiscovery Institute, University of North Texas, TX 76201, USA;
- Department of Biological Sciences, University of North Texas, TX 76201, USA
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Fernández-Ochoa Á, Borrás-Linares I, Baños A, García-López JD, Guillamón E, Nuñez-Lechado C, Quirantes-Piné R, Segura-Carretero A. A fingerprinting metabolomic approach reveals deregulation of endogenous metabolites after the intake of a bioactive garlic supplement. J Funct Foods 2018. [DOI: 10.1016/j.jff.2018.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Durazzo A, D'Addezio L, Camilli E, Piccinelli R, Turrini A, Marletta L, Marconi S, Lucarini M, Lisciani S, Gabrielli P, Gambelli L, Aguzzi A, Sette S. From Plant Compounds to Botanicals and Back: A Current Snapshot. Molecules 2018; 23:E1844. [PMID: 30042375 PMCID: PMC6222869 DOI: 10.3390/molecules23081844] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/20/2018] [Accepted: 07/21/2018] [Indexed: 02/07/2023] Open
Abstract
This work aims at giving an updated picture of the strict interaction between main plant biologically active compounds and botanicals. The main features of the emerging class of dietary supplements, the botanicals, are highlighted. Focus is also on the definition of actual possibilities of study approach and research strategies. Examples of innovative directions are given: assessment of interaction of bioactive compounds, chemometrics and the new goal of biorefineries. Current models of existing databases, such as plant metabolic pathways, food composition, bioactive compounds, dietary supplements, and dietary markers, are described as usable tools for health research. The need for categorization of botanicals as well as for the implementation of specific and dedicated databases emerged, based on both analytical data and collected data taken from literature throughout a harmonized and standardized approach for the evaluation of an adequate dietary intake.
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Affiliation(s)
| | - Laura D'Addezio
- CREA-Research Centre for Food and Nutrition, 00178 Rome, Italy.
| | | | | | - Aida Turrini
- CREA-Research Centre for Food and Nutrition, 00178 Rome, Italy.
| | - Luisa Marletta
- CREA-Research Centre for Food and Nutrition, 00178 Rome, Italy.
| | | | | | - Silvia Lisciani
- CREA-Research Centre for Food and Nutrition, 00178 Rome, Italy.
| | - Paolo Gabrielli
- CREA-Research Centre for Food and Nutrition, 00178 Rome, Italy.
| | | | - Altero Aguzzi
- CREA-Research Centre for Food and Nutrition, 00178 Rome, Italy.
| | - Stefania Sette
- CREA-Research Centre for Food and Nutrition, 00178 Rome, Italy.
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