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Haange SB, Riesbeck S, Aldehoff AS, Engelmann B, Jensen Pedersen K, Castaneda-Monsalve V, Rolle-Kampczyk U, von Bergen M, Jehmlich N. Chemical mixture effects on the simplified human intestinal microbiota: Assessing xenobiotics at environmentally realistic concentrations. JOURNAL OF HAZARDOUS MATERIALS 2024; 474:134683. [PMID: 38820745 DOI: 10.1016/j.jhazmat.2024.134683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/07/2024] [Accepted: 05/20/2024] [Indexed: 06/02/2024]
Abstract
The microbial community present in our intestines is pivotal for converting indigestible substances into vital nutrients and signaling molecules such as short-chain fatty acids (SCFAs). These compounds have considerable influence over our immune system and the development of diverse human diseases. However, ingested environmental contaminants, known as xenobiotics, can upset the delicate balance of the microbial gut community and enzymatic processes, consequently affecting the host organism. In our study, we employed an in vitro bioreactor model system based on the simplified human microbiome model (SIHUMIx) to investigate the direct effects of specific xenobiotics, such as perfluorooctanoic acid (PFOA), perfluorohexanoic acid (PFHxA) and perfluorobutanoic acid (PFBA) or bisphenol S (BPS) and bisphenol F (BPF), either individually or in combination, on the microbiota. We observed increased SCFA production, particularly acetate and butyrate, with PFAS exposure. Metaproteomics revealed pathway alterations across treatments, including changes in vitamin synthesis and fatty acid metabolism with BPX. This study underscores the necessity of assessing the combined effects of xenobiotics to better safeguard public health. It emphasizes the significance of considering adverse effects on the microbiome in the risk assessment of environmental chemicals.
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Affiliation(s)
- Sven-Bastiaan Haange
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany
| | - Sarah Riesbeck
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany
| | - Alix Sarah Aldehoff
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany
| | - Beatrice Engelmann
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany
| | - Kristian Jensen Pedersen
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany
| | - Victor Castaneda-Monsalve
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany
| | - Martin von Bergen
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany; Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research - UFZ GmbH, Department of Molecular Toxicology, Leipzig, Germany.
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2
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Lange E, Kranert L, Krüger J, Benndorf D, Heyer R. Microbiome modeling: a beginner's guide. Front Microbiol 2024; 15:1368377. [PMID: 38962127 PMCID: PMC11220171 DOI: 10.3389/fmicb.2024.1368377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/27/2024] [Indexed: 07/05/2024] Open
Abstract
Microbiomes, comprised of diverse microbial species and viruses, play pivotal roles in human health, environmental processes, and biotechnological applications and interact with each other, their environment, and hosts via ecological interactions. Our understanding of microbiomes is still limited and hampered by their complexity. A concept improving this understanding is systems biology, which focuses on the holistic description of biological systems utilizing experimental and computational methods. An important set of such experimental methods are metaomics methods which analyze microbiomes and output lists of molecular features. These lists of data are integrated, interpreted, and compiled into computational microbiome models, to predict, optimize, and control microbiome behavior. There exists a gap in understanding between microbiologists and modelers/bioinformaticians, stemming from a lack of interdisciplinary knowledge. This knowledge gap hinders the establishment of computational models in microbiome analysis. This review aims to bridge this gap and is tailored for microbiologists, researchers new to microbiome modeling, and bioinformaticians. To achieve this goal, it provides an interdisciplinary overview of microbiome modeling, starting with fundamental knowledge of microbiomes, metaomics methods, common modeling formalisms, and how models facilitate microbiome control. It concludes with guidelines and repositories for modeling. Each section provides entry-level information, example applications, and important references, serving as a valuable resource for comprehending and navigating the complex landscape of microbiome research and modeling.
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Affiliation(s)
- Emanuel Lange
- Multidimensional Omics Data Analysis, Department for Bioanalytics, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- Graduate School Digital Infrastructure for the Life Sciences, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Bielefeld, Germany
| | - Lena Kranert
- Institute for Automation Engineering, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Jacob Krüger
- Engineering of Software-Intensive Systems, Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Dirk Benndorf
- Applied Biosciences and Bioprocess Engineering, Anhalt University of Applied Sciences, Köthen, Germany
| | - Robert Heyer
- Multidimensional Omics Data Analysis, Department for Bioanalytics, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
- Graduate School Digital Infrastructure for the Life Sciences, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Bielefeld, Germany
- Multidimensional Omics Data Analysis, Faculty of Technology, Bielefeld University, Bielefeld, Germany
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3
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Vorländer D, Schultz G, Hoffmann K, Rasch D, Dohnt K. PETR: A novel peristaltic mixed tubular bioreactor simulating human colonic conditions. Biotechnol Bioeng 2024; 121:1118-1143. [PMID: 38151924 DOI: 10.1002/bit.28636] [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: 07/07/2023] [Revised: 12/08/2023] [Accepted: 12/09/2023] [Indexed: 12/29/2023]
Abstract
A novel bioreactor simulating human colonic conditions for in vitro cultivation of intestinal microbiota is presented. The PEristaltic mixed Tubular bioReactor (PETR) is modular designed and periodically kneaded to simulate intestinal peristalsis. The reactor is introduced, characterized from a bioprocess engineer's perspective and discussed in its ability to mimic colon conditions. PETR provides physiological temperature and appropriate anaerobic conditions, simulates intestinal peristalsis, and has a mean residence time of 32.8 ± 0.8 h comparable to the adult human colon. The single-tube design enables a time-constant and longitudinally progressive pH gradient from 5.5 to 7.0. Using a dialysis liquid containing high molecular weight polyethylene glycol, the integrated dialysis system efficiently absorbs short chain fatty acids (up to 60%) and water (on average 850 mL d-1 ). Cultivation of a typical gut bacterium (Bifidobacterium animalis) was performed to demonstrate the applicability for controlled microbiota cultivation. PETR is unique in combining simulation of the entire colon, peristaltic mixing, dialytic water and metabolite absorption, and a progressive pH gradient in a single-tube design. PETR is a further step to precise replication of colonic conditions in vitro for reliable and reproducible microbiota research, such as studying the effect of food compounds, prebiotics or probiotics, or the development and treatment of infections with enteric pathogens, but also for further medical applications such as drug delivery studies or to study the effect of drugs on and their degradation by the microbiota.
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Affiliation(s)
- David Vorländer
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Gábor Schultz
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Kristin Hoffmann
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Detlev Rasch
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Katrin Dohnt
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
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4
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Castañeda-Monsalve V, Fröhlich LF, Haange SB, Homsi MN, Rolle-Kampczyk U, Fu Q, von Bergen M, Jehmlich N. High-throughput screening of the effects of 90 xenobiotics on the simplified human gut microbiota model (SIHUMIx): a metaproteomic and metabolomic study. Front Microbiol 2024; 15:1349367. [PMID: 38444810 PMCID: PMC10912515 DOI: 10.3389/fmicb.2024.1349367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
The human gut microbiota is a complex microbial community with critical functions for the host, including the transformation of various chemicals. While effects on microorganisms has been evaluated using single-species models, their functional effects within more complex microbial communities remain unclear. In this study, we investigated the response of a simplified human gut microbiota model (SIHUMIx) cultivated in an in vitro bioreactor system in combination with 96 deep-well plates after exposure to 90 different xenobiotics, comprising 54 plant protection products and 36 food additives and dyes, at environmentally relevant concentrations. We employed metaproteomics and metabolomics to evaluate changes in bacterial abundances, the production of Short Chain Fatty Acids (SCFAs), and the regulation of metabolic pathways. Our findings unveiled significant changes induced by 23 out of 54 plant protection products and 28 out of 36 food additives across all three categories assessed. Notable highlights include azoxystrobin, fluroxypyr, and ethoxyquin causing a substantial reduction (log2FC < -0.5) in the concentrations of the primary SCFAs: acetate, butyrate, and propionate. Several food additives had significant effects on the relative abundances of bacterial species; for example, acid orange 7 and saccharin led to a 75% decrease in Clostridium butyricum, with saccharin causing an additional 2.5-fold increase in E. coli compared to the control. Furthermore, both groups exhibited up- and down-regulation of various pathways, including those related to the metabolism of amino acids such as histidine, valine, leucine, and isoleucine, as well as bacterial secretion systems and energy pathways like starch, sucrose, butanoate, and pyruvate metabolism. This research introduces an efficient in vitro technique that enables high-throughput screening of the structure and function of a simplified and well-defined human gut microbiota model against 90 chemicals using metaproteomics and metabolomics. We believe this approach will be instrumental in characterizing chemical-microbiota interactions especially important for regulatory chemical risk assessments.
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Affiliation(s)
- Victor Castañeda-Monsalve
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Laura-Fabienne Fröhlich
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Sven-Bastiaan Haange
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Masun Nabhan Homsi
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Qiuguo Fu
- Department of Analytical Chemistry, Helmholtz Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Toxicology, Helmholtz Centre for Environmental Research GmbH (UFZ), Leipzig, Germany
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5
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Jennings SAV, Clavel T. Synthetic Communities of Gut Microbes for Basic Research and Translational Approaches in Animal Health and Nutrition. Annu Rev Anim Biosci 2024; 12:283-300. [PMID: 37963399 DOI: 10.1146/annurev-animal-021022-025552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Microbes and animals have a symbiotic relationship that greatly influences nutrient uptake and animal health. This relationship can be studied using selections of microbes termed synthetic communities, or SynComs. SynComs are used in many different animal hosts, including agricultural animals, to investigate microbial interactions with nutrients and how these affect animal health. The most common host focuses for SynComs are currently mouse and human, from basic mechanistic research through to translational disease models and live biotherapeutic products (LBPs) as treatments. We discuss SynComs used in basic research models and findings that relate to human and animal health and nutrition. Translational use cases of SynComs are discussed, followed by LBPs, especially within the context of agriculture. SynComs still face challenges, such as standardization for reproducibility and contamination risks. However, the future of SynComs is hopeful, especially in the areas of genome-guided SynCom design and custom SynCom-based treatments.
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Affiliation(s)
- Susan A V Jennings
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany;
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany;
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6
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Van Den Bossche T, Verschaffelt P, Vande Moortele T, Dawyndt P, Martens L, Mesuere B. Biodiversity Analysis of Metaproteomics Samples with Unipept: A Comprehensive Tutorial. Methods Mol Biol 2024; 2836:183-215. [PMID: 38995542 DOI: 10.1007/978-1-0716-4007-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be , has emerged as a valuable resource for analyzing metaproteomic data. It offers in-depth insights into both taxonomic distributions and functional characteristics of complex ecosystems. This tutorial explains essential concepts like Lowest Common Ancestor (LCA) determination and the handling of peptides with missed cleavages. It also provides a detailed, step-by-step guide on using the Unipept Web application and Unipept Desktop for thorough metaproteomics analyses. By integrating theoretical principles with practical methodologies, this tutorial empowers researchers with the essential knowledge and tools needed to fully utilize metaproteomics in their microbiome studies.
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Affiliation(s)
- Tim Van Den Bossche
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
| | - Pieter Verschaffelt
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Tibo Vande Moortele
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Peter Dawyndt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Lennart Martens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.
| | - Bart Mesuere
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
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7
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Krause JL, Engelmann B, Schaepe SS, Rolle-Kampczyk U, Jehmlich N, Chang HD, Slanina U, Hoffman M, Lehmann J, Zenclussen AC, Herberth G, von Bergen M, Haange SB. DSS treatment does not affect murine colonic microbiota in absence of the host. Gut Microbes 2024; 16:2297831. [PMID: 38165179 PMCID: PMC10763643 DOI: 10.1080/19490976.2023.2297831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
The prevalence of inflammatory bowel disease (IBD) is rising globally; however, its etiology is still not fully understood. Patient genetics, immune system, and intestinal microbiota are considered critical factors contributing to IBD. Preclinical animal models are crucial to better understand the importance of individual contributing factors. Among these, the dextran sodium sulfate (DSS) colitis model is the most widely used. DSS treatment induces gut inflammation and dysbiosis. However, its exact mode of action remains unclear. To determine whether DSS treatment induces pathogenic changes in the microbiota, we investigated the microbiota-modulating effects of DSS on murine microbiota in vitro. For this purpose, we cultured murine microbiota from the colon in six replicate continuous bioreactors. Three bioreactors were supplemented with 1% DSS and compared with the remaining PBS-treated control bioreactors by means of microbiota taxonomy and functionality. Using metaproteomics, we did not identify significant changes in microbial taxonomy, either at the phylum or genus levels. No differences in the metabolic pathways were observed. Furthermore, the global metabolome and targeted short-chain fatty acid (SCFA) quantification did not reveal any DSS-related changes. DSS had negligible effects on microbial functionality and taxonomy in vitro in the absence of the host environment. Our results underline that the DSS colitis mouse model is a suitable model to study host-microbiota interactions, which may help to understand how intestinal inflammation modulates the microbiota at the taxonomic and functional levels.
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Affiliation(s)
- Jannike Lea Krause
- German Rheumatism Research Center Berlin, a Leibniz Institute – DRFZ, Schwiete laboratory for microbiota and inflammation, Berlin, Germany
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany
| | - Beatrice Engelmann
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Stephanie Serena Schaepe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hyun-Dong Chang
- German Rheumatism Research Center Berlin, a Leibniz Institute – DRFZ, Schwiete laboratory for microbiota and inflammation, Berlin, Germany
- Chair of Cytometry, Institute of Biotechnology, Technische Universität, Berlin, Germany
| | - Ulla Slanina
- Fraunhofer Cluster of Excellence Immune-mediated Diseases – CIMD, Leipzig, Germany
| | - Maximillian Hoffman
- Fraunhofer Cluster of Excellence Immune-mediated Diseases – CIMD, Leipzig, Germany
| | - Jörg Lehmann
- Fraunhofer Cluster of Excellence Immune-mediated Diseases – CIMD, Leipzig, Germany
- Department of Preclinical Development and Validation, Fraunhofer-Institute for Cell Therapy and Immunology – IZI, Leipzig, Germany
| | - Ana Claudia Zenclussen
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany
| | - Gunda Herberth
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany
| | - Sven-Bastiaan Haange
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
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8
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Yadav A, Ahlawat S, Sharma KK. Culturing the unculturables: strategies, challenges, and opportunities for gut microbiome study. J Appl Microbiol 2023; 134:lxad280. [PMID: 38006234 DOI: 10.1093/jambio/lxad280] [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: 08/08/2023] [Revised: 10/17/2023] [Accepted: 11/23/2023] [Indexed: 11/26/2023]
Abstract
Metagenome sequencing techniques revolutionized the field of gut microbiome study. However, it is equipped with experimental and computational biases, which affect the downstream analysis results. Also, live microbial strains are needed for a better understanding of host-microbial crosstalks and for designing next-generation treatment therapies based on probiotic strains and postbiotic molecules. Conventional culturing methodologies are insufficient to get the dark gut matter on the plate; therefore, there is an urgent need to propose novel culturing methods that can fill the limitations of metagenomics. The current work aims to provide a consolidated evaluation of the available methods for host-microbe interaction with an emphasis on in vitro culturing of gut microbes using organoids, gut on a chip, and gut bioreactor. Further, the knowledge of microbial crosstalk in the gut helps us to identify core microbiota, and key metabolites that will aid in designing culturing media and co-culturing systems for gut microbiome study. After the deeper mining of the current culturing methods, we recommend that 3D-printed intestinal cells in a multistage continuous flow reactor equipped with an extended organoid system might be a good practical choice for gut microbiota-based studies.
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Affiliation(s)
- Asha Yadav
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
| | - Shruti Ahlawat
- Department of Microbiology, Faculty of Allied Health Sciences, SGT University, Gurugram 122505, Haryana, India
| | - Krishna K Sharma
- Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India
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9
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Procházková N, Falony G, Dragsted LO, Licht TR, Raes J, Roager HM. Advancing human gut microbiota research by considering gut transit time. Gut 2023; 72:180-191. [PMID: 36171079 PMCID: PMC9763197 DOI: 10.1136/gutjnl-2022-328166] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/10/2022] [Indexed: 02/04/2023]
Abstract
Accumulating evidence indicates that gut transit time is a key factor in shaping the gut microbiota composition and activity, which are linked to human health. Both population-wide and small-scale studies have identified transit time as a top covariate contributing to the large interindividual variation in the faecal microbiota composition. Despite this, transit time is still rarely being considered in the field of the human gut microbiome. Here, we review the latest research describing how and why whole gut and segmental transit times vary substantially between and within individuals, and how variations in gut transit time impact the gut microbiota composition, diversity and metabolism. Furthermore, we discuss the mechanisms by which the gut microbiota may causally affect gut motility. We argue that by taking into account the interindividual and intraindividual differences in gut transit time, we can advance our understanding of diet-microbiota interactions and disease-related microbiome signatures, since these may often be confounded by transient or persistent alterations in transit time. Altogether, a better understanding of the complex, bidirectional interactions between the gut microbiota and transit time is required to better understand gut microbiome variations in health and disease.
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Affiliation(s)
- Nicola Procházková
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Gwen Falony
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Lars Ove Dragsted
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University, Kgs. Lyngby, Denmark
| | - Jeroen Raes
- Department of Microbiology and Immunology, KU Leuven - University of Leuven, Leuven, Belgium
- Center for Microbiology, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Henrik M Roager
- Department of Nutrition, Exercise and Sports, University of Copenhagen, Frederiksberg, Denmark
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10
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Biagini F, Daddi C, Calvigioni M, De Maria C, Zhang YS, Ghelardi E, Vozzi G. Designs and methodologies to recreate in vitro human gut microbiota models. Biodes Manuf 2022. [DOI: 10.1007/s42242-022-00210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AbstractThe human gut microbiota is widely considered to be a metabolic organ hidden within our bodies, playing a crucial role in the host’s physiology. Several factors affect its composition, so a wide variety of microbes residing in the gut are present in the world population. Individual excessive imbalances in microbial composition are often associated with human disorders and pathologies, and new investigative strategies to gain insight into these pathologies and define pharmaceutical therapies for their treatment are needed. In vitro models of the human gut microbiota are commonly used to study microbial fermentation patterns, community composition, and host-microbe interactions. Bioreactors and microfluidic devices have been designed to culture microorganisms from the human gut microbiota in a dynamic environment in the presence or absence of eukaryotic cells to interact with. In this review, we will describe the overall elements required to create a functioning, reproducible, and accurate in vitro culture of the human gut microbiota. In addition, we will analyze some of the devices currently used to study fermentation processes and relationships between the human gut microbiota and host eukaryotic cells.
Graphic abstract
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11
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Cheng K, Ning Z, Li L, Zhang X, Serrana JM, Mayne J, Figeys D. MetaLab-MAG: A Metaproteomic Data Analysis Platform for Genome-Level Characterization of Microbiomes from the Metagenome-Assembled Genomes Database. J Proteome Res 2022; 22:387-398. [PMID: 36508259 PMCID: PMC9903328 DOI: 10.1021/acs.jproteome.2c00554] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The studies of microbial communities have drawn increased attention in various research fields such as agriculture, environment, and human health. Recently, metaproteomics has become a powerful tool to interpret the roles of the community members by investigating the expressed proteins of the microbes. However, analyzing the metaproteomic data sets at genome resolution is still challenging because of the lack of efficient bioinformatics tools. Here we develop MetaLab-MAG, a specially designed tool for the characterization of microbiomes from metagenome-assembled genomes databases. MetaLab-MAG was evaluated by analyzing various human gut microbiota data sets and performed comparably or better than searching the gene catalog protein database directly. MetaLab-MAG can quantify the genome-level microbiota compositions and supports both label-free and isobaric labeling-based quantification strategies. MetaLab-MAG removes the obstacles of metaproteomic data analysis and provides the researchers with in-depth and comprehensive information from the microbiomes.
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12
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Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties. THE ISME JOURNAL 2022; 16:2144-2159. [PMID: 35717467 PMCID: PMC9381525 DOI: 10.1038/s41396-022-01255-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 04/30/2022] [Accepted: 05/25/2022] [Indexed: 11/08/2022]
Abstract
AbstractMicrobe–microbe interactions in the human gut are influenced by host-derived glycans and diet. The high complexity of the gut microbiome poses a major challenge for unraveling the metabolic interactions and trophic roles of key microbes. Synthetic minimal microbiomes provide a pragmatic approach to investigate their ecology including metabolic interactions. Here, we rationally designed a synthetic microbiome termed Mucin and Diet based Minimal Microbiome (MDb-MM) by taking into account known physiological features of 16 key bacteria. We combined 16S rRNA gene-based composition analysis, metabolite measurements and metatranscriptomics to investigate community dynamics, stability, inter-species metabolic interactions and their trophic roles. The 16 species co-existed in the in vitro gut ecosystems containing a mixture of complex substrates representing dietary fibers and mucin. The triplicate MDb-MM’s followed the Taylor’s power law and exhibited strikingly similar ecological and metabolic patterns. The MDb-MM exhibited resistance and resilience to temporal perturbations as evidenced by the abundance and metabolic end products. Microbe-specific temporal dynamics in transcriptional niche overlap and trophic interaction network explained the observed co-existence in a competitive minimal microbiome. Overall, the present study provides crucial insights into the co-existence, metabolic niches and trophic roles of key intestinal microbes in a highly dynamic and competitive in vitro ecosystem.
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13
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Lee JY, Mitchell HD, Burnet MC, Wu R, Jenson SC, Merkley ED, Nakayasu ES, Nicora CD, Jansson JK, Burnum-Johnson KE, Payne SH. Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics. J Proteome Res 2022; 21:2023-2035. [PMID: 35793793 PMCID: PMC9361346 DOI: 10.1021/acs.jproteome.2c00334] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
![]()
Metaproteomics has
been increasingly utilized for high-throughput
characterization of proteins in complex environments and has been
demonstrated to provide insights into microbial composition and functional
roles. However, significant challenges remain in metaproteomic data
analysis, including creation of a sample-specific protein sequence
database. A well-matched database is a requirement for successful
metaproteomics analysis, and the accuracy and sensitivity of PSM identification
algorithms suffer when the database is incomplete or contains extraneous
sequences. When matched DNA sequencing data of the sample is unavailable
or incomplete, creating the proteome database that accurately represents
the organisms in the sample is a challenge. Here, we leverage a de novo peptide sequencing approach to identify the sample
composition directly from metaproteomic data. First, we created a
deep learning model, Kaiko, to predict the peptide sequences from
mass spectrometry data and trained it on 5 million peptide–spectrum
matches from 55 phylogenetically diverse bacteria. After training,
Kaiko successfully identified organisms from soil isolates and synthetic
communities directly from proteomics data. Finally, we created a pipeline
for metaproteome database generation using Kaiko. We tested the pipeline
on native soils collected in Kansas, showing that the de novo sequencing model can be employed as an alternative and complementary
method to construct the sample-specific protein database instead of
relying on (un)matched metagenomes. Our pipeline identified all highly
abundant taxa from 16S rRNA sequencing of the soil samples and uncovered
several additional species which were strongly represented only in
proteomic data.
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Affiliation(s)
- Joon-Yong Lee
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Hugh D Mitchell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Meagan C Burnet
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ruonan Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Sarah C Jenson
- Signature Sciences and Technology Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Eric D Merkley
- Signature Sciences and Technology Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kristin E Burnum-Johnson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Samuel H Payne
- Biology Department, Brigham Young University, Provo, Utah 84602, United States
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14
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Schallert K, Verschaffelt P, Mesuere B, Benndorf D, Martens L, Van Den Bossche T. Pout2Prot: An Efficient Tool to Create Protein (Sub)groups from Percolator Output Files. J Proteome Res 2022; 21:1175-1180. [PMID: 35143215 DOI: 10.1021/acs.jproteome.1c00685] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In metaproteomics, the study of the collective proteome of microbial communities, the protein inference problem is more challenging than in single-species proteomics. Indeed, a peptide sequence can be present not only in multiple proteins or protein isoforms of the same species, but also in homologous proteins from closely related species. To assign the taxonomy and functions of the microbial species, specialized tools have been developed, such as Prophane. This tool, however, is not directly compatible with post-processing tools such as Percolator. In this manuscript we therefore present Pout2Prot, which takes Percolator Output (.pout) files from multiple experiments and creates protein group and protein subgroup output files (.tsv) that can be used directly with Prophane. We investigated different grouping strategies and compared existing protein grouping tools to develop an advanced protein grouping algorithm that offers a variety of different approaches, allows grouping for multiple files, and uses a weighted spectral count for protein (sub)groups to reflect abundance. Pout2Prot is available as a web application at https://pout2prot.ugent.be and is installable via pip as a standalone command line tool and reusable software library. All code is open source under the Apache License 2.0 and is available at https://github.com/compomics/pout2prot.
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Affiliation(s)
- Kay Schallert
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, 39104 Magdeburg, Germany.,Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39104 Magdeburg, Germany
| | - Pieter Verschaffelt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium.,VIB - UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
| | - Bart Mesuere
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium.,VIB - UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
| | - Dirk Benndorf
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, 39104 Magdeburg, Germany.,Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39104 Magdeburg, Germany.,Microbiology, Department of Applied Biosciences and Process Technology, Anhalt University of Applied Sciences, 06366 Köthen, Germany
| | - Lennart Martens
- VIB - UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Tim Van Den Bossche
- VIB - UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
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15
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Krause JL, Engelmann B, Nunes da Rocha U, Pierzchalski A, Chang HD, Zenclussen AC, von Bergen M, Rolle-Kampczyk U, Herberth G. MAIT cell activation is reduced by direct and microbiota-mediated exposure to bisphenols. ENVIRONMENT INTERNATIONAL 2022; 158:106985. [PMID: 34991247 DOI: 10.1016/j.envint.2021.106985] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/15/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Oral uptake is the primary route of human bisphenol exposure, resulting in an exposure of the intestinal microbiota and intestine-associated immune cells. Therefore, we compared the impact of bisphenol A (BPA), bisphenol F (BPF) and bisphenol S (BPS) on (i) intestinal microbiota, (ii) microbiota-mediated immunomodulatory effects and (iii) direct effects on mucosal-associated invariant T (MAIT) cells in vitro. We acutely exposed human fecal microbiota, Bacteroides thetaiotaomicron and Escherichia coli to BPA and its analogues BPF and BPS referring to the European tolerable daily intake (TDI), i.e. 2.3 µg/mL, 28.3 µg/mL and 354.0 µg/mL. Growth and viability of E. coli was most susceptible to BPF, whereas B.thetaiotaomicron and fecal microbiota were affected by BPA > BPF > BPS. At 354.0 µg/mL bisphenols altered microbial diversity in compound-specific manner and modulated microbial metabolism, with BPA already acting on metabolism at 28.3 µg/mL. Microbiota-mediated effects on MAIT cells were observed for the individual bacteria at 354.0 µg/mL only. However, BPA and BPF directly modulated MAIT cell responses at low concentrations, whereby bisphenols at concentrations equivalent for the current TDI had no modulatory effects for microbiota or for MAIT cells. Our findings indicate that acute bisphenol exposure may alter microbial metabolism and impact directly on immune cells.
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Affiliation(s)
- J L Krause
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany; present address: German Rheumatism Research Center Berlin, a Leibniz Institute - DRFZ, Schwiete laboratory for microbiota and inflammation, Berlin, Germany
| | - B Engelmann
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany
| | - U Nunes da Rocha
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Microbiology, Leipzig, Germany
| | - A Pierzchalski
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany
| | - H D Chang
- present address: German Rheumatism Research Center Berlin, a Leibniz Institute - DRFZ, Schwiete laboratory for microbiota and inflammation, Berlin, Germany; Chair of Cytometry, Institute of Biotechnology, Technische Universität Berlin, Germany
| | - A C Zenclussen
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany
| | - M 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
| | - U Rolle-Kampczyk
- Helmholtz-Centre for Environmental Research - UFZ, Department of Molecular Systems Biology, Leipzig, Germany
| | - G Herberth
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany.
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16
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Van Den Bossche T, Kunath BJ, Schallert K, Schäpe SS, Abraham PE, Armengaud J, Arntzen MØ, Bassignani A, Benndorf D, Fuchs S, Giannone RJ, Griffin TJ, Hagen LH, Halder R, Henry C, Hettich RL, Heyer R, Jagtap P, Jehmlich N, Jensen M, Juste C, Kleiner M, Langella O, Lehmann T, Leith E, May P, Mesuere B, Miotello G, Peters SL, Pible O, Queiros PT, Reichl U, Renard BY, Schiebenhoefer H, Sczyrba A, Tanca A, Trappe K, Trezzi JP, Uzzau S, Verschaffelt P, von Bergen M, Wilmes P, Wolf M, Martens L, Muth T. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nat Commun 2021; 12:7305. [PMID: 34911965 PMCID: PMC8674281 DOI: 10.1038/s41467-021-27542-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 11/24/2021] [Indexed: 12/17/2022] Open
Abstract
Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.
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Affiliation(s)
- Tim Van Den Bossche
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Benoit J Kunath
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Kay Schallert
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Stephanie S Schäpe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ariane Bassignani
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Dirk Benndorf
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Microbiology, Department of Applied Biosciences and Process Technology, Anhalt University of Applied Sciences, Köthen, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Stephan Fuchs
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | | | - Timothy J Griffin
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Céline Henry
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Robert Heyer
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Pratik Jagtap
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Marlene Jensen
- Department of Plant & Microbial Biology, North Carolina State University, Raleigh, USA
| | - Catherine Juste
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Manuel Kleiner
- Department of Plant & Microbial Biology, North Carolina State University, Raleigh, USA
| | - Olivier Langella
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Theresa Lehmann
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Emma Leith
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Bart Mesuere
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Guylaine Miotello
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Samantha L Peters
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Pedro T Queiros
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Udo Reichl
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Bernhard Y Renard
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany
| | - Henning Schiebenhoefer
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany
| | | | - Alessandro Tanca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Kathrin Trappe
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Jean-Pierre Trezzi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Integrated Biobank of Luxembourg, Luxembourg Institute of Health, 1, rue Louis Rech, L-3555, Dudelange, Luxembourg
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Pieter Verschaffelt
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6 avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Maximilian Wolf
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Lennart Martens
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
| | - Thilo Muth
- Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany
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17
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Van Den Bossche T, Kunath BJ, Schallert K, Schäpe SS, Abraham PE, Armengaud J, Arntzen MØ, Bassignani A, Benndorf D, Fuchs S, Giannone RJ, Griffin TJ, Hagen LH, Halder R, Henry C, Hettich RL, Heyer R, Jagtap P, Jehmlich N, Jensen M, Juste C, Kleiner M, Langella O, Lehmann T, Leith E, May P, Mesuere B, Miotello G, Peters SL, Pible O, Queiros PT, Reichl U, Renard BY, Schiebenhoefer H, Sczyrba A, Tanca A, Trappe K, Trezzi JP, Uzzau S, Verschaffelt P, von Bergen M, Wilmes P, Wolf M, Martens L, Muth T. Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows. Nat Commun 2021; 12:7305. [PMID: 34911965 DOI: 10.1101/2021.03.05.433915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 11/24/2021] [Indexed: 05/21/2023] Open
Abstract
Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.
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Affiliation(s)
- Tim Van Den Bossche
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Benoit J Kunath
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Kay Schallert
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Stephanie S Schäpe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Ariane Bassignani
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Dirk Benndorf
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Microbiology, Department of Applied Biosciences and Process Technology, Anhalt University of Applied Sciences, Köthen, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Stephan Fuchs
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | | | - Timothy J Griffin
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Rashi Halder
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Céline Henry
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Robert Heyer
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Pratik Jagtap
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Marlene Jensen
- Department of Plant & Microbial Biology, North Carolina State University, Raleigh, USA
| | - Catherine Juste
- INRAE, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Manuel Kleiner
- Department of Plant & Microbial Biology, North Carolina State University, Raleigh, USA
| | - Olivier Langella
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Theresa Lehmann
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Emma Leith
- Department of Biochemistry Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Bart Mesuere
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Guylaine Miotello
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Samantha L Peters
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, 30200, Bagnols-sur-Cèze, France
| | - Pedro T Queiros
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Udo Reichl
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Bernhard Y Renard
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany
| | - Henning Schiebenhoefer
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
- Data Analytics and Computational Statistics, Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Potsdam, Germany
| | | | - Alessandro Tanca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Kathrin Trappe
- Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Berlin, Germany
| | - Jean-Pierre Trezzi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Integrated Biobank of Luxembourg, Luxembourg Institute of Health, 1, rue Louis Rech, L-3555, Dudelange, Luxembourg
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Pieter Verschaffelt
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, 6 avenue du Swing, L-4367, Belvaux, Luxembourg
| | - Maximilian Wolf
- Bioprocess Engineering, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Lennart Martens
- VIB - UGent Center for Medical Biotechnology, VIB, Ghent, Belgium.
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
| | - Thilo Muth
- Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany
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18
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Development and Validation of a LC-MS/MS Technique for the Analysis of Short Chain Fatty Acids in Tissues and Biological Fluids without Derivatisation Using Isotope Labelled Internal Standards. Molecules 2021; 26:molecules26216444. [PMID: 34770853 PMCID: PMC8587764 DOI: 10.3390/molecules26216444] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/13/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
The gut microbiota is critical to the maintenance of physiological homeostasis and as such is implicated in a range of diseases such as colon cancer, ulcerative colitis, diabetes, cardiovascular diseases, and neurodegenerative diseases. Short chain fatty acids (SCFAs) are key metabolites produced by the gut microbiota from the fermentation of dietary fibre. Here we present a novel, sensitive, and direct LC-MS/MS technique using isotopically labelled internal standards without derivatisation for the analysis of SCFAs in different biological matrices. The technique has significant advantages over the current widely used techniques based on sample derivatization and GC-MS analysis, including fast and simple sample preparation and short LC runtime (10 min). The technique is specific and sensitive for the quantification of acetate, butyrate, isobutyrate, isovalerate, lactate, propionate and valerate. The limits of detection were all 0.001 mM except for acetate which was 0.003 mM. The calibration curves for all the analytes were linear with correlation coefficients r2 > 0.998. The intra- and inter-day precisions in three levels of known concentrations were <12% and <20%, respectively. The quantification accuracy ranged from 92% to 120%. The technique reported here offers a valuable analytical tool for use in studies of SCFA production in the gut and their distribution to host tissues.
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19
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Rodríguez-Daza MC, Pulido-Mateos EC, Lupien-Meilleur J, Guyonnet D, Desjardins Y, Roy D. Polyphenol-Mediated Gut Microbiota Modulation: Toward Prebiotics and Further. Front Nutr 2021; 8:689456. [PMID: 34268328 PMCID: PMC8276758 DOI: 10.3389/fnut.2021.689456] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/27/2021] [Indexed: 12/11/2022] Open
Abstract
The genome of gut microbes encodes a collection of enzymes whose metabolic functions contribute to the bioavailability and bioactivity of unabsorbed (poly)phenols. Datasets from high throughput sequencing, metabolome measurements, and other omics have expanded the understanding of the different modes of actions by which (poly)phenols modulate the microbiome conferring health benefits to the host. Progress have been made to identify direct prebiotic effects of (poly)phenols; albeit up to date, these compounds are not recognized as prebiotics sensu stricto. Interestingly, certain probiotics strains have an enzymatic repertoire, such as tannase, α-L-rhamnosidase, and phenolic acid reductase, involved in the transformation of different (poly)phenols into bioactive phenolic metabolites. In vivo studies have demonstrated that these (poly)phenol-transforming bacteria thrive when provided with phenolic substrates. However, other taxonomically distinct gut symbionts of which a phenolic-metabolizing activity has not been demonstrated are still significantly promoted by (poly)phenols. This is the case of Akkermansia muciniphila, a so-called antiobesity bacterium, which responds positively to (poly)phenols and may be partially responsible for the health benefits formerly attributed to these molecules. We surmise that (poly)phenols broad antimicrobial action free ecological niches occupied by competing bacteria, thereby allowing the bloom of beneficial gut bacteria. This review explores the capacity of (poly)phenols to promote beneficial gut bacteria through their direct and collaborative bacterial utilization and their inhibitory action on potential pathogenic species. We propose the term duplibiotic, to describe an unabsorbed substrate modulating the gut microbiota by both antimicrobial and prebiotic modes of action. (Poly)phenol duplibiotic effect could participate in blunting metabolic disturbance and gut dysbiosis, positioning these compounds as dietary strategies with therapeutic potential.
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Affiliation(s)
- Maria Carolina Rodríguez-Daza
- Faculty of Agriculture and Food Sciences, Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, QC, Canada.,Department of Food Science, Faculty of Agriculture and Food Sciences, Laval University, Québec, QC, Canada
| | - Elena C Pulido-Mateos
- Faculty of Agriculture and Food Sciences, Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, QC, Canada.,Department of Food Science, Faculty of Agriculture and Food Sciences, Laval University, Québec, QC, Canada
| | - Joseph Lupien-Meilleur
- Faculty of Agriculture and Food Sciences, Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, QC, Canada.,Department of Food Science, Faculty of Agriculture and Food Sciences, Laval University, Québec, QC, Canada
| | - Denis Guyonnet
- Diana Nova, Symrise Nutrition, Clichy-la-Garenne, France
| | - Yves Desjardins
- Faculty of Agriculture and Food Sciences, Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, QC, Canada.,Department of Plant Science, Faculty of Agriculture and Food Sciences, Laval University, Québec, QC, Canada
| | - Denis Roy
- Faculty of Agriculture and Food Sciences, Institute of Nutrition and Functional Foods (INAF), Laval University, Québec, QC, Canada.,Department of Food Science, Faculty of Agriculture and Food Sciences, Laval University, Québec, QC, Canada
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20
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A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations. BMC Bioinformatics 2021; 22:277. [PMID: 34039272 PMCID: PMC8157683 DOI: 10.1186/s12859-021-04159-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
Background Small Proteins have received increasing attention in recent years. They have in particular been implicated as signals contributing to the coordination of bacterial communities. In genome annotations they are often missing or hidden among large numbers of hypothetical proteins because genome annotation pipelines often exclude short open reading frames or over-predict hypothetical proteins based on simple models. The validation of novel proteins, and in particular of small proteins (sProteins), therefore requires additional evidence. Proteogenomics is considered the gold standard for this purpose. It extends beyond established annotations and includes all possible open reading frames (ORFs) as potential sources of peptides, thus allowing the discovery of novel, unannotated proteins. Typically this results in large numbers of putative novel small proteins fraught with large fractions of false-positive predictions. Results We observe that number and quality of the peptide-spectrum matches (PSMs) that map to a candidate ORF can be highly informative for the purpose of distinguishing proteins from spurious ORF annotations. We report here on a workflow that aggregates PSM quality information and local context into simple descriptors and reliably separates likely proteins from the large pool of false-positive, i.e., most likely untranslated ORFs. We investigated the artificial gut microbiome model SIHUMIx, comprising eight different species, for which we validate 5114 proteins that have previously been annotated only as hypothetical ORFs. In addition, we identified 37 non-annotated protein candidates for which we found evidence at the proteomic and transcriptomic level. Half (19) of these candidates have close functional homologs in other species. Another 12 candidates have homologs designated as hypothetical proteins in other species. The remaining six candidates are short (< 100 AA) and are most likely bona fide novel proteins. Conclusions The aggregation of PSM quality information for predicted ORFs provides a robust and efficient method to identify novel proteins in proteomics data. The workflow is in particular capable of identifying small proteins and frameshift variants. Since PSMs are explicitly mapped to genomic locations, it furthermore facilitates the integration of transcriptomics data and other sources of genome-level information. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04159-8.
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21
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Nissen L, Casciano F, Gianotti A. Intestinal fermentation in vitro models to study food-induced gut microbiota shift: an updated review. FEMS Microbiol Lett 2021; 367:5854534. [PMID: 32510557 DOI: 10.1093/femsle/fnaa097] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/06/2020] [Indexed: 12/12/2022] Open
Abstract
In vitro gut fermentation models were firstly introduced in nutrition and applied microbiology research back in the 1990s. These models have improved greatly during time, mainly over the resemblance to the complexity of digestion stages, the replication of experimental conditions, the multitude of ecological parameters to assay. The state of the science is that the most competitive models shall include a complex gut microbiota, small working volumes, distinct interconnected compartments and rigorous bio-chemical and ecological settings, controlled by a computer, as well as a free-hands accessibility, not to contaminate the mock microbiota. These models are a useful tool to study the impact of a given diet compound, e.g. prebiotics, on the human gut microbiota. The principal application is to focus on the shift of the core microbial groups and selected species together with their metabolites, assaying their diversity, richness and abundance in the community over time. Besides, it is possible to study how a compound is digested, which metabolic pathways are triggered, and the type and quantity of microbial metabolites produced. Further prospective should focus on challenges with pathogens as well as on ecology of gut syndromes. In this minireview an updated presentation of the most used intestinal models is presented, basing on their concept, technical features, as well as on research applications.
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Affiliation(s)
- Lorenzo Nissen
- CIRI-Interdepartmental Centre of Agri-Food Industrial Research, University of Bologna, P.za G. Goidanich 60, 47521 Cesena, FC, Italy
| | - Flavia Casciano
- DiSTAL-Department of Agricultural and Food Sciences, University of Bologna, V.le Fanin 50, 40127 Bologna, Italy
| | - Andrea Gianotti
- CIRI-Interdepartmental Centre of Agri-Food Industrial Research, University of Bologna, P.za G. Goidanich 60, 47521 Cesena, FC, Italy.,DiSTAL-Department of Agricultural and Food Sciences, University of Bologna, V.le Fanin 50, 40127 Bologna, Italy
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22
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Karaduta O, Dvanajscak Z, Zybailov B. Metaproteomics-An Advantageous Option in Studies of Host-Microbiota Interaction. Microorganisms 2021; 9:microorganisms9050980. [PMID: 33946610 PMCID: PMC8147213 DOI: 10.3390/microorganisms9050980] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/29/2021] [Accepted: 04/30/2021] [Indexed: 12/20/2022] Open
Abstract
Gut microbiome contributes to host health by maintaining homeostasis, increasing digestive efficiency, and facilitating the development of the immune system. Manipulating gut microbiota is being recognized as a therapeutic target to manage various chronic diseases. The therapeutic manipulation of the intestinal microbiome is achieved through diet modification, the administration of prebiotics, probiotics, or antibiotics, and more recently, fecal microbiome transplantation (FMT). In this opinion paper, we give a perspective on the current status of application of multi-omics technologies in the analysis of host-microbiota interactions. The aim of this paper was to highlight the strengths of metaproteomics, which integrates with and often relies on other approaches.
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Affiliation(s)
- Oleg Karaduta
- Department of Biochemistry and Molecular Biology, UAMS, Little Rock, AR 72205, USA;
- Correspondence: ; Tel.: +1-501-251-5381
| | | | - Boris Zybailov
- Department of Biochemistry and Molecular Biology, UAMS, Little Rock, AR 72205, USA;
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23
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Petruschke H, Schori C, Canzler S, Riesbeck S, Poehlein A, Daniel R, Frei D, Segessemann T, Zimmerman J, Marinos G, Kaleta C, Jehmlich N, Ahrens CH, von Bergen M. Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome. MICROBIOME 2021; 9:55. [PMID: 33622394 PMCID: PMC7903761 DOI: 10.1186/s40168-020-00981-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/16/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. RESULTS We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. CONCLUSIONS We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract. Video abstract.
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Affiliation(s)
- Hannes Petruschke
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Christian Schori
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Sebastian Canzler
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Sarah Riesbeck
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Anja Poehlein
- Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Georg-August University of Göttingen, Göttingen, Germany
| | - Daniel Frei
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Tina Segessemann
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Johannes Zimmerman
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Georgios Marinos
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Christian H Ahrens
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland.
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany.
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany.
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24
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Oba PM, Vidal S, Wyss R, Miao Y, Adesokan Y, Swanson KS. Effect of a novel animal milk oligosaccharide biosimilar on the gut microbial communities and metabolites of in vitro incubations using feline and canine fecal inocula. J Anim Sci 2020; 98:5897395. [PMID: 32845316 DOI: 10.1093/jas/skaa273] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/20/2020] [Indexed: 12/17/2022] Open
Abstract
Milk oligosaccharides (MO) confer multiple potential physiological benefits, such as the selective growth promotion of beneficial microbiota, inhibition of enteric pathogen growth and adhesion to enterocytes, maturation of the gut mucosal barrier, and modulation of the gastrointestinal immune system. This study was conducted to determine the fermentation potential of GNU100, an animal MO biosimilar, in an in vitro system using healthy canine and feline fecal inocula. Single feline and single canine fecal samples were used to inoculate a batch fermentation system. Tubes containing a blank control (BNC), GNU100 at 0.5% (5 g/L; GNU1), or GNU100 at 1.0% (10 g/L; GNU2) were incubated for 48 h. Gas pressure, pH, lactate, short-chain fatty acids (SCFA; acetate, propionate, and butyrate), and branched-chain fatty acids (BCFA; isobutyrate, isovalerate, and valerate) were measured after 6, 24, and 48 h. Ammonium and microbiota (total bacteria by flow cytometry and Pet-16Seq; Lactobacillus and Bifidobacterium by quantitative polymerase chain reaction ) were measured after 24 and 48 h. Data were analyzed using the Mixed Models procedure of SAS. Substrates were considered to be a fixed effect and replicates considered to be a random effect. Tukey's multiple comparison analysis was used to compare least squares means, with differences considered significant with P < 0.05. In feline and canine incubations, SCFA increases were greater (P < 0.0001) in GNU100 compared with BNC, with acetate making up the largest SCFA proportion (P < 0.0001). GNU100 cultures led to greater increases (P < 0.0001) in lactate and ammonium than BNC in the feline incubations. GNU100 cultures led to greater increases (P < 0.0001) in ammonium than BNC in canine incubations and greater increases (P < 0.0001) in BCFA than BNC in feline incubations. Pet-16Seq microbial profiles from the feline and canine fecal incubations exhibited a modulation after GNU100 fermentation, with a reduction of the genera Escherichia/Shigella and Salmonella. In feline incubations, Bifidobacterium populations had greater increases (P < 0.0001) in GNU100 than BNC. In feline incubations, Lactobacillus populations had greater increases (P = 0.01) in GNU100 than BNC, with GNU1 leading to greater increases (P = 0.02) in Lactobacillus than BNC tubes in canine incubations. Overall, this study demonstrated that GNU100 was fermented in an in vitro fermentation system inoculated with canine and feline microbiota, resulting in the growth of beneficial bacteria and the production of SCFA, BCFA, and ammonium.
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Affiliation(s)
- Patrícia M Oba
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL
| | - Sara Vidal
- Gnubiotics Sciences SA, Épalinges, Switzerland
| | - Romain Wyss
- Gnubiotics Sciences SA, Épalinges, Switzerland
| | - Yong Miao
- Gnubiotics Sciences SA, Épalinges, Switzerland
| | | | - Kelly S Swanson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL.,Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL.,Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, IL
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25
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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: 22] [Impact Index Per Article: 5.5] [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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26
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Schäpe SS, Krause JL, Masanetz RK, Riesbeck S, Starke R, Rolle-Kampczyk U, Eberlein C, Heipieper HJ, Herberth G, von Bergen M, Jehmlich N. Environmentally Relevant Concentration of Bisphenol S Shows Slight Effects on SIHUMIx. Microorganisms 2020; 8:microorganisms8091436. [PMID: 32961728 PMCID: PMC7564734 DOI: 10.3390/microorganisms8091436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/03/2020] [Accepted: 09/16/2020] [Indexed: 11/29/2022] Open
Abstract
Bisphenol S (BPS) is an industrial chemical used in the process of polymerization of polycarbonate plastics and epoxy resins and thus can be found in various plastic products and thermal papers. The microbiota disrupting effect of BPS on the community structure of the microbiome has already been reported, but little is known on how BPS affects bacterial activity and function. To analyze these effects, we cultivated the simplified human intestinal microbiota (SIHUMIx) in bioreactors at a concentration of 45 µM BPS. By determining biomass, growth of SIHUMIx was followed but no differences during BPS exposure were observed. To validate if the membrane composition was affected, fatty acid methyl esters (FAMEs) profiles were compared. Changes in the individual membrane fatty acid composition could not been described; however, the saturation level of the membranes slightly increased during BPS exposure. By applying targeted metabolomics to quantify short-chain fatty acids (SCFA), it was shown that the activity of SIHUMIx was unaffected. Metaproteomics revealed temporal effect on the community structure and function, showing that BPS has minor effects on the structure or functionality of SIHUMIx.
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Affiliation(s)
- Stephanie Serena Schäpe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (S.S.S.); (R.K.M.); (S.R.); (U.R.-K.); (M.v.B.)
| | - Jannike Lea Krause
- Department of Environmental Immunology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (J.L.K.); (G.H.)
| | - Rebecca Katharina Masanetz
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (S.S.S.); (R.K.M.); (S.R.); (U.R.-K.); (M.v.B.)
| | - Sarah Riesbeck
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (S.S.S.); (R.K.M.); (S.R.); (U.R.-K.); (M.v.B.)
| | - Robert Starke
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic;
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (S.S.S.); (R.K.M.); (S.R.); (U.R.-K.); (M.v.B.)
| | - Christian Eberlein
- Department of Environmental Biotechnology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (C.E.); (H.-J.H.)
| | - Hermann-Josef Heipieper
- Department of Environmental Biotechnology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (C.E.); (H.-J.H.)
| | - Gunda Herberth
- Department of Environmental Immunology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (J.L.K.); (G.H.)
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (S.S.S.); (R.K.M.); (S.R.); (U.R.-K.); (M.v.B.)
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, 04103 Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research GmbH – UFZ, 04318 Leipzig, Germany; (S.S.S.); (R.K.M.); (S.R.); (U.R.-K.); (M.v.B.)
- Correspondence: ; Tel.: +49-341-235-4767
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27
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Cytometric fingerprints of gut microbiota predict Crohn's disease state. ISME JOURNAL 2020; 15:354-358. [PMID: 32879459 DOI: 10.1038/s41396-020-00762-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 08/06/2020] [Accepted: 08/25/2020] [Indexed: 12/17/2022]
Abstract
Variations in the gut microbiome have been associated with changes in health state such as Crohn's disease (CD). Most surveys characterize the microbiome through analysis of the 16S rRNA gene. An alternative technology that can be used is flow cytometry. In this report, we reanalyzed a disease cohort that has been characterized by both technologies. Changes in microbial community structure are reflected in both types of data. We demonstrate that cytometric fingerprints can be used as a diagnostic tool in order to classify samples according to CD state. These results highlight the potential of flow cytometry to perform rapid diagnostics of microbiome-associated diseases.
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Van Den Bossche T, Verschaffelt P, Schallert K, Barsnes H, Dawyndt P, Benndorf D, Renard BY, Mesuere B, Martens L, Muth T. Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data Analysis. J Proteome Res 2020; 19:3562-3566. [DOI: 10.1021/acs.jproteome.0c00136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Tim Van Den Bossche
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, St. Pietersnieuwstraat 33, 9000 Ghent, Belgium
| | - Pieter Verschaffelt
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
- Department of Applied Mathematics, Computer Science, and Statistics, Ghent University, Krijgslaan 281-S9, 9000 Ghent, Belgium
| | - Kay Schallert
- Bioprocess Engineering, Faculty for Process and Systems Engineering, Otto von Guericke University, Universitaetsplatz 2, 39106 Magdeburg, Germany
- Microbiology, Department of Applied Biosciences and Process Technology, Anhalt University of Applied Sciences, Bernburger Straße 55, 06366 Köthen, Germany
| | - Harald Barsnes
- Proteomics Unit (PROBE), Department of Biomedicine, University of Bergen, Postboks 7804, NO-5020 Bergen, Norway
- Computational Biology Unit (CBU), Department of Informatics, University of Bergen, Postboks 7804, N-5020 Bergen, Norway
| | - Peter Dawyndt
- Department of Applied Mathematics, Computer Science, and Statistics, Ghent University, Krijgslaan 281-S9, 9000 Ghent, Belgium
| | - Dirk Benndorf
- Bioprocess Engineering, Faculty for Process and Systems Engineering, Otto von Guericke University, Universitaetsplatz 2, 39106 Magdeburg, Germany
- Microbiology, Department of Applied Biosciences and Process Technology, Anhalt University of Applied Sciences, Bernburger Straße 55, 06366 Köthen, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße, 39106 Magdeburg, Germany
| | - Bernhard Y. Renard
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
- Hasso-Plattner-Institute, Faculty of Digital Engineering, University of Potsdam, Prof.-Dr.-Helmert-Straße 2 – 3, 14482 Potsdam, Germany
| | - Bart Mesuere
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, St. Pietersnieuwstraat 33, 9000 Ghent, Belgium
- Department of Applied Mathematics, Computer Science, and Statistics, Ghent University, Krijgslaan 281-S9, 9000 Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, Technologiepark-Zwijnaarde 75, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, St. Pietersnieuwstraat 33, 9000 Ghent, Belgium
| | - Thilo Muth
- Bioinformatics Unit (MF 1), Department for Methods Development and Research Infrastructure, Robert Koch Institute, Nordufer 20, 13353 Berlin, Germany
- eScience Division (S.3), Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205 Berlin, Germany
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Krause JL, Schäpe SS, Schattenberg F, Müller S, Ackermann G, Rolle-Kampczyk UE, Jehmlich N, Pierzchalski A, von Bergen M, Herberth G. The Activation of Mucosal-Associated Invariant T (MAIT) Cells Is Affected by Microbial Diversity and Riboflavin Utilization in vitro. Front Microbiol 2020; 11:755. [PMID: 32390989 PMCID: PMC7189812 DOI: 10.3389/fmicb.2020.00755] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 03/30/2020] [Indexed: 12/16/2022] Open
Abstract
Recent research has demonstrated that MAIT cells are activated by individual bacterial or yeasts species that possess the riboflavin biosynthesis pathway. However, little is known about the MAIT cell activating potential of microbial communities and the contribution of individual community members. Here, we analyze the MAIT cell activating potential of a human intestinal model community (SIHUMIx) as well as intestinal microbiota after bioreactor cultivation. We determined the contribution of individual SIHUMIx community members to the MAIT cell activating potential and investigated whether microbial stress can influence their MAIT cell activating potential. The MAIT cell activating potential of SIHUMIx was directly related to the relative species abundances in the community. We therefore suggest an additive relationship between the species abundances and their MAIT cell activating potential. In diverse microbial communities, we found that a low MAIT cell activating potential was associated with high microbial diversity and a high level of riboflavin demand and vice versa. We suggest that microbial diversity might affect MAIT cell activation via riboflavin utilization within the community. Microbial acid stress significantly reduced the MAIT cell activating potential of SIHUMIx by impairing riboflavin availability through increasing the riboflavin demand. We show that MAIT cells can perceive microbial stress due to changes in riboflavin utilization and that riboflavin availability might also play a central role for the MAIT cell activating potential of diverse microbiota.
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Affiliation(s)
- Jannike L Krause
- Department of Environmental Immunology, Helmholtz-Centre for Environmental Research - UFZ Leipzig, Germany
| | - Stephanie S Schäpe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Florian Schattenberg
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | | | - Ulrike E Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Arkadiusz Pierzchalski
- Department of Environmental Immunology, Helmholtz-Centre for Environmental Research - UFZ Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany.,Faculty of Biosciences, Pharmacy and Psychology, Institute of Biochemistry, University of Leipzig, Leipzig, Germany
| | - Gunda Herberth
- Department of Environmental Immunology, Helmholtz-Centre for Environmental Research - UFZ Leipzig, Germany
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Fritz-Wallace K, Engelmann B, Krause JL, Schäpe SS, Pöppe J, Herberth G, Rösler U, Jehmlich N, von Bergen M, Rolle-Kampczyk U. Quantification of glyphosate and aminomethylphosphonic acid from microbiome reactor fluids. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8668. [PMID: 31961458 DOI: 10.1002/rcm.8668] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/20/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
RATIONALE Glyphosate is one of the most widely used herbicides and it is suspected to affect the intestinal microbiota through inhibition of aromatic amino acid synthesis via the shikimate pathway. In vitro microbiome bioreactors are increasingly used as model systems to investigate effects on intestinal microbiota and consequently methods for the quantitation of glyphosate and its degradation product aminomethylphosphonic acid (AMPA) in microbiome model systems are required. METHODS An optimized protocol enables the analysis of both glyphosate and AMPA by simple extraction with methanol:acetonitrile:water (2:3:1) without further enrichment steps. Glyphosate and AMPA are separated by liquid chromatography on an amide column and identified and quantified with a targeted tandem mass spectrometry method using a QTRAP 5500 system (AB Sciex). RESULTS Our method has a limit of detection (LOD) in extracted water samples of <2 ng/mL for both glyphosate and AMPA. In complex intestinal medium, the LOD is 2 and 5 ng/mL for glyphosate and AMPA, respectively. These LODs allow for measurement at exposure-relevant concentrations. Glyphosate levels in a bioreactor model of porcine colon were determined and consequently it was verified whether AMPA was produced by porcine gut microbiota. CONCLUSIONS The method presented here allows quantitation of glyphosate and AMPA in complex bioreactor fluids and thus enables studies of the impact of glyphosate and its metabolism on intestinal microbiota. In addition, the extraction protocol is compatible with an untargeted metabolomics analysis, thus allowing one to look for other perturbations caused by glyphosate in the same sample.
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Affiliation(s)
- Katarina Fritz-Wallace
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Beatrice Engelmann
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Jannike L Krause
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Stephanie S Schäpe
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Judith Pöppe
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - Gunda Herberth
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Uwe Rösler
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, Berlin, Germany
| | - 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, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, 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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Petruschke H, Anders J, Stadler PF, Jehmlich N, von Bergen M. Enrichment and identification of small proteins in a simplified human gut microbiome. J Proteomics 2020; 213:103604. [DOI: 10.1016/j.jprot.2019.103604] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/22/2019] [Accepted: 12/07/2019] [Indexed: 02/06/2023]
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Liu Z, Müller S. Bacterial Community Diversity Dynamics Highlight Degrees of Nestedness and Turnover Patterns. Cytometry A 2020; 97:742-748. [PMID: 31944547 DOI: 10.1002/cyto.a.23965] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/27/2019] [Accepted: 12/20/2019] [Indexed: 11/07/2022]
Abstract
Bacterial communities change their structure rapidly due to short generation times of their members. How bacteria assemble to certain structures provides insight into ecological mechanisms that shape a bacterial community. Microbial community flow cytometry was used to create community fingerprints based on subcommunity distributions and to visualize the dynamic variations of 10 independently grown communities under equal conditions. Inventory diversity values were recorded by α- and γ-diversity whereas the degree of subsistence of subcommunities (nestedness) and the degree of gain or loss of subcommunities (turnover) was calculated as multi-sites ß-diversity terms ßNES and ßSIM . Numbers of unique subcommunities of pairwise samples were determined by intra- and inter-community ß-diversity values. Although all communities were exposed to niche-differentiating conditions they assembled to disparate structures. In our study, the turnover coefficients were high (> 0.6), while the nestedness coefficients were complementary low in the separate 10 bioreactors. Intra- and inter-community ß-diversity values indicated fast community shifts. Microbial community flow cytometry straightforwardly identifies the dominance and subsistence of subsets of cells in a community or the degree of their replacement. The calculation of either turnover or nestedness patterns might have implications in medical, biotechnological, or environmental research. © 2020 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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Affiliation(s)
- Zishu Liu
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Susann Müller
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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