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Zimmermann J, Piecyk A, Sieber M, Petersen C, Johnke J, Moitinho-Silva L, Künzel S, Bluhm L, Traulsen A, Kaleta C, Schulenburg H. Gut-associated functions are favored during microbiome assembly across a major part of C. elegans life. mBio 2024; 15:e0001224. [PMID: 38634692 PMCID: PMC11077962 DOI: 10.1128/mbio.00012-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
The microbiome expresses a variety of functions that influence host biology. The range of functions depends on the microbiome's composition, which can change during the host's lifetime due to neutral assembly processes, host-mediated selection, and environmental conditions. To date, the exact dynamics of microbiome assembly, the underlying determinants, and the effects on host-associated functions remain poorly understood. Here, we used the nematode Caenorhabditis elegans and a defined community of fully sequenced, naturally associated bacteria to study microbiome dynamics and functions across a major part of the worm's lifetime of hosts under controlled experimental conditions. Bacterial community composition initially shows strongly declining levels of stochasticity, which increases during later time points, suggesting selective effects in younger animals as opposed to more random processes in older animals. The adult microbiome is enriched in genera Ochrobactrum and Enterobacter compared to the direct substrate and a host-free control environment. Using pathway analysis, metabolic, and ecological modeling, we further find that the lifetime assembly dynamics increase competitive strategies and gut-associated functions in the host-associated microbiome, indicating that the colonizing bacteria benefit the worm. Overall, our study introduces a framework for studying microbiome assembly dynamics based on stochastic, ecological, and metabolic models, yielding new insights into the processes that determine host-associated microbiome composition and function. IMPORTANCE The microbiome plays a crucial role in host biology. Its functions depend on the microbiome composition that can change during a host's lifetime. To date, the dynamics of microbiome assembly and the resulting functions still need to be better understood. This study introduces a new approach to characterize the functional consequences of microbiome assembly by modeling both the relevance of stochastic processes and metabolic characteristics of microbial community changes. The approach was applied to experimental time-series data obtained for the microbiome of the nematode Caenorhabditis elegans across the major part of its lifetime. Stochastic processes played a minor role, whereas beneficial bacteria as well as gut-associated functions enriched in hosts. This indicates that the host might actively shape the composition of its microbiome. Overall, this study provides a framework for studying microbiome assembly dynamics and yields new insights into C. elegans microbiome functions.
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Affiliation(s)
- Johannes Zimmermann
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Max Planck Fellow Group Antibiotic Resistance Evolution, Max Planck Institute for Evolutionary Biology, Ploen, Germany
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Agnes Piecyk
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Michael Sieber
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Carola Petersen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Julia Johnke
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Lucas Moitinho-Silva
- />Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Lena Bluhm
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
| | - Arne Traulsen
- Department for Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Hinrich Schulenburg
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Germany
- Max Planck Fellow Group Antibiotic Resistance Evolution, Max Planck Institute for Evolutionary Biology, Ploen, Germany
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Olecka M, van Bömmel A, Best L, Haase M, Foerste S, Riege K, Dost T, Flor S, Witte OW, Franzenburg S, Groth M, von Eyss B, Kaleta C, Frahm C, Hoffmann S. Nonlinear DNA methylation trajectories in aging male mice. Nat Commun 2024; 15:3074. [PMID: 38594255 PMCID: PMC11004021 DOI: 10.1038/s41467-024-47316-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 03/25/2024] [Indexed: 04/11/2024] Open
Abstract
Although DNA methylation data yields highly accurate age predictors, little is known about the dynamics of this quintessential epigenomic biomarker during lifespan. To narrow the gap, we investigate the methylation trajectories of male mouse colon at five different time points of aging. Our study indicates the existence of sudden hypermethylation events at specific stages of life. Precisely, we identify two epigenomic switches during early-to-midlife (3-9 months) and mid-to-late-life (15-24 months) transitions, separating the rodents' life into three stages. These nonlinear methylation dynamics predominantly affect genes associated with the nervous system and enrich in bivalently marked chromatin regions. Based on groups of nonlinearly modified loci, we construct a clock-like classifier STageR (STage of aging estimatoR) that accurately predicts murine epigenetic stage. We demonstrate the universality of our clock in an independent mouse cohort and with publicly available datasets.
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Affiliation(s)
- Maja Olecka
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Alena van Bömmel
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Lena Best
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Madlen Haase
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Silke Foerste
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Konstantin Riege
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Thomas Dost
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Stefano Flor
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Otto W Witte
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Marco Groth
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Björn von Eyss
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, University of Kiel and University Medical Center Schleswig-Holstein, 24105, Kiel, Germany
| | - Christiane Frahm
- Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747, Jena, Germany
| | - Steve Hoffmann
- Hoffmann Lab, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany.
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Marinos G, Hamerich IK, Debray R, Obeng N, Petersen C, Taubenheim J, Zimmermann J, Blackburn D, Samuel BS, Dierking K, Franke A, Laudes M, Waschina S, Schulenburg H, Kaleta C. Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics. Microbiol Spectr 2024; 12:e0114423. [PMID: 38230938 PMCID: PMC10846184 DOI: 10.1128/spectrum.01144-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 12/13/2023] [Indexed: 01/18/2024] Open
Abstract
While numerous health-beneficial interactions between host and microbiota have been identified, there is still a lack of targeted approaches for modulating these interactions. Thus, we here identify precision prebiotics that specifically modulate the abundance of a microbiome member species of interest. In the first step, we show that defining precision prebiotics by compounds that are only taken up by the target species but no other species in a community is usually not possible due to overlapping metabolic niches. Subsequently, we use metabolic modeling to identify precision prebiotics for a two-member Caenorhabditis elegans microbiome community comprising the immune-protective target species Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71. We experimentally confirm four of the predicted precision prebiotics, L-serine, L-threonine, D-mannitol, and γ-aminobutyric acid, to specifically increase the abundance of MYb11. L-serine was further assessed in vivo, leading to an increase in MYb11 abundance also in the worm host. Overall, our findings demonstrate that metabolic modeling is an effective tool for the design of precision prebiotics as an important cornerstone for future microbiome-targeted therapies.IMPORTANCEWhile various mechanisms through which the microbiome influences disease processes in the host have been identified, there are still only few approaches that allow for targeted manipulation of microbiome composition as a first step toward microbiome-based therapies. Here, we propose the concept of precision prebiotics that allow to boost the abundance of already resident health-beneficial microbial species in a microbiome. We present a constraint-based modeling pipeline to predict precision prebiotics for a minimal microbial community in the worm Caenorhabditis elegans comprising the host-beneficial Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71 with the aim to boost the growth of MYb11. Experimentally testing four of the predicted precision prebiotics, we confirm that they are specifically able to increase the abundance of MYb11 in vitro and in vivo. These results demonstrate that constraint-based modeling could be an important tool for the development of targeted microbiome-based therapies against human diseases.
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Affiliation(s)
- Georgios Marinos
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Inga K. Hamerich
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Reena Debray
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Nancy Obeng
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Carola Petersen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Jan Taubenheim
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Johannes Zimmermann
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
- Max-Planck Institute for Evolutionary Biology, Ploen, Schleswig-Holstein, Germany
| | - Dana Blackburn
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Buck S. Samuel
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Katja Dierking
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Matthias Laudes
- Institute of Diabetes and Clinical Metabolic Research, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Silvio Waschina
- Nutriinformatics, Institute for Human Nutrition and Food Science, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Hinrich Schulenburg
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
- Max-Planck Institute for Evolutionary Biology, Ploen, Schleswig-Holstein, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
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Forero-Rodríguez J, Zimmermann J, Taubenheim J, Arias-Rodríguez N, Caicedo-Narvaez JD, Best L, Mendieta CV, López-Castiblanco J, Gómez-Muñoz LA, Gonzalez-Santos J, Arboleda H, Fernandez W, Kaleta C, Pinzón A. Changes in Bacterial Gut Composition in Parkinson's Disease and Their Metabolic Contribution to Disease Development: A Gut Community Reconstruction Approach. Microorganisms 2024; 12:325. [PMID: 38399728 PMCID: PMC10893096 DOI: 10.3390/microorganisms12020325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 02/25/2024] Open
Abstract
Parkinson's disease (PD) is a chronic and progressive neurodegenerative disease with the major symptoms comprising loss of movement coordination (motor dysfunction) and non-motor dysfunction, including gastrointestinal symptoms. Alterations in the gut microbiota composition have been reported in PD patients vs. controls. However, it is still unclear how these compositional changes contribute to disease etiology and progression. Furthermore, most of the available studies have focused on European, Asian, and North American cohorts, but the microbiomes of PD patients in Latin America have not been characterized. To address this problem, we obtained fecal samples from Colombian participants (n = 25 controls, n = 25 PD idiopathic cases) to characterize the taxonomical community changes during disease via 16S rRNA gene sequencing. An analysis of differential composition, diversity, and personalized computational modeling was carried out, given the fecal bacterial composition and diet of each participant. We found three metabolites that differed in dietary habits between PD patients and controls: carbohydrates, trans fatty acids, and potassium. We identified six genera that changed significantly in their relative abundance between PD patients and controls, belonging to the families Lachnospiraceae, Lactobacillaceae, Verrucomicrobioaceae, Peptostreptococcaceae, and Streptococcaceae. Furthermore, personalized metabolic modeling of the gut microbiome revealed changes in the predicted production of seven metabolites (Indole, tryptophan, fructose, phenylacetic acid, myristic acid, 3-Methyl-2-oxovaleric acid, and N-Acetylneuraminic acid). These metabolites are associated with the metabolism of aromatic amino acids and their consumption in the diet. Therefore, this research suggests that each individual's diet and intestinal composition could affect host metabolism. Furthermore, these findings open the door to the study of microbiome-host interactions and allow us to contribute to personalized medicine.
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Affiliation(s)
- Johanna Forero-Rodríguez
- Bioinformatics and Systems Biology Research Group, Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (J.F.-R.); (J.D.C.-N.); (J.L.-C.)
- Medical Systems Biology Research Group, Institute of Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany (J.T.)
| | - Johannes Zimmermann
- Medical Systems Biology Research Group, Institute of Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany (J.T.)
| | - Jan Taubenheim
- Medical Systems Biology Research Group, Institute of Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany (J.T.)
| | - Natalia Arias-Rodríguez
- Bioinformatics and Systems Biology Research Group, Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (J.F.-R.); (J.D.C.-N.); (J.L.-C.)
| | - Juan David Caicedo-Narvaez
- Bioinformatics and Systems Biology Research Group, Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (J.F.-R.); (J.D.C.-N.); (J.L.-C.)
- Neurosciences Research Group, Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Lena Best
- Medical Systems Biology Research Group, Institute of Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany (J.T.)
| | - Cindy V. Mendieta
- PhD Program in Clinical Epidemiology, Department of Clinical Epidemiology and Biostatistics, Faculty of Medicine, Pontificia Universidad Javeriana, Bogotá 110231, Colombia;
- Department of Nutrition and Biochemistry, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Julieth López-Castiblanco
- Bioinformatics and Systems Biology Research Group, Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (J.F.-R.); (J.D.C.-N.); (J.L.-C.)
| | - Laura Alejandra Gómez-Muñoz
- Neurosciences Research Group, Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia
- Cell Death Research Group, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Janneth Gonzalez-Santos
- Structural Biochemistry and Bioinformatics Laboratory, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Humberto Arboleda
- Cell Death Research Group, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - William Fernandez
- Neurosciences Research Group, Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia
- Cell Death Research Group, Medical School and Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Christoph Kaleta
- Medical Systems Biology Research Group, Institute of Experimental Medicine, Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany (J.T.)
| | - Andrés Pinzón
- Bioinformatics and Systems Biology Research Group, Genetic Institute, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (J.F.-R.); (J.D.C.-N.); (J.L.-C.)
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Pfefferkorn RM, Mortzfeld BM, Fink C, von Frieling J, Bossen J, Esser D, Kaleta C, Rosenstiel P, Heine H, Roeder T. Recurrent Phases of Strict Protein Limitation Inhibit Tumor Growth and Restore Lifespan in A Drosophila Intestinal Cancer Model. Aging Dis 2024; 15:226-244. [PMID: 37962464 PMCID: PMC10796089 DOI: 10.14336/ad.2023.0517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 05/17/2023] [Indexed: 11/15/2023] Open
Abstract
Diets that restrict caloric or protein intake offer a variety of benefits, including decreasing the incidence of cancer. However, whether such diets pose a substantial therapeutic benefit as auxiliary cancer treatments remains unclear. We determined the effects of severe protein depletion on tumorigenesis in a Drosophila melanogaster intestinal tumor model, using a human RAF gain-of-function allele. Severe and continuous protein restriction significantly reduced tumor growth but resulted in premature death. Therefore, we developed a diet in which short periods of severe protein restriction alternated cyclically with periods of complete feeding. This nutritional regime reduced tumor mass, restored gut functionality, and rescued the lifespan of oncogene-expressing flies to the levels observed in healthy flies on a continuous, fully nutritious diet. Furthermore, this diet reduced the chemotherapy-induced stem cell activity associated with tumor recurrence. Transcriptome analysis revealed long-lasting changes in the expression of key genes involved in multiple major developmental signaling pathways. Overall, the data suggest that recurrent severe protein depletion effectively mimics the health benefits of continuous protein restriction, without undesired nutritional shortcomings. This provides seminal insights into the mechanisms of the memory effect required to maintain the positive effects of protein restriction throughout the phases of a full diet. Finally, the repetitive form of strict protein restriction is an ideal strategy for adjuvant cancer therapy that is useful in many tumor contexts.
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Affiliation(s)
- Roxana M. Pfefferkorn
- Department of Molecular Physiology, Zoological Institute, Kiel University, Kiel, Germany.
| | - Benedikt M. Mortzfeld
- Department of Cell and Developmental Biology, Zoological Institute, Kiel University, Kiel, Germany.
| | - Christine Fink
- Department of Molecular Physiology, Zoological Institute, Kiel University, Kiel, Germany.
| | - Jakob von Frieling
- Department of Molecular Physiology, Zoological Institute, Kiel University, Kiel, Germany.
| | - Judith Bossen
- Department of Molecular Physiology, Zoological Institute, Kiel University, Kiel, Germany.
| | - Daniela Esser
- Department of Neuroimmunology, Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, Kiel, Germany.
| | - Christoph Kaleta
- Department Medical Systems Biology, Institute for Experimental Medicine, Kiel University, Germany.
| | - Philip Rosenstiel
- Department Molecular Cell Biology, Institute for Clinical Molecular Biology, Kiel University, Germany.
| | - Holger Heine
- Division of Innate Immunity, Research Center Borstel - Leibniz Lung Center, Borstel, Germany.
| | - Thomas Roeder
- Department of Molecular Physiology, Zoological Institute, Kiel University, Kiel, Germany.
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Unni R, Andreani NA, Vallier M, Heinzmann SS, Taubenheim J, Guggeis MA, Tran F, Vogler O, Künzel S, Hövener JB, Rosenstiel P, Kaleta C, Dempfle A, Unterweger D, Baines JF. Evolution of E. coli in a mouse model of inflammatory bowel disease leads to a disease-specific bacterial genotype and trade-offs with clinical relevance. Gut Microbes 2023; 15:2286675. [PMID: 38059748 PMCID: PMC10730162 DOI: 10.1080/19490976.2023.2286675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/17/2023] [Indexed: 12/08/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a persistent inflammatory condition that affects the gastrointestinal tract and presents significant challenges in its management and treatment. Despite the knowledge that within-host bacterial evolution occurs in the intestine, the disease has rarely been studied from an evolutionary perspective. In this study, we aimed to investigate the evolution of resident bacteria during intestinal inflammation and whether- and how disease-related bacterial genetic changes may present trade-offs with potential therapeutic importance. Here, we perform an in vivo evolution experiment of E. coli in a gnotobiotic mouse model of IBD, followed by multiomic analyses to identify disease-specific genetic and phenotypic changes in bacteria that evolved in an inflamed versus a non-inflamed control environment. Our results demonstrate distinct evolutionary changes in E. coli specific to inflammation, including a single nucleotide variant that independently reached high frequency in all inflamed mice. Using ex vivo fitness assays, we find that these changes are associated with a higher fitness in an inflamed environment compared to isolates derived from non-inflamed mice. Further, using large-scale phenotypic assays, we show that bacterial adaptation to inflammation results in clinically relevant phenotypes, which intriguingly include collateral sensitivity to antibiotics. Bacterial evolution in an inflamed gut yields specific genetic and phenotypic signatures. These results may serve as a basis for developing novel evolution-informed treatment approaches for patients with intestinal inflammation.
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Affiliation(s)
- Rahul Unni
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Nadia Andrea Andreani
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Marie Vallier
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Silke S. Heinzmann
- Research Unit Analytical BioGeoChemistry, Helmholtz Munich, Neuherberg, Germany
| | - Jan Taubenheim
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Martina A. Guggeis
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Olga Vogler
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Sven Künzel
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Jan-Bernd Hövener
- Section Biomedical Imaging, Molecular Imaging North Competence Center (MOIN CC), Department of Radiology and Neuroradiology, University Medical Center Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - Astrid Dempfle
- Institute of Medical Informatics and Statistics, Kiel University, Kiel, Germany
| | - Daniel Unterweger
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
| | - John F. Baines
- Section Evolutionary Medicine, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Kiel, Germany
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7
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Domin H, Zimmermann J, Taubenheim J, Fuentes Reyes G, Saueressig L, Prasse D, Höppner M, Schmitz RA, Hentschel U, Kaleta C, Fraune S. Sequential host-bacteria and bacteria-bacteria interactions determine the microbiome establishment of Nematostella vectensis. Microbiome 2023; 11:257. [PMID: 37978412 PMCID: PMC10656924 DOI: 10.1186/s40168-023-01701-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 10/17/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND The microbiota of multicellular organisms undergoes considerable changes during host ontogeny but the general mechanisms that control community assembly and succession are poorly understood. Here, we use bacterial recolonization experiments in Nematostella vectensis as a model to understand general mechanisms determining bacterial establishment and succession. We compared the dynamic establishment of the microbiome on the germfree host and on inert silicone tubes. RESULTS Following the dynamic reconstruction of microbial communities on both substrates, we show that the initial colonization events are strongly influenced by the host but not by the silicone tube, while the subsequent bacteria-bacteria interactions are the main driver of bacterial succession. Interestingly, the recolonization pattern on adult hosts resembles the ontogenetic colonization succession. This process occurs independently of the bacterial composition of the inoculum and can be followed at the level of individual bacteria. To identify potential metabolic traits associated with initial colonization success and potential metabolic interactions among bacteria associated with bacterial succession, we reconstructed the metabolic networks of bacterial colonizers based on their genomes. These analyses revealed that bacterial metabolic capabilities reflect the recolonization pattern, and the degradation of chitin might be a selection factor during early recolonization of the animal. Concurrently, transcriptomic analyses revealed that Nematostella possesses two chitin synthase genes, one of which is upregulated during early recolonization. CONCLUSIONS Our results show that early recolonization events are strongly controlled by the host while subsequent colonization depends on metabolic bacteria-bacteria interactions largely independent of host ontogeny. Video Abstract.
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Affiliation(s)
- H Domin
- Institute for Zoology and Organismic Interactions, Heinrich-Heine-University Düsseldorf, Düsseldorf, 40225, Germany
| | - J Zimmermann
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, 24105, Germany
| | - J Taubenheim
- Institute for Zoology and Organismic Interactions, Heinrich-Heine-University Düsseldorf, Düsseldorf, 40225, Germany
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, 24105, Germany
| | - G Fuentes Reyes
- Institute for Zoology and Organismic Interactions, Heinrich-Heine-University Düsseldorf, Düsseldorf, 40225, Germany
| | - L Saueressig
- Institute for Zoology and Organismic Interactions, Heinrich-Heine-University Düsseldorf, Düsseldorf, 40225, Germany
| | - D Prasse
- Institute for General Microbiology, Christian-Albrechts-University Kiel, Kiel, 24105, Germany
| | - M Höppner
- Institute for Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, 24105, Germany
| | - R A Schmitz
- Institute for General Microbiology, Christian-Albrechts-University Kiel, Kiel, 24105, Germany
| | - U Hentschel
- RD3 Marine Symbioses, GEOMAR Helmholtz Centre for Ocean Research, Kiel, 24105, Germany
- Christian-Albrechts-University Kiel, Kiel, 24105, Germany
| | - C Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, 24105, Germany
| | - S Fraune
- Institute for Zoology and Organismic Interactions, Heinrich-Heine-University Düsseldorf, Düsseldorf, 40225, Germany.
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8
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Schrenk SJ, Brodoehl S, Flor S, Frahm C, Gaser C, Hamdan RA, Herbsleb M, Kaleta C, Kattlun F, Müller HJ, Puta C, Radscheidt M, Ruiz-Rizzo AL, Saraei T, Scherag A, Steidten T, Witte OW, Finke K. Impact of an online guided physical activity training on cognition and gut-brain axis interactions in older adults: protocol of a randomized controlled trial. Front Aging Neurosci 2023; 15:1254194. [PMID: 37781101 PMCID: PMC10539595 DOI: 10.3389/fnagi.2023.1254194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
Introduction By 2050, the worldwide percentage of people 65 years and older is assumed to have doubled compared to current numbers. Therefore, finding ways of promoting healthy (cognitive) aging is crucial. Physical activity is considered an effective approach to counteract not only physical but also cognitive decline. However, the underlying mechanisms that drive the benefits of regular physical activity on cognitive function are not fully understood. This randomized controlled trial aims to analyze the effect of an eight-week standardized physical activity training program in older humans on cognitive, brain, and gut-barrier function as well as the relationship between the resulting changes. Methods and analysis One-hundred healthy participants aged 60 to 75 years will be recruited. First, participants will undergo an extensive baseline assessment consisting of neurocognitive tests, functional and structural brain imaging, physical fitness tests, and gut-microbiome profiling. Next, participants will be randomized into either a multi-component physical activity group (experimental condition) or a relaxation group (active control condition), with each training lasting 8 weeks and including an equal number and duration of exercises. The whole intervention will be online-based, i.e., participants will find their intervention schedule and all materials needed on the study website. After the intervention phase, participants will have their post-intervention assessment, which consists of the same measures and tests as the baseline assessment. The primary outcome of this study is the change in the cognitive parameter of visual processing speed from baseline to post-measurement, which will on average take place 10 weeks after the randomization. Secondary outcomes related to cognitive, brain, and microbiome data will be analyzed exploratory. Clinical trial registration: https://drks.de/search/de/trial/DRKS00028022.
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Affiliation(s)
- Simon J. Schrenk
- Department of Neurology, Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
| | - Stefan Brodoehl
- Department of Neurology, Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
| | - Stefano Flor
- Institute of Experimental Medicine, Christian-Albrechts-University zu Kiel, Kiel, Germany
| | - Christiane Frahm
- Department of Neurology, Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
| | - Christian Gaser
- Department of Neurology, Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
- Department of Psychiatry and Psychotherapy, Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
| | - Rami Abou Hamdan
- Department of Sports Medicine and Health Promotion, Friedrich-Schiller-University Jena, Jena, Germany
| | - Marco Herbsleb
- Department of Sports Medicine and Health Promotion, Friedrich-Schiller-University Jena, Jena, Germany
- Department of Psychosomatic Medicine and Psychotherapy, Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
| | - Christoph Kaleta
- Institute of Experimental Medicine, Christian-Albrechts-University zu Kiel, Kiel, Germany
| | - Fabian Kattlun
- Department of Neurology, Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
| | - Hans-Josef Müller
- Department of Sports Medicine and Health Promotion, Friedrich-Schiller-University Jena, Jena, Germany
| | - Christian Puta
- Department of Sports Medicine and Health Promotion, Friedrich-Schiller-University Jena, Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
- Center for Interdisciplinary Prevention of Diseases Related to Professional Activities, Friedrich-Schiller-University Jena, Jena, Germany
| | - Monique Radscheidt
- Department of Neurology, Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
| | - Adriana L. Ruiz-Rizzo
- Department of Neurology, Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
| | - Tannaz Saraei
- Department of Neurology, Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
| | - André Scherag
- Center for Sepsis Control and Care (CSCC), Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
- Center for Clinical Studies, Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
- Institute of Medical Statistics, Computer and Data Sciences, Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
| | - Thomas Steidten
- Department of Sports Medicine and Health Promotion, Friedrich-Schiller-University Jena, Jena, Germany
| | - Otto W. Witte
- Department of Neurology, Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
| | - Kathrin Finke
- Department of Neurology, Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
- Center for Sepsis Control and Care (CSCC), Jena University Hospital – Friedrich Schiller University of Jena, Jena, Germany
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9
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Beder T, Hansen BT, Hartmann AM, Zimmermann J, Amelunxen E, Wolgast N, Walter W, Zaliova M, Antić Ž, Chouvarine P, Bartsch L, Barz MJ, Bultmann M, Horns J, Bendig S, Kässens J, Kaleta C, Cario G, Schrappe M, Neumann M, Gökbuget N, Bergmann AK, Trka J, Haferlach C, Brüggemann M, Baldus CD, Bastian L. The Gene Expression Classifier ALLCatchR Identifies B-cell Precursor ALL Subtypes and Underlying Developmental Trajectories Across Age. Hemasphere 2023; 7:e939. [PMID: 37645423 PMCID: PMC10461941 DOI: 10.1097/hs9.0000000000000939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/26/2023] [Indexed: 08/31/2023] Open
Abstract
Current classifications (World Health Organization-HAEM5/ICC) define up to 26 molecular B-cell precursor acute lymphoblastic leukemia (BCP-ALL) disease subtypes by genomic driver aberrations and corresponding gene expression signatures. Identification of driver aberrations by transcriptome sequencing (RNA-Seq) is well established, while systematic approaches for gene expression analysis are less advanced. Therefore, we developed ALLCatchR, a machine learning-based classifier using RNA-Seq gene expression data to allocate BCP-ALL samples to all 21 gene expression-defined molecular subtypes. Trained on n = 1869 transcriptome profiles with established subtype definitions (4 cohorts; 55% pediatric / 45% adult), ALLCatchR allowed subtype allocation in 3 independent hold-out cohorts (n = 1018; 75% pediatric / 25% adult) with 95.7% accuracy (averaged sensitivity across subtypes: 91.1% / specificity: 99.8%). High-confidence predictions were achieved in 83.7% of samples with 98.9% accuracy. Only 1.2% of samples remained unclassified. ALLCatchR outperformed existing tools and identified novel driver candidates in previously unassigned samples. Additional modules provided predictions of samples blast counts, patient's sex, and immunophenotype, allowing the imputation in cases where these information are missing. We established a novel RNA-Seq reference of human B-lymphopoiesis using 7 FACS-sorted progenitor stages from healthy bone marrow donors. Implementation in ALLCatchR enabled projection of BCP-ALL samples to this trajectory. This identified shared proximity patterns of BCP-ALL subtypes to normal lymphopoiesis stages, extending immunophenotypic classifications with a novel framework for developmental comparisons of BCP-ALL. ALLCatchR enables RNA-Seq routine application for BCP-ALL diagnostics with systematic gene expression analysis for accurate subtype allocation and novel insights into underlying developmental trajectories.
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Affiliation(s)
- Thomas Beder
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Björn-Thore Hansen
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Alina M Hartmann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Johannes Zimmermann
- Institute of Experimental Medicine, Research Group Medical Systems Biology, Christian-Albrechts-University Kiel, Germany
| | - Eric Amelunxen
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Nadine Wolgast
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | | | - Marketa Zaliova
- Childhood Leukaemia Investigation Prague, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | - Željko Antić
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Philippe Chouvarine
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Lorenz Bartsch
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Malwine J Barz
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Miriam Bultmann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Johanna Horns
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Sonja Bendig
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Jan Kässens
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Christoph Kaleta
- Institute of Experimental Medicine, Research Group Medical Systems Biology, Christian-Albrechts-University Kiel, Germany
| | - Gunnar Cario
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
- Department of Pediatrics, University Hospital Schleswig-Holstein Kiel, Germany
| | - Martin Schrappe
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
- Department of Pediatrics, University Hospital Schleswig-Holstein Kiel, Germany
| | - Martin Neumann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Nicola Gökbuget
- Department of Medicine II, Hematology/Oncology, Goethe University Hospital, Frankfurt/M., Germany
| | | | - Jan Trka
- Childhood Leukaemia Investigation Prague, Second Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | | | - Monika Brüggemann
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Claudia D Baldus
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
| | - Lorenz Bastian
- Medical Department II, Hematology and Oncology, University Hospital Schleswig-Holstein, Kiel, Germany
- Clinical Research Unit "CATCH ALL" (KFO 5010/1) funded by the Deutsche Forschungsgemeinschaft, Bonn, Germany
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10
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Marinos G, Hamerich IK, Debray R, Obeng N, Petersen C, Taubenheim J, Zimmermann J, Blackburn D, Samuel BS, Dierking K, Franke A, Laudes M, Waschina S, Schulenburg H, Kaleta C. Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics. bioRxiv 2023:2023.02.17.528811. [PMID: 36824941 PMCID: PMC9949166 DOI: 10.1101/2023.02.17.528811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
The microbiome is increasingly receiving attention as an important modulator of host health and disease. However, while numerous mechanisms through which the microbiome influences its host have been identified, there is still a lack of approaches that allow to specifically modulate the abundance of individual microbes or microbial functions of interest. Moreover, current approaches for microbiome manipulation such as fecal transfers often entail a non-specific transfer of entire microbial communities with potentially unwanted side effects. To overcome this limitation, we here propose the concept of precision prebiotics that specifically modulate the abundance of a microbiome member species of interest. In a first step, we show that defining precision prebiotics by compounds that are only taken up by the target species but no other species in a community is usually not possible due to overlapping metabolic niches. Subsequently, we present a metabolic modeling network framework that allows us to define precision prebiotics for a two-member C. elegans microbiome model community comprising the immune-protective Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71. Thus, we predicted compounds that specifically boost the abundance of the host-beneficial MYb11, four of which were experimentally validated in vitro (L-serine, L-threonine, D-mannitol, and γ-aminobutyric acid). L-serine was further assessed in vivo, leading to an increase in MYb11 abundance also in the worm host. Overall, our findings demonstrate that constraint-based metabolic modeling is an effective tool for the design of precision prebiotics as an important cornerstone for future microbiome-targeted therapies.
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Affiliation(s)
- Georgios Marinos
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Inga K Hamerich
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Reena Debray
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Nancy Obeng
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Carola Petersen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Jan Taubenheim
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Johannes Zimmermann
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
- Max-Planck Institute for Evolutionary Biology, Ploen, Schleswig-Holstein, Germany
| | - Dana Blackburn
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, Texas, USA
| | - Katja Dierking
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Matthias Laudes
- Institute of Diabetes and Clinical Metabolic Research, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Schleswig-Holstein, Germany
| | - Silvio Waschina
- Nutriinformatics, Institute for Human Nutrition and Food Science, Kiel University, Kiel, Schleswig-Holstein, Germany
| | - Hinrich Schulenburg
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Kiel University, Kiel, Schleswig-Holstein, Germany
- Max-Planck Institute for Evolutionary Biology, Ploen, Schleswig-Holstein, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, University Hospital Schleswig-Holstein Campus Kiel, Kiel University, Kiel, Schleswig-Holstein, Germany
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11
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Zacharias HU, Kaleta C, Cossais F, Schaeffer E, Berndt H, Best L, Dost T, Glüsing S, Groussin M, Poyet M, Heinzel S, Bang C, Siebert L, Demetrowitsch T, Leypoldt F, Adelung R, Bartsch T, Bosy-Westphal A, Schwarz K, Berg D. Microbiome and Metabolome Insights into the Role of the Gastrointestinal-Brain Axis in Parkinson's and Alzheimer's Disease: Unveiling Potential Therapeutic Targets. Metabolites 2022; 12:metabo12121222. [PMID: 36557259 PMCID: PMC9786685 DOI: 10.3390/metabo12121222] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Neurodegenerative diseases such as Parkinson's (PD) and Alzheimer's disease (AD), the prevalence of which is rapidly rising due to an aging world population and westernization of lifestyles, are expected to put a strong socioeconomic burden on health systems worldwide. Clinical trials of therapies against PD and AD have only shown limited success so far. Therefore, research has extended its scope to a systems medicine point of view, with a particular focus on the gastrointestinal-brain axis as a potential main actor in disease development and progression. Microbiome and metabolome studies have already revealed important insights into disease mechanisms. Both the microbiome and metabolome can be easily manipulated by dietary and lifestyle interventions, and might thus offer novel, readily available therapeutic options to prevent the onset as well as the progression of PD and AD. This review summarizes our current knowledge on the interplay between microbiota, metabolites, and neurodegeneration along the gastrointestinal-brain axis. We further illustrate state-of-the art methods of microbiome and metabolome research as well as metabolic modeling that facilitate the identification of disease pathomechanisms. We conclude with therapeutic options to modulate microbiome composition to prevent or delay neurodegeneration and illustrate potential future research directions to fight PD and AD.
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Affiliation(s)
- Helena U. Zacharias
- Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, 30625 Hannover, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Correspondence: (H.U.Z.); (C.K.)
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Kiel University, 24105 Kiel, Germany
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Correspondence: (H.U.Z.); (C.K.)
| | | | - Eva Schaeffer
- Department of Neurology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Henry Berndt
- Research Group Comparative Immunobiology, Zoological Institute, Kiel University, 24118 Kiel, Germany
| | - Lena Best
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Kiel University, 24105 Kiel, Germany
| | - Thomas Dost
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Kiel University, 24105 Kiel, Germany
| | - Svea Glüsing
- Institute of Human Nutrition and Food Science, Food Technology, Kiel University, 24118 Kiel, Germany
| | - Mathieu Groussin
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Mathilde Poyet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sebastian Heinzel
- Department of Neurology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Institute of Medical Informatics and Statistics, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Leonard Siebert
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Functional Nanomaterials, Department of Materials Science, Kiel University, 24143 Kiel, Germany
| | - Tobias Demetrowitsch
- Institute of Human Nutrition and Food Science, Food Technology, Kiel University, 24118 Kiel, Germany
- Kiel Network of Analytical Spectroscopy and Mass Spectrometry, Kiel University, 24118 Kiel, Germany
| | - Frank Leypoldt
- Department of Neurology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Neuroimmunology, Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Rainer Adelung
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Functional Nanomaterials, Department of Materials Science, Kiel University, 24143 Kiel, Germany
| | - Thorsten Bartsch
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Department of Neurology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Anja Bosy-Westphal
- Institute of Human Nutrition and Food Science, Kiel University, 24107 Kiel, Germany
| | - Karin Schwarz
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Institute of Human Nutrition and Food Science, Food Technology, Kiel University, 24118 Kiel, Germany
- Kiel Network of Analytical Spectroscopy and Mass Spectrometry, Kiel University, 24118 Kiel, Germany
| | - Daniela Berg
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Department of Neurology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
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12
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Henneke L, Schlicht K, Andreani NA, Hollstein T, Demetrowitsch T, Knappe C, Hartmann K, Jensen-Kroll J, Rohmann N, Pohlschneider D, Geisler C, Schulte DM, Settgast U, Türk K, Zimmermann J, Kaleta C, Baines JF, Shearer J, Shah S, Shen-Tu G, Schwarz K, Franke A, Schreiber S, Laudes M. A dietary carbohydrate - gut Parasutterella - human fatty acid biosynthesis metabolic axis in obesity and type 2 diabetes. Gut Microbes 2022; 14:2057778. [PMID: 35435797 PMCID: PMC9037427 DOI: 10.1080/19490976.2022.2057778] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Recent rodent microbiome experiments suggest that besides Akkermansia, Parasutterella sp. are important in type 2 diabetes and obesity development. In the present translational human study, we aimed to characterize Parasutterella in our European cross-sectional FoCus cohort (n = 1,544) followed by validation of the major results in an independent Canadian cohort (n = 438). In addition, we examined Parasutterella abundance in response to a weight loss intervention (n = 55). Parasutterella was positively associated with BMI and type 2 diabetes independently of the reduced microbiome α/β diversity and low-grade inflammation commonly found in obesity. Nutritional analysis revealed a positive association with the dietary intake of carbohydrates but not with fat or protein consumption. Out of 126 serum metabolites differentially detectable by untargeted HPLC-based MS-metabolomics, L-cysteine showed the strongest reduction in subjects with high Parasutterella abundance. This is of interest, since Parasutterella is a known high L-cysteine consumer and L-cysteine is known to improve blood glucose levels in rodents. Furthermore, metabolic network enrichment analysis identified an association of high Parasutterella abundance with the activation of the human fatty acid biosynthesis pathway suggesting a mechanism for body weight gain. This is supported by a significant reduction of the Parasutterella abundance during our weight loss intervention. Together, these data indicate a role for Parasutterella in human type 2 diabetes and obesity, whereby the link to L-cysteine might be relevant in type 2 diabetes development and the link to the fatty acid biosynthesis pathway for body weight gain in response to a carbohydrate-rich diet in obesity development.
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Affiliation(s)
- Lea Henneke
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, Kiel, Germany
| | - Kristina Schlicht
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, Kiel, Germany
| | - Nadia A. Andreani
- Section of Evolutionary Medicine, Institute for Experimental Medicine University of Kiel, Kiel, Germany,Guest group for evolutionary medicine Max-Planck-Institute of Evolutionary Biology, Plön, Germany
| | - Tim Hollstein
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, Kiel, Germany
| | - Tobias Demetrowitsch
- Division of Food Technology, Department of Human Nutrition, University of Kiel, Kiel, Germany
| | - Carina Knappe
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, Kiel, Germany
| | - Katharina Hartmann
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, Kiel, Germany
| | - Julia Jensen-Kroll
- Division of Food Technology, Department of Human Nutrition, University of Kiel, Kiel, Germany
| | - Nathalie Rohmann
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, Kiel, Germany
| | - Daniela Pohlschneider
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, Kiel, Germany
| | - Corinna Geisler
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, Kiel, Germany
| | - Dominik M. Schulte
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, Kiel, Germany
| | - Ute Settgast
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, Kiel, Germany
| | - Kathrin Türk
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, Kiel, Germany
| | - Johannes Zimmermann
- Research Group Medical System Biology, Institute of Experimental Medicine, University of Kiel, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical System Biology, Institute of Experimental Medicine, University of Kiel, Kiel, Germany
| | - John F. Baines
- Section of Evolutionary Medicine, Institute for Experimental Medicine University of Kiel, Kiel, Germany,Guest group for evolutionary medicine Max-Planck-Institute of Evolutionary Biology, Plön, Germany
| | - Jane Shearer
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, Faculty Kinesiology, University of Calgary, Calgary, Alberta, Canada
| | - Shrushti Shah
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, Faculty Kinesiology, University of Calgary, Calgary, Alberta, Canada
| | - Grace Shen-Tu
- Alberta’s Tomorrow Project, Cancer Control Alberta, Alberta Health Services, Edmonton, AB, Canada
| | - Karin Schwarz
- Division of Food Technology, Department of Human Nutrition, University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Matthias Laudes
- Institute of Diabetes and Clinical Metabolic Research, University of Kiel, Kiel, Germany,Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Medicine 1, University Medical Centre Schleswig-Holstein, Kiel University, Kiel, Germany,CONTACT Matthias Laudes Institute of Diabetes and Clinical Metabolic Research, University of Kiel, Düsternbrooker Weg 17, 24105Kiel, Germany
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13
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Forero-Rodríguez LJ, Josephs-Spaulding J, Flor S, Pinzón A, Kaleta C. Parkinson's Disease and the Metal-Microbiome-Gut-Brain Axis: A Systems Toxicology Approach. Antioxidants (Basel) 2021; 11:71. [PMID: 35052575 PMCID: PMC8773335 DOI: 10.3390/antiox11010071] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/02/2021] [Accepted: 12/17/2021] [Indexed: 12/14/2022] Open
Abstract
Parkinson's Disease (PD) is a neurodegenerative disease, leading to motor and non-motor complications. Autonomic alterations, including gastrointestinal symptoms, precede motor defects and act as early warning signs. Chronic exposure to dietary, environmental heavy metals impacts the gastrointestinal system and host-associated microbiome, eventually affecting the central nervous system. The correlation between dysbiosis and PD suggests a functional and bidirectional communication between the gut and the brain. The bioaccumulation of metals promotes stress mechanisms by increasing reactive oxygen species, likely altering the bidirectional gut-brain link. To better understand the differing molecular mechanisms underlying PD, integrative modeling approaches are necessary to connect multifactorial perturbations in this heterogeneous disorder. By exploring the effects of gut microbiota modulation on dietary heavy metal exposure in relation to PD onset, the modification of the host-associated microbiome to mitigate neurological stress may be a future treatment option against neurodegeneration through bioremediation. The progressive movement towards a systems toxicology framework for precision medicine can uncover molecular mechanisms underlying PD onset such as metal regulation and microbial community interactions by developing predictive models to better understand PD etiology to identify options for novel treatments and beyond. Several methodologies recently addressed the complexity of this interaction from different perspectives; however, to date, a comprehensive review of these approaches is still lacking. Therefore, our main aim through this manuscript is to fill this gap in the scientific literature by reviewing recently published papers to address the surrounding questions regarding the underlying molecular mechanisms between metals, microbiota, and the gut-brain-axis, as well as the regulation of this system to prevent neurodegeneration.
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Affiliation(s)
- Lady Johanna Forero-Rodríguez
- Research Group Bioinformatics and Systems Biology, Instituto de Genetica, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (L.J.F.-R.); (A.P.)
- Research Group Medical Systems Biology, Christian-Albrechts-Universität Kiel, Brunswiker Straße 10, 24105 Kiel, Germany; (S.F.); (C.K.)
| | - Jonathan Josephs-Spaulding
- Research Group Medical Systems Biology, Christian-Albrechts-Universität Kiel, Brunswiker Straße 10, 24105 Kiel, Germany; (S.F.); (C.K.)
| | - Stefano Flor
- Research Group Medical Systems Biology, Christian-Albrechts-Universität Kiel, Brunswiker Straße 10, 24105 Kiel, Germany; (S.F.); (C.K.)
| | - Andrés Pinzón
- Research Group Bioinformatics and Systems Biology, Instituto de Genetica, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (L.J.F.-R.); (A.P.)
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Christian-Albrechts-Universität Kiel, Brunswiker Straße 10, 24105 Kiel, Germany; (S.F.); (C.K.)
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14
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Ewald J, Rivieccio F, Radosa L, Schuster S, Brakhage AA, Kaleta C. Dynamic optimization reveals alveolar epithelial cells as key mediators of host defense in invasive aspergillosis. PLoS Comput Biol 2021; 17:e1009645. [PMID: 34898608 PMCID: PMC8699926 DOI: 10.1371/journal.pcbi.1009645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 12/23/2021] [Accepted: 11/15/2021] [Indexed: 11/18/2022] Open
Abstract
Aspergillus fumigatus is an important human fungal pathogen and its conidia are constantly inhaled by humans. In immunocompromised individuals, conidia can grow out as hyphae that damage lung epithelium. The resulting invasive aspergillosis is associated with devastating mortality rates. Since infection is a race between the innate immune system and the outgrowth of A. fumigatus conidia, we use dynamic optimization to obtain insight into the recruitment and depletion of alveolar macrophages and neutrophils. Using this model, we obtain key insights into major determinants of infection outcome on host and pathogen side. On the pathogen side, we predict in silico and confirm in vitro that germination speed is an important virulence trait of fungal pathogens due to the vulnerability of conidia against host defense. On the host side, we found that epithelial cells, which have been underappreciated, play a role in fungal clearance and are potent mediators of cytokine release. Both predictions were confirmed by in vitro experiments on established cell lines as well as primary lung cells. Further, our model affirms the importance of neutrophils in invasive aspergillosis and underlines that the role of macrophages remains elusive. We expect that our model will contribute to improvement of treatment protocols by focusing on the critical components of immune response to fungi but also fungal virulence traits.
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Affiliation(s)
- Jan Ewald
- Department of Bioinformatics, Friedrich Schiller University Jena, Jena, Germany.,Center for Scalable Data Analytics and Artificial Intelligence (ScaDS.AI), University of Leipzig, Leipzig, Germany
| | - Flora Rivieccio
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Lukáš Radosa
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Friedrich Schiller University Jena, Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute (HKI), Jena, Germany.,Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
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15
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Hinrichsen F, Hamm J, Westermann M, Schröder L, Shima K, Mishra N, Walker A, Sommer N, Klischies K, Prasse D, Zimmermann J, Kaiser S, Bordoni D, Fazio A, Marinos G, Laue G, Imm S, Tremaroli V, Basic M, Häsler R, Schmitz RA, Krautwald S, Wolf A, Stecher B, Schmitt-Kopplin P, Kaleta C, Rupp J, Bäckhed F, Rosenstiel P, Sommer F. Microbial regulation of hexokinase 2 links mitochondrial metabolism and cell death in colitis. Cell Metab 2021; 33:2355-2366.e8. [PMID: 34847376 DOI: 10.1016/j.cmet.2021.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 08/07/2021] [Accepted: 11/09/2021] [Indexed: 12/14/2022]
Abstract
Hexokinases (HK) catalyze the first step of glycolysis limiting its pace. HK2 is highly expressed in gut epithelium, contributes to immune responses, and is upregulated during inflammation. We examined the microbial regulation of HK2 and its impact on inflammation using mice lacking HK2 in intestinal epithelial cells (Hk2ΔIEC). Hk2ΔIEC mice were less susceptible to acute colitis. Analyzing the epithelial transcriptome from Hk2ΔIEC mice during colitis and using HK2-deficient intestinal organoids and Caco-2 cells revealed reduced mitochondrial respiration and epithelial cell death in the absence of HK2. The microbiota strongly regulated HK2 expression and activity. The microbially derived short-chain fatty acid (SCFA) butyrate repressed HK2 expression via histone deacetylase 8 (HDAC8) and reduced mitochondrial respiration in wild-type but not in HK2-deficient Caco-2 cells. Butyrate supplementation protected wild-type but not Hk2ΔIEC mice from colitis. Our findings define a mechanism how butyrate promotes intestinal homeostasis and suggest targeted HK2-inhibition as therapeutic avenue for inflammation.
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Affiliation(s)
- Finn Hinrichsen
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Jacob Hamm
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Magdalena Westermann
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Lena Schröder
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Kensuke Shima
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany
| | - Neha Mishra
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Alesia Walker
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Centre for Environmental Health (GmbH), 85764 Neuherberg, Germany
| | - Nina Sommer
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Kenneth Klischies
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Daniela Prasse
- Institute of General Microbiology, University of Kiel, 24118 Kiel, Germany
| | | | - Sina Kaiser
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Dora Bordoni
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Antonella Fazio
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Georgios Marinos
- Institute of Experimental Medicine, University of Kiel, 24105 Kiel, Germany
| | - Georg Laue
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Simon Imm
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Valentina Tremaroli
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, 41345 Gothenburg, Sweden
| | - Marijana Basic
- Institute for Laboratory Animal Science, Hannover Medical School, 30625 Hannover, Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany; Department of Dermatology and Allergy, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Ruth A Schmitz
- Institute of General Microbiology, University of Kiel, 24118 Kiel, Germany
| | - Stefan Krautwald
- Department of Nephrology and Hypertension, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Andrea Wolf
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich, 80336 Munich, Germany; German Center for Infection Research (DZIF), partner site LMU Munich, Munich Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, German Research Centre for Environmental Health (GmbH), 85764 Neuherberg, Germany
| | - Christoph Kaleta
- Institute of Experimental Medicine, University of Kiel, 24105 Kiel, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, University of Gothenburg, 41345 Gothenburg, Sweden; Department of Clinical Physiology, Sahlgrenska University Hospital, Gothenburg, Sweden; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany
| | - Felix Sommer
- Institute of Clinical Molecular Biology, University of Kiel, 24105 Kiel, Germany.
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16
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Giri S, Oña L, Waschina S, Shitut S, Yousif G, Kaleta C, Kost C. Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria. Curr Biol 2021; 31:5547-5557.e6. [PMID: 34731676 DOI: 10.1016/j.cub.2021.10.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 09/01/2021] [Accepted: 10/08/2021] [Indexed: 12/19/2022]
Abstract
The exchange of metabolites among different bacterial genotypes profoundly impacts the structure and function of microbial communities. However, the factors governing the establishment of these cross-feeding interactions remain poorly understood. While shared physiological features may facilitate interactions among more closely related individuals, a lower relatedness should reduce competition and thus increase the potential for synergistic interactions. Here, we investigate how the relationship between a metabolite donor and recipient affects the propensity of strains to engage in unidirectional cross-feeding interactions. For this, we performed pairwise cocultivation experiments between four auxotrophic recipients and 25 species of potential amino acid donors. Auxotrophic recipients grew in the vast majority of pairs tested (63%), suggesting metabolic cross-feeding interactions are readily established. Strikingly, both the phylogenetic distance between donor and recipient and the dissimilarity of their metabolic networks were positively associated with the growth of auxotrophic recipients. Analyzing the co-growth of species from a gut microbial community in silico also revealed that recipient genotypes benefitted more from interacting with metabolically dissimilar partners, thus corroborating the empirical results. Together, our work identifies the metabolic dissimilarity between bacterial genotypes as a key factor determining the establishment of metabolic cross-feeding interactions in microbial communities.
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Affiliation(s)
- Samir Giri
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.
| | - Leonardo Oña
- Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Silvio Waschina
- Institute for Human Nutrition and Food Science, Nutriinformatics, Christian-Albrechts-University Kiel, 24105 Kiel, Germany; Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, 24105 Kiel, Germany
| | - Shraddha Shitut
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany
| | - Ghada Yousif
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany; Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, 24105 Kiel, Germany
| | - Christian Kost
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany; Department of Ecology, School of Biology/Chemistry, University of Osnabrück, 49076 Osnabrück, Germany.
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17
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Josephs-Spaulding J, Krogh TJ, Rettig HC, Lyng M, Chkonia M, Waschina S, Graspeuntner S, Rupp J, Møller-Jensen J, Kaleta C. Recurrent Urinary Tract Infections: Unraveling the Complicated Environment of Uncomplicated rUTIs. Front Cell Infect Microbiol 2021; 11:562525. [PMID: 34368008 PMCID: PMC8340884 DOI: 10.3389/fcimb.2021.562525] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
Urinary tract infections (UTIs) are frequent in humans, affecting the upper and lower urinary tract. Present diagnosis relies on the positive culture of uropathogenic bacteria from urine and clinical markers of inflammation of the urinary tract. The bladder is constantly challenged by adverse environmental stimuli which influence urinary tract physiology, contributing to a dysbiotic environment. Simultaneously, pathogens are primed by environmental stressors such as antibiotics, favoring recurrent UTIs (rUTIs), resulting in chronic illness. Due to different confounders for UTI onset, a greater understanding of the fundamental environmental mechanisms and microbial ecology of the human urinary tract is required. Such advancements could promote the tandem translation of bench and computational studies for precision treatments and clinical management of UTIs. Therefore, there is an urgent need to understand the ecological interactions of the human urogenital microbial communities which precede rUTIs. This review aims to outline the mechanistic aspects of rUTI ecology underlying dysbiosis between both the human microbiome and host physiology which predisposes humans to rUTIs. By assessing the applications of next generation and systems level methods, we also recommend novel approaches to elucidate the systemic consequences of rUTIs which requires an integrated approach for successful treatment. To this end, we will provide an outlook towards the so-called 'uncomplicated environment of UTIs', a holistic and systems view that applies ecological principles to define patient-specific UTIs. This perspective illustrates the need to withdraw from traditional reductionist perspectives in infection biology and instead, a move towards a systems-view revolving around patient-specific pathophysiology during UTIs.
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Affiliation(s)
- Jonathan Josephs-Spaulding
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-Universität, Kiel, Germany
| | - Thøger Jensen Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Hannah Clara Rettig
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Mark Lyng
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Mariam Chkonia
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Silvio Waschina
- Research Group Nutriinformatics, Institute of Human Nutrition and Food Science, Christian-Albrechts-Universität, Kiel, Germany
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-Universität, Kiel, Germany
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18
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Schuster S, Ewald J, Kaleta C. Modeling the energy metabolism in immune cells. Curr Opin Biotechnol 2021; 68:282-291. [PMID: 33770632 DOI: 10.1016/j.copbio.2021.03.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/16/2021] [Accepted: 03/01/2021] [Indexed: 02/08/2023]
Abstract
In this review, we summarize and briefly discuss various approaches to modeling the metabolism in human immune cells, with a focus on energy metabolism. These approaches include metabolic reconstruction, elementary modes, and flux balance analysis, which are often subsumed under constraint-based modeling. Further approaches are evolutionary game theory and kinetic modeling. Many immune cells such as macrophages show the Warburg effect, meaning that glycolysis is upregulated upon activation. We outline a minimal model for explaining that effect using optimization. The effect of a confrontation with pathogen cells on immunometabolism is highlighted. Models describing the differences between M1 and M2 macrophages, ROS production in neutrophils, and tryptophan metabolism are discussed. Obstacles and future prospects are outlined.
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Affiliation(s)
- Stefan Schuster
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Pl. 2, 07743 Jena, Germany.
| | - Jan Ewald
- Department of Bioinformatics, Matthias Schleiden Institute, Friedrich Schiller University Jena, Ernst-Abbe-Pl. 2, 07743 Jena, Germany
| | - Christoph Kaleta
- Medical Systems Biology Group, Institute of Experimental Medicine, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany
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19
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Zimmermann J, Kaleta C, Waschina S. gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models. Genome Biol 2021; 22:81. [PMID: 33691770 PMCID: PMC7949252 DOI: 10.1186/s13059-021-02295-1] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/10/2021] [Indexed: 12/21/2022] Open
Abstract
Genome-scale metabolic models of microorganisms are powerful frameworks to predict phenotypes from an organism's genotype. While manual reconstructions are laborious, automated reconstructions often fail to recapitulate known metabolic processes. Here we present gapseq ( https://github.com/jotech/gapseq ), a new tool to predict metabolic pathways and automatically reconstruct microbial metabolic models using a curated reaction database and a novel gap-filling algorithm. On the basis of scientific literature and experimental data for 14,931 bacterial phenotypes, we demonstrate that gapseq outperforms state-of-the-art tools in predicting enzyme activity, carbon source utilisation, fermentation products, and metabolic interactions within microbial communities.
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Affiliation(s)
- Johannes Zimmermann
- Christian-Albrechts-University Kiel, Institute of Experimental Medicine, Research Group Medical Systems Biology, Michaelis-Str. 5, Kiel, 24105 Germany
| | - Christoph Kaleta
- Christian-Albrechts-University Kiel, Institute of Experimental Medicine, Research Group Medical Systems Biology, Michaelis-Str. 5, Kiel, 24105 Germany
| | - Silvio Waschina
- Christian-Albrechts-University Kiel, Institute of Experimental Medicine, Research Group Medical Systems Biology, Michaelis-Str. 5, Kiel, 24105 Germany
- Christian-Albrechts-University Kiel, Institute of Human Nutrition and Food Science, Nutriinformatics, Heinrich-Hecht-Platz 10, Kiel, 24118 Germany
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20
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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21
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Bernardes JP, Mishra N, Tran F, Bahmer T, Best L, Blase JI, Bordoni D, Franzenburg J, Geisen U, Josephs-Spaulding J, Köhler P, Künstner A, Rosati E, Aschenbrenner AC, Bacher P, Baran N, Boysen T, Brandt B, Bruse N, Dörr J, Dräger A, Elke G, Ellinghaus D, Fischer J, Forster M, Franke A, Franzenburg S, Frey N, Friedrichs A, Fuß J, Glück A, Hamm J, Hinrichsen F, Hoeppner MP, Imm S, Junker R, Kaiser S, Kan YH, Knoll R, Lange C, Laue G, Lier C, Lindner M, Marinos G, Markewitz R, Nattermann J, Noth R, Pickkers P, Rabe KF, Renz A, Röcken C, Rupp J, Schaffarzyk A, Scheffold A, Schulte-Schrepping J, Schunk D, Skowasch D, Ulas T, Wandinger KP, Wittig M, Zimmermann J, Busch H, Hoyer BF, Kaleta C, Heyckendorf J, Kox M, Rybniker J, Schreiber S, Schultze JL, Rosenstiel P. Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19. Immunity 2020; 53:1296-1314.e9. [PMID: 33296687 PMCID: PMC7689306 DOI: 10.1016/j.immuni.2020.11.017] [Citation(s) in RCA: 224] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/15/2020] [Accepted: 11/19/2020] [Indexed: 01/08/2023]
Abstract
Temporal resolution of cellular features associated with a severe COVID-19 disease trajectory is needed for understanding skewed immune responses and defining predictors of outcome. Here, we performed a longitudinal multi-omics study using a two-center cohort of 14 patients. We analyzed the bulk transcriptome, bulk DNA methylome, and single-cell transcriptome (>358,000 cells, including BCR profiles) of peripheral blood samples harvested from up to 5 time points. Validation was performed in two independent cohorts of COVID-19 patients. Severe COVID-19 was characterized by an increase of proliferating, metabolically hyperactive plasmablasts. Coinciding with critical illness, we also identified an expansion of interferon-activated circulating megakaryocytes and increased erythropoiesis with features of hypoxic signaling. Megakaryocyte- and erythroid-cell-derived co-expression modules were predictive of fatal disease outcome. The study demonstrates broad cellular effects of SARS-CoV-2 infection beyond adaptive immune cells and provides an entry point toward developing biomarkers and targeted treatments of patients with COVID-19. SARS-CoV2 infection elicits dynamic changes of circulating cells in the blood Severe COVID-19 is characterized by increased metabolically active plasmablasts Elevation of IFN-activated megakaryocytes and erythroid cells in severe COVID-19 Cell-type-specific expression signatures are associated with a fatal COVID-19 outcome
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Affiliation(s)
- Joana P Bernardes
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Neha Mishra
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; Department of Internal Medicine I, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Thomas Bahmer
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Lena Best
- Institute for Experimental Medicine, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Johanna I Blase
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Dora Bordoni
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Jeanette Franzenburg
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, 24105 Kiel and 23562 Lübeck, Germany
| | - Ulf Geisen
- Section for Rheumatology, Department of Internal Medicine I, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Jonathan Josephs-Spaulding
- Institute for Experimental Medicine, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Philipp Köhler
- Department I of Internal Medicine, University of Cologne and University Hospital Cologne; German Center for Infection Research, Partner Site Bonn-Cologne and Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50937 Cologne, Germany
| | - Axel Künstner
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Germany
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Anna C Aschenbrenner
- Genomics & Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; Departments of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, 53127 Bonn, Germany
| | - Petra Bacher
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; Institute of Immunology, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Nathan Baran
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Teide Boysen
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Burkhard Brandt
- Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, 24105 Kiel and 23562 Lübeck, Germany
| | - Niklas Bruse
- Departments of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Jonathan Dörr
- Section for Rheumatology, Department of Internal Medicine I, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Andreas Dräger
- Department of Computer Science, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen and German Center for Infection Research (DZIF), Partner site Tübingen, 72076 Tübingen, Germany
| | - Gunnar Elke
- Department of Anaesthesiology and Intensive Care Medicine, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Julia Fischer
- Department I of Internal Medicine, University of Cologne and University Hospital Cologne; German Center for Infection Research, Partner Site Bonn-Cologne and Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Norbert Frey
- Department of Internal Medicine III, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Anette Friedrichs
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Janina Fuß
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Andreas Glück
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Jacob Hamm
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Finn Hinrichsen
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Marc P Hoeppner
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Simon Imm
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Ralf Junker
- Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, 24105 Kiel and 23562 Lübeck, Germany
| | - Sina Kaiser
- Section for Rheumatology, Department of Internal Medicine I, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Ying H Kan
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Rainer Knoll
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, 53127 Bonn, Germany
| | - Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel and German Center for Infection Research (DZIF), TTU-TB, 23845 Borstel, Germany
| | - Georg Laue
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Clemens Lier
- Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, 24105 Kiel and 23562 Lübeck, Germany
| | - Matthias Lindner
- Department of Anaesthesiology and Intensive Care Medicine, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Georgios Marinos
- Institute for Experimental Medicine, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Robert Markewitz
- Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, 24105 Kiel and 23562 Lübeck, Germany
| | - Jacob Nattermann
- Department of Internal Medicine I and German Center for Infection Research (DZIF), University of Bonn, 53217 Bonn, Germany
| | - Rainer Noth
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Peter Pickkers
- Departments of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Klaus F Rabe
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; LungenClinic Grosshansdorf, Airway Research Centre North, German Centre for Lung Research, 22927 Grosshansdorf, Germany
| | - Alina Renz
- Department of Computer Science, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen and German Center for Infection Research (DZIF), Partner site Tübingen, 72076 Tübingen, Germany
| | - Christoph Röcken
- Department of Pathology, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23562 Lübeck, Germany
| | - Annika Schaffarzyk
- Section for Rheumatology, Department of Internal Medicine I, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Alexander Scheffold
- Institute of Immunology, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Jonas Schulte-Schrepping
- Genomics & Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany
| | - Domagoj Schunk
- Department for Emergency Medicine, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Dirk Skowasch
- Section of Pneumology, Department of Internal Medicine II, University Hospital Bonn, , 53127 Bonn, Germany
| | - Thomas Ulas
- Genomics & Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, 53127 Bonn, Germany
| | - Klaus-Peter Wandinger
- Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, 24105 Kiel and 23562 Lübeck, Germany
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Johannes Zimmermann
- Institute for Experimental Medicine, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Hauke Busch
- Lübeck Institute of Experimental Dermatology, University of Lübeck, 23562 Lübeck, Germany
| | - Bimba F Hoyer
- Section for Rheumatology, Department of Internal Medicine I, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Christoph Kaleta
- Institute for Experimental Medicine, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Jan Heyckendorf
- Department of Internal Medicine III, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Matthijs Kox
- Genomics & Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Jan Rybniker
- Department I of Internal Medicine, University of Cologne and University Hospital Cologne; German Center for Infection Research, Partner Site Bonn-Cologne and Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany; Department of Internal Medicine I, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Joachim L Schultze
- Genomics & Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany; Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), 53127 Bonn, Germany; German Center for Neurodegenerative Diseases (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE, and University of Bonn, 53127 Bonn, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany.
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22
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Demetrowitsch TJ, Schlicht K, Knappe C, Zimmermann J, Jensen-Kroll J, Pisarevskaja A, Brix F, Brandes J, Geisler C, Marinos G, Sommer F, Schulte DM, Kaleta C, Andersen V, Laudes M, Schwarz K, Waschina S. Precision Nutrition in Chronic Inflammation. Front Immunol 2020; 11:587895. [PMID: 33329569 PMCID: PMC7719806 DOI: 10.3389/fimmu.2020.587895] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/22/2020] [Indexed: 12/11/2022] Open
Abstract
The molecular foundation of chronic inflammatory diseases (CIDs) can differ markedly between individuals. As our understanding of the biochemical mechanisms underlying individual disease manifestations and progressions expands, new strategies to adjust treatments to the patient's characteristics will continue to profoundly transform clinical practice. Nutrition has long been recognized as an important determinant of inflammatory disease phenotypes and treatment response. Yet empirical work demonstrating the therapeutic effectiveness of patient-tailored nutrition remains scarce. This is mainly due to the challenges presented by long-term effects of nutrition, variations in inter-individual gastrointestinal microbiota, the multiplicity of human metabolic pathways potentially affected by food ingredients, nutrition behavior, and the complexity of food composition. Historically, these challenges have been addressed in both human studies and experimental model laboratory studies primarily by using individual nutrition data collection in tandem with large-scale biomolecular data acquisition (e.g. genomics, metabolomics, etc.). This review highlights recent findings in the field of precision nutrition and their potential implications for the development of personalized treatment strategies for CIDs. It emphasizes the importance of computational approaches to integrate nutritional information into multi-omics data analysis and to predict which molecular mechanisms may explain how nutrients intersect with disease pathways. We conclude that recent findings point towards the unexhausted potential of nutrition as part of personalized medicine in chronic inflammation.
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Affiliation(s)
- Tobias J. Demetrowitsch
- Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - Kristina Schlicht
- Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Medicine 1, Kiel University, Kiel, Germany
| | - Carina Knappe
- Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Medicine 1, Kiel University, Kiel, Germany
| | - Johannes Zimmermann
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Julia Jensen-Kroll
- Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - Alina Pisarevskaja
- Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
- Division of Nutriinformatics, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - Fynn Brix
- Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - Juliane Brandes
- Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Medicine 1, Kiel University, Kiel, Germany
| | - Corinna Geisler
- Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Medicine 1, Kiel University, Kiel, Germany
| | - Georgios Marinos
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Felix Sommer
- Institute of Clinical Molecular Biology (IKMB), Kiel University, Kiel, Germany
| | - Dominik M. Schulte
- Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Medicine 1, Kiel University, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, Kiel, Germany
| | - Vibeke Andersen
- Institute of Regional Research, University of Southern Denmark, Odense, Denmark
- Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
- Focused Research Unit for Molecular Diagnostic and Clinical Research, University Hospital of Southern Denmark, Aabenraa, Denmark
| | - Matthias Laudes
- Division of Endocrinology, Diabetes and Clinical Nutrition, Department of Medicine 1, Kiel University, Kiel, Germany
| | - Karin Schwarz
- Division of Food Technology, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
| | - Silvio Waschina
- Division of Nutriinformatics, Institute of Human Nutrition and Food Science, Kiel University, Kiel, Germany
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23
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Dirksen P, Assié A, Zimmermann J, Zhang F, Tietje AM, Marsh SA, Félix MA, Shapira M, Kaleta C, Schulenburg H, Samuel BS. CeMbio - The Caenorhabditis elegans Microbiome Resource. G3 (Bethesda) 2020; 10:3025-3039. [PMID: 32669368 PMCID: PMC7466993 DOI: 10.1534/g3.120.401309] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 07/07/2020] [Indexed: 12/23/2022]
Abstract
The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships in host-microbiome systems. Yet the available communities suffer from several drawbacks, such as artificial (thus non-natural) choice of microbes, microbe-host mismatch (e.g., human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified natural Caenorhabditis elegans microbiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of the C. elegans model system, strains included are readily culturable, they all colonize the worm gut individually, and comprise a robust community that distinctly affects nematode life-history. Several tools have additionally been developed for the CeMbio strains, including diagnostic PCR primers, completely sequenced genomes, and metabolic network models. With CeMbio, we provide a versatile resource and toolbox for the in-depth dissection of naturally relevant host-microbiome interactions in C. elegans.
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Affiliation(s)
- Philipp Dirksen
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts University, Kiel, Germany
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston TX
| | - Johannes Zimmermann
- Medical Systems Biology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Fan Zhang
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston TX
| | - Adina-Malin Tietje
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts University, Kiel, Germany
| | | | - Marie-Anne Félix
- Institute of Biology of the Ecole Normale Supérieure, Paris, France
| | - Michael Shapira
- Department of Integrative Biology, University of California, Berkeley CA
| | - Christoph Kaleta
- Medical Systems Biology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Christian-Albrechts University, Kiel, Germany
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston TX
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24
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Krogh TJ, Franke A, Møller-Jensen J, Kaleta C. Elucidating the Influence of Chromosomal Architecture on Transcriptional Regulation in Prokaryotes - Observing Strong Local Effects of Nucleoid Structure on Gene Regulation. Front Microbiol 2020; 11:2002. [PMID: 32983020 PMCID: PMC7491251 DOI: 10.3389/fmicb.2020.02002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/29/2020] [Indexed: 11/13/2022] Open
Abstract
Both intrinsic and extrinsic mechanisms regulating bacterial expression have been elucidated and described, however, such studies have mainly focused on local effects on the two-dimensional structure of the prokaryote genome while long-range as well as spatial interactions influencing gene expression are still only poorly understood. In this paper, we investigate the association between co-expression and distance between genes, using RNA-seq data at multiple growth phases in order to illuminate whether such conserved patterns are an indication of a gene regulatory mechanism relevant for prokaryotic cell proliferation, adaption, and evolution. We observe recurrent sinusoidal patterns in correlation of pairwise expression as function of genomic distance and rule out that these are caused by transcription-induced supercoiling gradients, gene clustering in operons, or association with regulatory transcription factors (TFs). By comparing spatial proximity for pairs of genomic bins with their correlation of pairwise expression, we further observe a high co-expression proportional with the spatial proximity. Based on these observations, we propose that the observed patterns are related to nucleoid structure as a product of transcriptional spilling, where genes actively influence transcription of spatially proximal genes through increases within shared local pools of RNA polymerases (RNAP), and actively spilling transcription onto neighboring genes.
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Affiliation(s)
- Thøger Jensen Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Andre Franke
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University Kiel, Kiel, Germany
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
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25
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Abstract
The reconstruction and application of genome-scale metabolic network models is a central topic in the field of systems biology with numerous applications in biotechnology, ecology, and medicine. However, there is no agreed upon standard for the definition of the nutritional environment for these models. The objective of this article is to provide a guideline and a clear paradigm on how to translate nutritional information into an in-silico representation of the chemical environment. Step-by-step procedures explain how to characterise and categorise the nutritional input and to successfully apply it to constraint-based metabolic models. In parallel, we illustrate the proposed procedure with a case study of the growth of Escherichia coli in a complex nutritional medium and show that an accurate representation of the medium is crucial for physiological predictions. The proposed framework will assist researchers to expand their existing metabolic models of their microbial systems of interest with detailed representations of the nutritional environment, which allows more accurate and reproducible predictions of microbial metabolic processes.
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Affiliation(s)
- Georgios Marinos
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, University Medical Center Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Kiel University, University Medical Center Schleswig-Holstein, Kiel, Schleswig-Holstein, Germany
| | - Silvio Waschina
- Division of Nutriinformatics, Institute for Human Nutrition and Food Sciences, Kiel University, Kiel, Schleswig-Holstein, Germany
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26
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Graspeuntner S, Waschina S, Künzel S, Twisselmann N, Rausch TK, Cloppenborg-Schmidt K, Zimmermann J, Viemann D, Herting E, Göpel W, Baines JF, Kaleta C, Rupp J, Härtel C, Pagel J. Gut Dysbiosis With Bacilli Dominance and Accumulation of Fermentation Products Precedes Late-onset Sepsis in Preterm Infants. Clin Infect Dis 2020; 69:268-277. [PMID: 30329017 DOI: 10.1093/cid/ciy882] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/12/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Gut dysbiosis has been suggested as a major risk factor for the development of late-onset sepsis (LOS), a main cause of mortality and morbidity in preterm infants. We aimed to assess specific signatures of the gut microbiome, including metabolic profiles, in preterm infants <34 weeks of gestation preceding LOS. METHODS In a single-center cohort, fecal samples from preterm infants were prospectively collected during the period of highest vulnerability for LOS (days 7, 14, and 21 of life). Following 16S rRNA gene profiling, we assessed microbial community function using microbial metabolic network modeling. Data were adjusted for gestational age and use of probiotics. RESULTS We studied stool samples from 71 preterm infants with LOS and 164 unaffected controls (no LOS/necrotizing enterocolitis). In most cases, the bacteria isolated in diagnostic blood culture corresponded to the genera in the gut microbiome. LOS cases had a decelerated development of microbial diversity. Before onset of disease, LOS cases had specific gut microbiome signatures with higher abundance of Bacilli (specifically coagulase-negative Staphylococci) and a lack of anaerobic bacteria. In silico modeling of bacterial community metabolism suggested accumulation of the fermentation products ethanol and formic acid in LOS cases before the onset of disease. CONCLUSIONS Intestinal dysbiosis preceding LOS is characterized by an accumulation of Bacilli and their fermentation products and a paucity of anaerobic bacteria. Early microbiome and metabolic patterns may become a valuable biomarker to guide individualized prevention strategies of LOS in highly vulnerable populations.
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Affiliation(s)
- S Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Plön
| | - S Waschina
- Research Group Medical Systems Biology, Christian Albrechts University of Kiel, Plön
| | - S Künzel
- Max Planck Institute for Evolutionary Biology, Evolutionary Genomics, Plön
| | - N Twisselmann
- Department of Pediatrics, University of Lübeck, Lübeck, Germany
| | - T K Rausch
- Department of Pediatrics, University of Lübeck, Lübeck, Germany.,Institute for Medical Biometry and Statistics, University of Lübeck, Lübeck, Germany
| | - K Cloppenborg-Schmidt
- Institute for Experimental Medicine, Christian Albrechts University of Kiel, Lübeck, Germany
| | - J Zimmermann
- Research Group Medical Systems Biology, Christian Albrechts University of Kiel, Plön
| | - D Viemann
- Department of Pediatric Pneumology, Allergy and Neonatology, Hannover Medical School, Lübeck, Germany
| | - E Herting
- Department of Pediatrics, University of Lübeck, Lübeck, Germany
| | - W Göpel
- Department of Pediatrics, University of Lübeck, Lübeck, Germany
| | - J F Baines
- Max Planck Institute for Evolutionary Biology, Evolutionary Genomics, Plön.,Institute for Medical Biometry and Statistics, University of Lübeck, Lübeck, Germany
| | - C Kaleta
- Research Group Medical Systems Biology, Christian Albrechts University of Kiel, Plön
| | - J Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Plön.,German Center for Infection Research, partner site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
| | - C Härtel
- Department of Pediatrics, University of Lübeck, Lübeck, Germany
| | - J Pagel
- Department of Infectious Diseases and Microbiology, University of Lübeck, Plön.,Department of Pediatrics, University of Lübeck, Lübeck, Germany.,German Center for Infection Research, partner site Hamburg-Lübeck-Borstel-Riems, Lübeck, Germany
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27
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van Dam E, van Leeuwen LAG, Dos Santos E, James J, Best L, Lennicke C, Vincent AJ, Marinos G, Foley A, Buricova M, Mokochinski JB, Kramer HB, Lieb W, Laudes M, Franke A, Kaleta C, Cochemé HM. Sugar-Induced Obesity and Insulin Resistance Are Uncoupled from Shortened Survival in Drosophila. Cell Metab 2020; 31:710-725.e7. [PMID: 32197072 PMCID: PMC7156915 DOI: 10.1016/j.cmet.2020.02.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 01/29/2020] [Accepted: 02/24/2020] [Indexed: 12/24/2022]
Abstract
High-sugar diets cause thirst, obesity, and metabolic dysregulation, leading to diseases including type 2 diabetes and shortened lifespan. However, the impact of obesity and water imbalance on health and survival is complex and difficult to disentangle. Here, we show that high sugar induces dehydration in adult Drosophila, and water supplementation fully rescues their lifespan. Conversely, the metabolic defects are water-independent, showing uncoupling between sugar-induced obesity and insulin resistance with reduced survival in vivo. High-sugar diets promote accumulation of uric acid, an end-product of purine catabolism, and the formation of renal stones, a process aggravated by dehydration and physiological acidification. Importantly, regulating uric acid production impacts on lifespan in a water-dependent manner. Furthermore, metabolomics analysis in a human cohort reveals that dietary sugar intake strongly predicts circulating purine levels. Our model explains the pathophysiology of high-sugar diets independently of obesity and insulin resistance and highlights purine metabolism as a pro-longevity target.
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Affiliation(s)
- Esther van Dam
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Lucie A G van Leeuwen
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Eliano Dos Santos
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Joel James
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Lena Best
- Institute for Experimental Medicine, Kiel University, 24105 Kiel, Germany
| | - Claudia Lennicke
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Alec J Vincent
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Georgios Marinos
- Institute for Experimental Medicine, Kiel University, 24105 Kiel, Germany
| | - Andrea Foley
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Marcela Buricova
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Joao B Mokochinski
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Holger B Kramer
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Wolfgang Lieb
- Institute of Epidemiology, Kiel University, 24105 Kiel, Germany
| | - Matthias Laudes
- Department of Internal Medicine I, University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany
| | - Christoph Kaleta
- Institute for Experimental Medicine, Kiel University, 24105 Kiel, Germany
| | - Helena M Cochemé
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.
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28
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Aden K, Rehman A, Waschina S, Pan WH, Walker A, Lucio M, Nunez AM, Bharti R, Zimmerman J, Bethge J, Schulte B, Schulte D, Franke A, Nikolaus S, Schroeder JO, Vandeputte D, Raes J, Szymczak S, Waetzig GH, Zeuner R, Schmitt-Kopplin P, Kaleta C, Schreiber S, Rosenstiel P. Metabolic Functions of Gut Microbes Associate With Efficacy of Tumor Necrosis Factor Antagonists in Patients With Inflammatory Bowel Diseases. Gastroenterology 2019; 157:1279-1292.e11. [PMID: 31326413 DOI: 10.1053/j.gastro.2019.07.025] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/18/2019] [Accepted: 07/04/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Altered interactions between the mucosal immune system and intestinal microbiota contribute to pathogenesis of inflammatory bowel diseases (IBD). It is not clear how inhibitors of cytokines, such as antagonists of tumor necrosis factor (anti-TNF), affect the intestinal microbiome. We investigated the effects of anti-TNF agents on gut microbe community structure and function in a longitudinal 2-step study of patients with IBD. We correlated our findings with outcomes of treatment and investigated patterns of metabolites in fecal samples before and after anti-TNF therapy. METHODS We performed a prospective study of 2 cohorts of patients in Germany; the discovery cohort comprised 12 patients with IBD, 17 patients with rheumatic disease, and 19 healthy individuals (controls); fecal samples were collected at baseline and 2, 6, and 30 weeks after induction of anti-TNF therapy. The validation cohort comprised 23 patients with IBD treated with anti-TNF or vedolizumab (anti-α4β7 integrin) and 99 healthy controls; fecal samples were collected at baseline and at weeks 2, 6, and 14. Fecal microbiota were analyzed by V3-V4 16S ribosomal RNA gene amplicon sequencing. Clinical response and remission were determined by clinical disease activity scores. Metabolic network reconstruction and associated fecal metabolite level inference was performed in silico using the AGORA (Assembly of Gut Organisms through Reconstruction and Analysis) resource. Metabolomic analyses of fecal samples from a subset of patients were performed to validate metabolites associated with treatment outcomes. RESULTS Anti-TNF therapy shifted the diversity of fecal microbiota in patients with IBD, but not with rheumatic disease, toward that of controls. Across timepoints, diversity indices did not vary significantly between patients with IBD who did or did not achieve clinical remission after therapy. In contrast, in silico modeling of metabolic interactions between gut microbes found metabolite exchange to be significantly reduced at baseline in fecal samples from patients with IBD and to be associated with later clinical remission. Predicted levels of butyrate and substrates involved in butyrate synthesis (ethanol or acetaldehyde) were significantly associated with clinical remission following anti-TNF therapy, verified by fecal metabolomic analyses. CONCLUSIONS Metabolic network reconstruction and assessment of metabolic profiles of fecal samples might be used to identify patients with IBD likely to achieve clinical remission following anti-TNF therapy and increase our understanding of the heterogeneity of IBD.
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Affiliation(s)
- Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Ateequr Rehman
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Silvio Waschina
- Institute for Experimental Medicine, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Wei-Hung Pan
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Alesia Walker
- Research Unit Analytical BioGeoChemistry, Helmholtz ZentrumMünchen, German Research Centre for Environmental Health (GmbH), Neuherberg, Germany
| | - Marianna Lucio
- Research Unit Analytical BioGeoChemistry, Helmholtz ZentrumMünchen, German Research Centre for Environmental Health (GmbH), Neuherberg, Germany
| | - Alejandro Mena Nunez
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Richa Bharti
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Johannes Zimmerman
- Institute for Experimental Medicine, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Johannes Bethge
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Berenice Schulte
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Dominik Schulte
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Susanna Nikolaus
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Johann Oltmann Schroeder
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Doris Vandeputte
- VIB-KU Leuven Center for Microbiology, Campus Gasthuisberg, Leuven, Belgium
| | - Jeroen Raes
- VIB-KU Leuven Center for Microbiology, Campus Gasthuisberg, Leuven, Belgium
| | - Silke Szymczak
- Institute of Medical Informatics and Statistics, University of Kiel, Kiel, Germany
| | | | - Rainald Zeuner
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz ZentrumMünchen, German Research Centre for Environmental Health (GmbH), Neuherberg, Germany
| | - Christoph Kaleta
- Institute for Experimental Medicine, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
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29
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Zimmermann J, Obeng N, Yang W, Pees B, Petersen C, Waschina S, Kissoyan KA, Aidley J, Hoeppner MP, Bunk B, Spröer C, Leippe M, Dierking K, Kaleta C, Schulenburg H. The functional repertoire contained within the native microbiota of the model nematode Caenorhabditis elegans. ISME J 2019; 14:26-38. [PMID: 31484996 PMCID: PMC6908608 DOI: 10.1038/s41396-019-0504-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 06/11/2019] [Accepted: 07/17/2019] [Indexed: 02/07/2023]
Abstract
The microbiota is generally assumed to have a substantial influence on the biology of multicellular organisms. The exact functional contributions of the microbes are often unclear and cannot be inferred easily from 16S rRNA genotyping, which is commonly used for taxonomic characterization of bacterial associates. In order to bridge this knowledge gap, we here analyzed the metabolic competences of the native microbiota of the model nematode Caenorhabditis elegans. We integrated whole-genome sequences of 77 bacterial microbiota members with metabolic modeling and experimental characterization of bacterial physiology. We found that, as a community, the microbiota can synthesize all essential nutrients for C. elegans. Both metabolic models and experimental analyses revealed that nutrient context can influence how bacteria interact within the microbiota. We identified key bacterial traits that are likely to influence the microbe’s ability to colonize C. elegans (i.e., the ability of bacteria for pyruvate fermentation to acetoin) and affect nematode fitness (i.e., bacterial competence for hydroxyproline degradation). Considering that the microbiota is usually neglected in C. elegans research, the resource presented here will help our understanding of this nematode’s biology in a more natural context. Our integrative approach moreover provides a novel, general framework to characterize microbiota-mediated functions.
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Affiliation(s)
- Johannes Zimmermann
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts University, Kiel, Germany
| | - Nancy Obeng
- Research Group of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Wentao Yang
- Research Group of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Barbara Pees
- Research Group of Comparative Immunobiology, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Carola Petersen
- Research Group of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Kiel, Germany.,Research Group of Comparative Immunobiology, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Silvio Waschina
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts University, Kiel, Germany
| | - Kohar A Kissoyan
- Research Group of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Jack Aidley
- Research Group of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Marc P Hoeppner
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Kiel, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Matthias Leippe
- Research Group of Comparative Immunobiology, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Katja Dierking
- Research Group of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts University, Kiel, Germany.
| | - Hinrich Schulenburg
- Research Group of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Kiel, Germany. .,Max-Planck Institute for Evolutionary Biology, Ploen, Germany.
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30
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Yang W, Petersen C, Pees B, Zimmermann J, Waschina S, Dirksen P, Rosenstiel P, Tholey A, Leippe M, Dierking K, Kaleta C, Schulenburg H. The Inducible Response of the Nematode Caenorhabditis elegans to Members of Its Natural Microbiota Across Development and Adult Life. Front Microbiol 2019; 10:1793. [PMID: 31440221 PMCID: PMC6693516 DOI: 10.3389/fmicb.2019.01793] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022] Open
Abstract
The biology of all organisms is influenced by the associated community of microorganisms. In spite of its importance, it is usually not well understood how exactly this microbiota affects host functions and what are the underlying molecular processes. To rectify this knowledge gap, we took advantage of the nematode Caenorhabditis elegans as a tractable, experimental model system and assessed the inducible transcriptome response after colonization with members of its native microbiota. For this study, we focused on two isolates of the genus Ochrobactrum. These bacteria are known to be abundant in the nematode’s microbiota and are capable of colonizing and persisting in the nematode gut, even under stressful conditions. The transcriptome response was assessed across development and three time points of adult life, using general and C. elegans-specific enrichment analyses to identify affected functions. Our assessment revealed an influence of the microbiota members on the nematode’s dietary response, development, fertility, immunity, and energy metabolism. This response is mainly regulated by a GATA transcription factor, most likely ELT-2, as indicated by the enrichment of (i) the GATA motif in the promoter regions of inducible genes and (ii) of ELT-2 targets among the differentially expressed genes. We compared our transcriptome results with a corresponding previously characterized proteome data set, highlighting a significant overlap in the differentially expressed genes, the affected functions, and ELT-2 target genes. Our analysis further identified a core set of 86 genes that consistently responded to the microbiota members across development and adult life, including several C-type lectin-like genes and genes known to be involved in energy metabolism or fertility. We additionally assessed the consequences of induced gene expression with the help of metabolic network model analysis, using a previously established metabolic network for C. elegans. This analysis complemented the enrichment analyses by revealing an influence of the Ochrobactrum isolates on C. elegans energy metabolism and furthermore metabolism of specific amino acids, fatty acids, and also folate biosynthesis. Our findings highlight the multifaceted impact of naturally colonizing microbiota isolates on C. elegans life history and thereby provide a framework for further analysis of microbiota-mediated host functions.
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Affiliation(s)
- Wentao Yang
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Carola Petersen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Research Group Comparative Immunobiology, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Barbara Pees
- Research Group Comparative Immunobiology, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Johannes Zimmermann
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Silvio Waschina
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Philipp Dirksen
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute for Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Andreas Tholey
- Research Group Proteomics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Matthias Leippe
- Research Group Comparative Immunobiology, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Katja Dierking
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Hinrich Schulenburg
- Research Group Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, Plön, Germany
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31
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Giri S, Waschina S, Kaleta C, Kost C. Defining Division of Labor in Microbial Communities. J Mol Biol 2019; 431:4712-4731. [PMID: 31260694 DOI: 10.1016/j.jmb.2019.06.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 06/13/2019] [Accepted: 06/19/2019] [Indexed: 11/15/2022]
Abstract
In order to survive and reproduce, organisms must perform a multitude of tasks. However, trade-offs limit their ability to allocate energy and resources to all of these different processes. One strategy to solve this problem is to specialize in some traits and team up with other organisms that can help by providing additional, complementary functions. By reciprocally exchanging metabolites and/or services in this way, both parties benefit from the interaction. This phenomenon, which has been termed functional specialization or division of labor, is very common in nature and exists on all levels of biological organization. Also, microorganisms have evolved different types of synergistic interactions. However, very often, it remains unclear whether or not a given example represents a true case of division of labor. Here we aim at filling this gap by providing a list of criteria that clearly define division of labor in microbial communities. Furthermore, we propose a set of diagnostic experiments to verify whether a given interaction fulfills these conditions. In contrast to the common use of the term, our analysis reveals that both intraspecific and interspecific interactions meet the criteria defining division of labor. Moreover, our analysis identified non-cooperators of intraspecific public goods interactions as growth specialists that divide labor with conspecific producers, rather than being social parasites. By providing a conceptual toolkit, our work will help to unambiguously identify cases of division of labor and stimulate more detailed investigations of this important and widespread type of inter-microbial interaction.
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Affiliation(s)
- Samir Giri
- Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Silvio Waschina
- 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
| | - Christian Kost
- Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany.
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32
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Fabian A, Stegner S, Miarka L, Zimmermann J, Lenk L, Rahn S, Buttlar J, Viol F, Knaack H, Esser D, Schäuble S, Großmann P, Marinos G, Häsler R, Mikulits W, Saur D, Kaleta C, Schäfer H, Sebens S. Metastasis of pancreatic cancer: An uninflamed liver micromilieu controls cell growth and cancer stem cell properties by oxidative phosphorylation in pancreatic ductal epithelial cells. Cancer Lett 2019; 453:95-106. [PMID: 30930235 DOI: 10.1016/j.canlet.2019.03.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/08/2019] [Accepted: 03/21/2019] [Indexed: 12/11/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is commonly diagnosed when liver metastases already emerged. We recently demonstrated that hepatic stromal cells determine the dormancy status along with cancer stem cell (CSC) properties of pancreatic ductal epithelial cells (PDECs) during metastasis. This study investigated the influence of the hepatic microenvironment - and its inflammatory status - on metabolic alterations and how these impact cell growth and CSC-characteristics of PDECs. Coculture with hepatic stellate cells (HSCs), simulating a physiological liver stroma, but not with hepatic myofibroblasts (HMFs) representing liver inflammation promoted expression of Succinate Dehydrogenase subunit B (SDHB) and an oxidative metabolism along with a quiescent phenotype in PDECs. SiRNA-mediated SDHB knockdown increased cell growth and CSC-properties. Moreover, liver micrometastases of tumor bearing KPC mice strongly expressed SDHB while expression of the CSC-marker Nestin was exclusively found in macrometastases. Consistently, RNA-sequencing and in silico modeling revealed significantly altered metabolic fluxes and enhanced SDH activity predominantly in premalignant PDECs in the presence of HSC compared to HMF. Overall, these data emphasize that the hepatic microenvironment determines the metabolism of disseminated PDECs thereby controlling cell growth and CSC-properties during liver metastasis.
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Affiliation(s)
- Alexander Fabian
- Group Inflammatory Carcinogenesis, Institute for Experimental Cancer Research, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein (UKSH) Campus Kiel, Arnold-Heller-Str. 3, Building 17, 24105, Kiel, Germany
| | - Simon Stegner
- Group Inflammatory Carcinogenesis, Institute for Experimental Cancer Research, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein (UKSH) Campus Kiel, Arnold-Heller-Str. 3, Building 17, 24105, Kiel, Germany
| | - Lauritz Miarka
- Group Inflammatory Carcinogenesis, Institute for Experimental Cancer Research, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein (UKSH) Campus Kiel, Arnold-Heller-Str. 3, Building 17, 24105, Kiel, Germany
| | - Johannes Zimmermann
- Group Medical Systems Biology, Institute for Experimental Medicine, Michaelisstr. 5, Building 17, 24105, Kiel, Germany
| | - Lennart Lenk
- Department of Pediatrics, Christian-Albrechts-University Kiel and University Medical Center Schleswig-Holstein, Schwanenweg 20, 24105, Kiel, Germany
| | - Sascha Rahn
- Group Inflammatory Carcinogenesis, Institute for Experimental Cancer Research, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein (UKSH) Campus Kiel, Arnold-Heller-Str. 3, Building 17, 24105, Kiel, Germany
| | - Jann Buttlar
- Group Inflammatory Carcinogenesis, Institute for Experimental Cancer Research, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein (UKSH) Campus Kiel, Arnold-Heller-Str. 3, Building 17, 24105, Kiel, Germany
| | - Fabrice Viol
- Department of Medicine I, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hendrike Knaack
- Group Inflammatory Carcinogenesis, Institute for Experimental Cancer Research, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein (UKSH) Campus Kiel, Arnold-Heller-Str. 3, Building 17, 24105, Kiel, Germany
| | - Daniela Esser
- Group Medical Systems Biology, Institute for Experimental Medicine, Michaelisstr. 5, Building 17, 24105, Kiel, Germany
| | - Sascha Schäuble
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11A, 07745, Jena, Germany
| | - Peter Großmann
- Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute (HKI), Beutenbergstraße 11A, 07745, Jena, Germany
| | - Georgios Marinos
- Group Medical Systems Biology, Institute for Experimental Medicine, Michaelisstr. 5, Building 17, 24105, Kiel, Germany
| | - Robert Häsler
- Group Molecular Cell Biology, Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Rosalind-Franklin-Straße 12, 24105, Kiel, Germany
| | - Wolfgang Mikulits
- Department of Medicine I, Division: Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Dieter Saur
- II. Medizinische Klinik und Poliklinik, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
| | - Christoph Kaleta
- Group Medical Systems Biology, Institute for Experimental Medicine, Michaelisstr. 5, Building 17, 24105, Kiel, Germany
| | - Heiner Schäfer
- Group Inflammatory Carcinogenesis, Institute for Experimental Cancer Research, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein (UKSH) Campus Kiel, Arnold-Heller-Str. 3, Building 17, 24105, Kiel, Germany
| | - Susanne Sebens
- Group Inflammatory Carcinogenesis, Institute for Experimental Cancer Research, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein (UKSH) Campus Kiel, Arnold-Heller-Str. 3, Building 17, 24105, Kiel, Germany.
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Aden K, Bartsch K, Dahl J, Reijns MA, Esser D, Sheibani-Tezerji R, Sinha A, Wottawa F, Ito G, Mishra N, Knittler K, Burkholder A, Welz L, van Es J, Tran F, Lipinski S, Kakavand N, Boeger C, Lucius R, von Schoenfels W, Schafmayer C, Lenk L, Chalaris A, Clevers H, Röcken C, Kaleta C, Rose-John S, Schreiber S, Kunkel T, Rabe B, Rosenstiel P. Epithelial RNase H2 Maintains Genome Integrity and Prevents Intestinal Tumorigenesis in Mice. Gastroenterology 2019; 156:145-159.e19. [PMID: 30273559 PMCID: PMC6311085 DOI: 10.1053/j.gastro.2018.09.047] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 09/06/2018] [Accepted: 09/24/2018] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS RNase H2 is a holoenzyme, composed of 3 subunits (ribonuclease H2 subunits A, B, and C), that cleaves RNA:DNA hybrids and removes mis-incorporated ribonucleotides from genomic DNA through ribonucleotide excision repair. Ribonucleotide incorporation by eukaryotic DNA polymerases occurs during every round of genome duplication and produces the most frequent type of naturally occurring DNA lesion. We investigated whether intestinal epithelial proliferation requires RNase H2 function and whether RNase H2 activity is disrupted during intestinal carcinogenesis. METHODS We generated mice with epithelial-specific deletion of ribonuclease H2 subunit B (H2bΔIEC) and mice that also had deletion of tumor-suppressor protein p53 (H2b/p53ΔIEC); we compared phenotypes with those of littermate H2bfl/fl or H2b/p53fl/fl (control) mice at young and old ages. Intestinal tissues were collected and analyzed by histology. We isolated epithelial cells, generated intestinal organoids, and performed RNA sequence analyses. Mutation signatures of spontaneous tumors from H2b/p53ΔIEC mice were characterized by exome sequencing. We collected colorectal tumor specimens from 467 patients, measured levels of ribonuclease H2 subunit B, and associated these with patient survival times and transcriptome data. RESULTS The H2bΔIEC mice had DNA damage to intestinal epithelial cells and proliferative exhaustion of the intestinal stem cell compartment compared with controls and H2b/p53ΔIEC mice. However, H2b/p53ΔIEC mice spontaneously developed small intestine and colon carcinomas. DNA from these tumors contained T>G base substitutions at GTG trinucleotides. Analyses of transcriptomes of human colorectal tumors associated lower levels of RNase H2 with shorter survival times. CONCLUSIONS In analyses of mice with disruption of the ribonuclease H2 subunit B gene and colorectal tumors from patients, we provide evidence that RNase H2 functions as a colorectal tumor suppressor. H2b/p53ΔIEC mice can be used to study the roles of RNase H2 in tissue-specific carcinogenesis.
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Affiliation(s)
- Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany; First Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany.
| | - Kareen Bartsch
- Institute of Biochemistry, Christian-Albrechts-University, Kiel, Germany
| | - Joseph Dahl
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, North Carolina
| | - Martin A.M. Reijns
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Daniela Esser
- Institute for Experimental Medicine, Christian-Albrechts-University, Kiel, Germany
| | - Raheleh Sheibani-Tezerji
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Anupam Sinha
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Felix Wottawa
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Go Ito
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Neha Mishra
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Katharina Knittler
- Institute of Biochemistry, Christian-Albrechts-University, Kiel, Germany
| | - Adam Burkholder
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, North Carolina
| | - Lina Welz
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Johan van Es
- Hubrecht Institute/Royal Netherlands Academy of Arts and Sciences, Princess Maxima Centre and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany,First Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Simone Lipinski
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Nassim Kakavand
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Christine Boeger
- Department of Pathology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ralph Lucius
- Anatomical Institute, Christian-Albrechts-University, Kiel, Germany
| | | | - Clemens Schafmayer
- Department of Surgery, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Lennart Lenk
- Department of Pediatrics, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Athena Chalaris
- Institute of Biochemistry, Christian-Albrechts-University, Kiel, Germany
| | - Hans Clevers
- Hubrecht Institute/Royal Netherlands Academy of Arts and Sciences, Princess Maxima Centre and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Christoph Röcken
- Department of Pathology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Christoph Kaleta
- Institute for Experimental Medicine, Christian-Albrechts-University, Kiel, Germany
| | - Stefan Rose-John
- Institute of Biochemistry, Christian-Albrechts-University, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany,First Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Thomas Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, North Carolina
| | - Björn Rabe
- Institute of Biochemistry, Christian-Albrechts-University, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Kiel, Germany
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Witting M, Hastings J, Rodriguez N, Joshi CJ, Hattwell JPN, Ebert PR, van Weeghel M, Gao AW, Wakelam MJO, Houtkooper RH, Mains A, Le Novère N, Sadykoff S, Schroeder F, Lewis NE, Schirra HJ, Kaleta C, Casanueva O. Modeling Meets Metabolomics-The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans. Front Mol Biosci 2018; 5:96. [PMID: 30488036 PMCID: PMC6246695 DOI: 10.3389/fmolb.2018.00096] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/22/2018] [Indexed: 02/05/2023] Open
Abstract
Metabolism is one of the attributes of life and supplies energy and building blocks to organisms. Therefore, understanding metabolism is crucial for the understanding of complex biological phenomena. Despite having been in the focus of research for centuries, our picture of metabolism is still incomplete. Metabolomics, the systematic analysis of all small molecules in a biological system, aims to close this gap. In order to facilitate such investigations a blueprint of the metabolic network is required. Recently, several metabolic network reconstructions for the model organism Caenorhabditis elegans have been published, each having unique features. We have established the WormJam Community to merge and reconcile these (and other unpublished models) into a single consensus metabolic reconstruction. In a series of workshops and annotation seminars this model was refined with manual correction of incorrect assignments, metabolite structure and identifier curation as well as addition of new pathways. The WormJam consensus metabolic reconstruction represents a rich data source not only for in silico network-based approaches like flux balance analysis, but also for metabolomics, as it includes a database of metabolites present in C. elegans, which can be used for annotation. Here we present the process of model merging, correction and curation and give a detailed overview of the model. In the future it is intended to expand the model toward different tissues and put special emphasizes on lipid metabolism and secondary metabolism including ascaroside metabolism in accordance to their central role in C. elegans physiology.
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Affiliation(s)
- Michael Witting
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Neuherberg, Germany
- Chair of Analytical Food Chemistry, Technische Universtität München, Freising, Germany
| | - Janna Hastings
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
| | - Nicolas Rodriguez
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
| | - Chintan J. Joshi
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
| | - Jake P. N. Hattwell
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Paul R. Ebert
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Michel van Weeghel
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Arwen W. Gao
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | | | - Riekelt H. Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology and Metabolism, Amsterdam Cardiovascular Sciences, Amsterdam, Netherlands
| | - Abraham Mains
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
| | - Nicolas Le Novère
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
| | - Sean Sadykoff
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
| | | | - Nathan E. Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States
- Novo Nordisk Foundation Center for Biosustainability at University of California, San Diego, La Jolla, CA, United States
| | | | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Olivia Casanueva
- Epigenetics Department, Babraham Institute, Cambridge, United Kingdom
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35
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Krogh TJ, Møller-Jensen J, Kaleta C. Impact of Chromosomal Architecture on the Function and Evolution of Bacterial Genomes. Front Microbiol 2018; 9:2019. [PMID: 30210483 PMCID: PMC6119826 DOI: 10.3389/fmicb.2018.02019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 08/09/2018] [Indexed: 12/14/2022] Open
Abstract
The bacterial nucleoid is highly condensed and forms compartment-like structures within the cell. Much attention has been devoted to investigating the dynamic topology and organization of the nucleoid. In contrast, the specific nucleoid organization, and the relationship between nucleoid structure and function is often neglected with regard to importance for adaption to changing environments and horizontal gene acquisition. In this review, we focus on the structure-function relationship in the bacterial nucleoid. We provide an overview of the fundamental properties that shape the chromosome as a structured yet dynamic macromolecule. These fundamental properties are then considered in the context of the living cell, with focus on how the informational flow affects the nucleoid structure, which in turn impacts on the genetic output. Subsequently, the dynamic living nucleoid will be discussed in the context of evolution. We will address how the acquisition of foreign DNA impacts nucleoid structure, and conversely, how nucleoid structure constrains the successful and sustainable chromosomal integration of novel DNA. Finally, we will discuss current challenges and directions of research in understanding the role of chromosomal architecture in bacterial survival and adaptation.
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Affiliation(s)
- Thøger J Krogh
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Jakob Møller-Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Christoph Kaleta
- Institute of Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
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36
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Dühring S, Ewald J, Germerodt S, Kaleta C, Dandekar T, Schuster S. Modelling the host-pathogen interactions of macrophages and Candida albicans using Game Theory and dynamic optimization. J R Soc Interface 2018; 14:rsif.2017.0095. [PMID: 28701506 PMCID: PMC5550964 DOI: 10.1098/rsif.2017.0095] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/16/2017] [Indexed: 12/21/2022] Open
Abstract
The release of fungal cells following macrophage phagocytosis, called non-lytic expulsion, is reported for several fungal pathogens. On one hand, non-lytic expulsion may benefit the fungus in escaping the microbicidal environment of the phagosome. On the other hand, the macrophage could profit in terms of avoiding its own lysis and being able to undergo proliferation. To analyse the causes of non-lytic expulsion and the relevance of macrophage proliferation in the macrophage–Candida albicans interaction, we employ Evolutionary Game Theory and dynamic optimization in a sequential manner. We establish a game-theoretical model describing the different strategies of the two players after phagocytosis. Depending on the parameter values, we find four different Nash equilibria and determine the influence of the systems state of the host upon the game. As our Nash equilibria are a direct consequence of the model parameterization, we can depict several biological scenarios. A parameter region, where the host response is robust against the fungal infection, is determined. We further apply dynamic optimization to analyse whether macrophage mitosis is relevant in the host–pathogen interaction of macrophages and C. albicans. For this, we study the population dynamics of the macrophage–C. albicans interactions and the corresponding optimal controls for the macrophages, indicating the best macrophage strategy of switching from proliferation to attacking fungal cells.
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Affiliation(s)
- Sybille Dühring
- Department of Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany
| | - Jan Ewald
- Department of Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany
| | - Sebastian Germerodt
- Department of Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Thomas Dandekar
- Biocenter, Department of Bioinformatics, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Friedrich-Schiller-University Jena, Jena, Germany
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37
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Aramillo Irizar P, Schäuble S, Esser D, Groth M, Frahm C, Priebe S, Baumgart M, Hartmann N, Marthandan S, Menzel U, Müller J, Schmidt S, Ast V, Caliebe A, König R, Krawczak M, Ristow M, Schuster S, Cellerino A, Diekmann S, Englert C, Hemmerich P, Sühnel J, Guthke R, Witte OW, Platzer M, Ruppin E, Kaleta C. Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly. Nat Commun 2018; 9:327. [PMID: 29382830 PMCID: PMC5790807 DOI: 10.1038/s41467-017-02395-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 11/27/2017] [Indexed: 02/07/2023] Open
Abstract
Disease epidemiology during ageing shows a transition from cancer to degenerative chronic disorders as dominant contributors to mortality in the old. Nevertheless, it has remained unclear to what extent molecular signatures of ageing reflect this phenomenon. Here we report on the identification of a conserved transcriptomic signature of ageing based on gene expression data from four vertebrate species across four tissues. We find that ageing-associated transcriptomic changes follow trajectories similar to the transcriptional alterations observed in degenerative ageing diseases but are in opposite direction to the transcriptomic alterations observed in cancer. We confirm the existence of a similar antagonism on the genomic level, where a majority of shared risk alleles which increase the risk of cancer decrease the risk of chronic degenerative disorders and vice versa. These results reveal a fundamental trade-off between cancer and degenerative ageing diseases that sheds light on the pronounced shift in their epidemiology during ageing. Ageing is associated with a pronounced shift in mortality from cancer to degenerative diseases. Here, the authors show that in concordance with this shift, conserved transcriptional alterations during ageing across four vertebrates align with degenerative diseases but are opposite to those in cancer.
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Affiliation(s)
- Peer Aramillo Irizar
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, D-24105, Kiel, Germany
| | - Sascha Schäuble
- Jena University Language and Information Engineering Lab, Friedrich-Schiller-University Jena, D-07743, Jena, Germany.,GerontoSys JenAge Consortium, D-07745, Jena, Germany
| | - Daniela Esser
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, D-24105, Kiel, Germany
| | - Marco Groth
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Genome Analysis Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Christiane Frahm
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Hans Berger Department of Neurology, Jena University Hospital, D-07747, Jena, Germany
| | - Steffen Priebe
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, D-07745, Jena, Germany
| | - Mario Baumgart
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Biology of Ageing Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Nils Hartmann
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Molecular Genetics Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Shiva Marthandan
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Imageing Facility, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Uwe Menzel
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, D-07745, Jena, Germany
| | - Jule Müller
- Hans Berger Department of Neurology, Jena University Hospital, D-07747, Jena, Germany
| | - Silvio Schmidt
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Hans Berger Department of Neurology, Jena University Hospital, D-07747, Jena, Germany
| | - Volker Ast
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, D-07747, Jena, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, D-07745, Jena, Germany
| | - Amke Caliebe
- Institute for Medical Informatics and Statistics, Christian-Albrechts-University Kiel, D-24105, Kiel, Germany
| | - Rainer König
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, D-07747, Jena, Germany.,Network Modeling, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knöll Institute, D-07745, Jena, Germany
| | - Michael Krawczak
- Institute for Medical Informatics and Statistics, Christian-Albrechts-University Kiel, D-24105, Kiel, Germany
| | - Michael Ristow
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Energy Metabolism Laboratory, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach/Zürich, CH-8603, Switzerland
| | - Stefan Schuster
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Department of Bioinformatics, Friedrich-Schiller-University Jena, D-07743, Jena, Germany
| | - Alessandro Cellerino
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Biology of Ageing Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany.,Laboratory of Neurobiology, Scuola Normale Superiore, University of Pisa, I-56100, Pisa, Italy
| | - Stephan Diekmann
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Molecular Biology Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Christoph Englert
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Molecular Genetics Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany.,Faculty of Biology and Pharmacy, Friedrich-Schiller-University Jena, D-07743, Jena, Germany
| | - Peter Hemmerich
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Imageing Facility, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Jürgen Sühnel
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Biocomputing Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Reinhard Guthke
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology-Hans-Knöll-Institute, D-07745, Jena, Germany
| | - Otto W Witte
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Hans Berger Department of Neurology, Jena University Hospital, D-07747, Jena, Germany
| | - Matthias Platzer
- GerontoSys JenAge Consortium, D-07745, Jena, Germany.,Genome Analysis Lab, Leibniz Institute on Aging-Fritz-Lipmann-Institute, D-07745, Jena, Germany
| | - Eytan Ruppin
- Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute of Experimental Medicine, Christian-Albrechts-University Kiel, D-24105, Kiel, Germany. .,GerontoSys JenAge Consortium, D-07745, Jena, Germany.
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38
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Lück A, Klimmasch L, Großmann P, Germerodt S, Kaleta C. Computational Investigation of Environment-Noise Interaction in Single-Cell Organisms: The Merit of Expression Stochasticity Depends on the Quality of Environmental Fluctuations. Sci Rep 2018; 8:333. [PMID: 29321537 PMCID: PMC5762857 DOI: 10.1038/s41598-017-17441-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/27/2017] [Indexed: 11/23/2022] Open
Abstract
Organisms need to adapt to changing environments and they do so by using a broad spectrum of strategies. These strategies include finding the right balance between expressing genes before or when they are needed, and adjusting the degree of noise inherent in gene expression. We investigated the interplay between different nutritional environments and the inhabiting organisms’ metabolic and genetic adaptations by applying an evolutionary algorithm to an agent-based model of a concise bacterial metabolism. Our results show that constant environments and rapidly fluctuating environments produce similar adaptations in the organisms, making the predictability of the environment a major factor in determining optimal adaptation. We show that exploitation of expression noise occurs only in some types of fluctuating environment and is strongly dependent on the quality and availability of nutrients: stochasticity is generally detrimental in fluctuating environments and beneficial only at equal periods of nutrient availability and above a threshold environmental richness. Moreover, depending on the availability and nutritional value of nutrients, nutrient-dependent and stochastic expression are both strategies used to deal with environmental changes. Overall, we comprehensively characterize the interplay between the quality and periodicity of an environment and the resulting optimal deterministic and stochastic regulation strategies of nutrient-catabolizing pathways.
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Affiliation(s)
- Anja Lück
- Department of Bioinformatics, Friedrich Schiller University, Jena, 07743, Germany
| | - Lukas Klimmasch
- Research Group Theoretical Systems Biology, Friedrich Schiller University, Jena, 07743, Germany
| | - Peter Großmann
- Department of Bioinformatics, Friedrich Schiller University, Jena, 07743, Germany
| | - Sebastian Germerodt
- Department of Bioinformatics, Friedrich Schiller University, Jena, 07743, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University, Kiel, 24105, Germany.
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39
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Großmann P, Lück A, Kaleta C. Model-based genome-wide determination of RNA chain elongation rates in Escherichia coli. Sci Rep 2017; 7:17213. [PMID: 29222445 PMCID: PMC5722913 DOI: 10.1038/s41598-017-17408-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/24/2017] [Indexed: 11/17/2022] Open
Abstract
Dynamics in the process of transcription are often simplified, yet they play an important role in transcript folding, translation into functional protein and DNA supercoiling. While the modulation of the speed of transcription of individual genes and its role in regulation and proper protein folding has been analyzed in depth, the functional relevance of differences in transcription speeds as well as the factors influencing it have not yet been determined on a genome-wide scale. Here we determined transcription speeds for the majority of E. coli genes based on experimental data. We find large differences in transcription speed between individual genes and a strong influence of both cellular location as well as the relative importance of genes for cellular function on transcription speeds. Investigating factors influencing transcription speeds we observe both codon composition as well as factors associated to DNA topology as most important factors influencing transcription speeds. Moreover, we show that differences in transcription speeds are sufficient to explain the timing of regulatory responses during environmental shifts and highlight the importance of the consideration of transcription speeds in the design of experiments measuring transcriptomic responses to perturbations.
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Affiliation(s)
- Peter Großmann
- Research Group Theoretical Systems Biology, Friedrich-Schiller-University Jena, Ernst-Abbe-Platz 2, 07747, Jena, Germany
| | - Anja Lück
- Research Group Theoretical Systems Biology, Friedrich-Schiller-University Jena, Ernst-Abbe-Platz 2, 07747, Jena, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, c/o Transfusionsmedizin, Institut für Experimentelle Medizin, Christian-Albrechts-University Kiel, Michaelis-Straße 5, Haus 17, 24105, Kiel, Germany.
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40
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Häsler R, Sheibani-Tezerji R, Sinha A, Barann M, Rehman A, Esser D, Aden K, Knecht C, Brandt B, Nikolaus S, Schäuble S, Kaleta C, Franke A, Fretter C, Müller W, Hütt MT, Krawczak M, Schreiber S, Rosenstiel P. Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease. Gut 2017; 66:2087-2097. [PMID: 27694142 PMCID: PMC5749366 DOI: 10.1136/gutjnl-2016-311651] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 07/15/2016] [Accepted: 08/14/2016] [Indexed: 12/26/2022]
Abstract
OBJECTIVE An inadequate host response to the intestinal microbiota likely contributes to the manifestation and progression of human inflammatory bowel disease (IBD). However, molecular approaches to unravelling the nature of the defective crosstalk and its consequences for intestinal metabolic and immunological networks are lacking. We assessed the mucosal transcript levels, splicing architecture and mucosa-attached microbial communities of patients with IBD to obtain a comprehensive view of the underlying, hitherto poorly characterised interactions, and how these are altered in IBD. DESIGN Mucosal biopsies from Crohn's disease and patients with UC, disease controls and healthy individuals (n=63) were subjected to microbiome, transcriptome and splicing analysis, employing next-generation sequencing. The three data levels were integrated by different bioinformatic approaches, including systems biology-inspired network and pathway analysis. RESULTS Microbiota, host transcript levels and host splicing patterns were influenced most strongly by tissue differences, followed by the effect of inflammation. Both factors point towards a substantial disease-related alteration of metabolic processes. We also observed a strong enrichment of splicing events in inflamed tissues, accompanied by an alteration of the mucosa-attached bacterial taxa. Finally, we noted a striking uncoupling of the three molecular entities when moving from healthy individuals via disease controls to patients with IBD. CONCLUSIONS Our results provide strong evidence that the interplay between microbiome and host transcriptome, which normally characterises a state of intestinal homeostasis, is drastically perturbed in Crohn's disease and UC. Consequently, integrating multiple OMICs levels appears to be a promising approach to further disentangle the complexity of IBD.
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Affiliation(s)
- Robert Häsler
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | | | - Anupam Sinha
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Matthias Barann
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Ateequr Rehman
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Daniela Esser
- Institute for Experimental Medicine, Christian Albrechts University of Kiel, Kiel, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Carolin Knecht
- Institute of Medical Informatics and Statistics, Christian Albrechts University of Kiel, Kiel, Germany
| | - Berenice Brandt
- Department of General Internal Medicine, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Susanna Nikolaus
- Department of General Internal Medicine, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Sascha Schäuble
- Language and Information Engineering Lab, Friedrich-Schiller-University Jena, Jena, Germany
| | - Christoph Kaleta
- Institute for Experimental Medicine, Christian Albrechts University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Christoph Fretter
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Werner Müller
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Marc-Thorsten Hütt
- Department of Life Sciences and Chemistry, Jacobs University, Bremen, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian Albrechts University of Kiel, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany,Department of General Internal Medicine, University Hospital Schleswig-Holstein Campus Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
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41
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Sommer F, Rühlemann MC, Bang C, Höppner M, Rehman A, Kaleta C, Schmitt-Kopplin P, Dempfle A, Weidinger S, Ellinghaus E, Krauss-Etschmann S, Schmidt-Arras D, Aden K, Schulte D, Ellinghaus D, Schreiber S, Tholey A, Rupp J, Laudes M, Baines JF, Rosenstiel P, Franke A. Microbiomarkers in inflammatory bowel diseases: caveats come with caviar. Gut 2017; 66:1734-1738. [PMID: 28733278 PMCID: PMC5595102 DOI: 10.1136/gutjnl-2016-313678] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/07/2017] [Accepted: 06/08/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Felix Sommer
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | | | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Marc Höppner
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Ateequr Rehman
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Christoph Kaleta
- Institute for Experimental Medicine, Christian Albrechts University of Kiel, Kiel, Germany
| | - Phillippe Schmitt-Kopplin
- Helmholtz Zentrum München, Research Unit Analytical BioGeoChemistry, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Astrid Dempfle
- Institute of Medical Informatics and Statistics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Stephan Weidinger
- Department of Dermatology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Susanne Krauss-Etschmann
- Institute for Experimental Medicine, Christian Albrechts University of Kiel, Kiel, Germany,Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
| | - Dirk Schmidt-Arras
- Institute of Biochemistry, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Dominik Schulte
- Clinic of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany,Clinic of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Andreas Tholey
- Institute for Experimental Medicine, Christian Albrechts University of Kiel, Kiel, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lubeck, Lubeck, Germany
| | - Matthias Laudes
- Clinic of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | - John F Baines
- Institute for Experimental Medicine, Christian Albrechts University of Kiel, Kiel, Germany,Evolutionary Genomics, Max Planck Institute for Evolutionary Biology, Plon, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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42
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Hastings J, Mains A, Artal-Sanz M, Bergmann S, Braeckman BP, Bundy J, Cabreiro F, Dobson P, Ebert P, Hattwell J, Hefzi H, Houtkooper RH, Jelier R, Joshi C, Kothamachu VB, Lewis N, Lourenço AB, Nie Y, Norvaisas P, Pearce J, Riccio C, Rodriguez N, Santermans T, Scarcia P, Schirra HJ, Sheng M, Smith R, Suriyalaksh M, Towbin B, Tuli MA, van Weeghel M, Weinkove D, Zečić A, Zimmermann J, le Novère N, Kaleta C, Witting M, Casanueva O. WormJam: A consensusC. elegansMetabolic Reconstruction and Metabolomics Community and Workshop Series. Worm 2017. [PMCID: PMC5612476 DOI: 10.1080/21624054.2017.1373939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Janna Hastings
- Epigenetics, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Abraham Mains
- Epigenetics, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Marta Artal-Sanz
- Developmental Biology, Andalusian Center for Developmental Biology. Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, Seville, Spain
| | - Sven Bergmann
- Computational Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Jake Bundy
- Computational and Systems Medicine, Imperial College London, London, UK
| | - Filipe Cabreiro
- Structural and Molecular Biology, University College London, London, UK
| | - Paul Dobson
- School of Computer Science, University of Manchester, Manchester, UK
| | - Paul Ebert
- School of Biological Sciences, University of Queensland, Queensland, Australia
| | - Jake Hattwell
- Centre for Advanced Imaging, University of Queensland, Queensland, Australia
| | - Hooman Hefzi
- Department of Bioengineering, Novo Nordisk Center for Biosustainability at UC San Diego, University of California, San Diego, USA
| | - Riekelt H. Houtkooper
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, Amsterdam, Netherlands
| | - Rob Jelier
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Chintan Joshi
- Department of Pediatrics, Novo Nordisk Center for Biosustainability at UC San Diego, University of California, San Diego, USA
| | | | - Nathan Lewis
- Department of Pediatrics, Novo Nordisk Center for Biosustainability at UC San Diego, University of California, San Diego, USA
| | - Artur Bastos Lourenço
- Developmental Biology, Andalusian Center for Developmental Biology. Consejo Superior de Investigaciones Científicas/Junta de Andalucia/Universidad Pablo de Olavide, Seville, Spain
| | - Yu Nie
- School of Human and Life Sciences, Canterbury Christ Church University, Canterbury, UK
| | - Povilas Norvaisas
- Structural and Molecular Biology, University College London, London, UK
| | - Juliette Pearce
- Epigenetics, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | | | - Nicolas Rodriguez
- Signalling, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Toon Santermans
- Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium
| | - Pasquale Scarcia
- Dep. Biosciences Biotechnologies Biopharmaceutics, University of Bari, Bari, Italy
| | | | | | - Reuben Smith
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, Amsterdam, Netherlands
| | | | | | | | - Michel van Weeghel
- Epigenetics, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - David Weinkove
- Department of Biosciences, Durham University, Durham, UK
| | - Aleksandra Zečić
- Computational Biology, University of Lausanne, Lausanne, Switzerland
| | | | - Nicolas le Novère
- Signalling, Babraham Institute, Babraham Research Campus, Cambridge, UK
| | - Christoph Kaleta
- Medical Systems Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Michael Witting
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum Muenchen, Muenchen, Germany
| | - Olivia Casanueva
- Epigenetics, Babraham Institute, Babraham Research Campus, Cambridge, UK
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43
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Ewald J, Bartl M, Dandekar T, Kaleta C. Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism. PLoS Comput Biol 2017; 13:e1005371. [PMID: 28212377 PMCID: PMC5315294 DOI: 10.1371/journal.pcbi.1005371] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 01/19/2017] [Indexed: 11/18/2022] Open
Abstract
A precise and rapid adjustment of fluxes through metabolic pathways is crucial for organisms to prevail in changing environmental conditions. Based on this reasoning, many guiding principles that govern the evolution of metabolic networks and their regulation have been uncovered. To this end, methods from dynamic optimization are ideally suited since they allow to uncover optimality principles behind the regulation of metabolic networks. We used dynamic optimization to investigate the influence of toxic intermediates in connection with the efficiency of enzymes on the regulation of a linear metabolic pathway. Our results predict that transcriptional regulation favors the control of highly efficient enzymes with less toxic upstream intermediates to reduce accumulation of toxic downstream intermediates. We show that the derived optimality principles hold by the analysis of the interplay between intermediate toxicity and pathway regulation in the metabolic pathways of over 5000 sequenced prokaryotes. Moreover, using the lipopolysaccharide biosynthesis in Escherichia coli as an example, we show how knowledge about the relation of regulation, kinetic efficiency and intermediate toxicity can be used to identify drug targets, which control endogenous toxic metabolites and prevent microbial growth. Beyond prokaryotes, we discuss the potential of our findings for the development of antifungal drugs.
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Affiliation(s)
- Jan Ewald
- Research Group Theoretical Systems Biology, Department of Bioinformatics, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Martin Bartl
- Research Group Theoretical Systems Biology, Department of Bioinformatics, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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44
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Germerodt S, Bohl K, Lück A, Pande S, Schröter A, Kaleta C, Schuster S, Kost C. Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities. PLoS Comput Biol 2016; 12:e1004986. [PMID: 27314840 PMCID: PMC4912067 DOI: 10.1371/journal.pcbi.1004986] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 05/16/2016] [Indexed: 11/21/2022] Open
Abstract
Bacterial communities are taxonomically highly diverse, yet the mechanisms that maintain this diversity remain poorly understood. We hypothesized that an obligate and mutual exchange of metabolites, as is very common among bacterial cells, could stabilize different genotypes within microbial communities. To test this, we developed a cellular automaton to model interactions among six empirically characterized genotypes that differ in their ability and propensity to produce amino acids. By systematically varying intrinsic (i.e. benefit-to-cost ratio) and extrinsic parameters (i.e. metabolite diffusion level, environmental amino acid availability), we show that obligate cross-feeding of essential metabolites is selected for under a broad range of conditions. In spatially structured environments, positive assortment among cross-feeders resulted in the formation of cooperative clusters, which limited exploitation by non-producing auxotrophs, yet allowed them to persist at the clusters' periphery. Strikingly, cross-feeding helped to maintain genotypic diversity within populations, while amino acid supplementation to the environment decoupled obligate interactions and favored auxotrophic cells that saved amino acid production costs over metabolically autonomous prototrophs. Together, our results suggest that spatially structured environments and limited nutrient availabilities should facilitate the evolution of metabolic interactions, which can help to maintain genotypic diversity within natural microbial populations.
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Affiliation(s)
| | - Katrin Bohl
- Department of Bioinformatics, Friedrich Schiller University Jena, Germany
- Research Group Theoretical Systems Biology, Friedrich Schiller University Jena, Germany
| | - Anja Lück
- Department of Bioinformatics, Friedrich Schiller University Jena, Germany
- Research Group Theoretical Systems Biology, Friedrich Schiller University Jena, Germany
| | - Samay Pande
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Anja Schröter
- Department of Bioinformatics, Friedrich Schiller University Jena, Germany
| | - Christoph Kaleta
- Research Group Theoretical Systems Biology, Friedrich Schiller University Jena, Germany
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Friedrich Schiller University Jena, Germany
| | - Christian Kost
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
- Department of Ecology and Evolution, School of Biology/Chemistry, Osnabrück University, Germany
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45
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Gebauer J, Gentsch C, Mansfeld J, Schmeißer K, Waschina S, Brandes S, Klimmasch L, Zamboni N, Zarse K, Schuster S, Ristow M, Schäuble S, Kaleta C. A Genome-Scale Database and Reconstruction of Caenorhabditis elegans Metabolism. Cell Syst 2016; 2:312-22. [PMID: 27211858 DOI: 10.1016/j.cels.2016.04.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 04/20/2016] [Accepted: 04/27/2016] [Indexed: 12/23/2022]
Abstract
We present a genome-scale model of Caenorhabditis elegans metabolism along with the public database ElegCyc (http://elegcyc.bioinf.uni-jena.de:1100), which represents a reference for metabolic pathways in the worm and allows for the visualization as well as analysis of omics datasets. Our model reflects the metabolic peculiarities of C. elegans that make it distinct from other higher eukaryotes and mammals, including mice and humans. We experimentally verify one of these peculiarities by showing that the lifespan-extending effect of L-tryptophan supplementation is dose dependent (hormetic). Finally, we show the utility of our model for analyzing omics datasets through predicting changes in amino acid concentrations after genetic perturbations and analyzing metabolic changes during normal aging as well as during two distinct, reactive oxygen species (ROS)-related lifespan-extending treatments. Our analyses reveal a notable similarity in metabolic adaptation between distinct lifespan-extending interventions and point to key pathways affecting lifespan in nematodes.
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Affiliation(s)
- Juliane Gebauer
- Research Group Theoretical Systems Biology, Friedrich Schiller-University (FSU) Jena, 07745 Jena, Germany; Department of Bioinformatics, Friedrich Schiller-University (FSU) Jena, 07743 Jena, Germany
| | - Christoph Gentsch
- Research Group Theoretical Systems Biology, Friedrich Schiller-University (FSU) Jena, 07745 Jena, Germany
| | - Johannes Mansfeld
- Department of Human Nutrition, Friedrich Schiller-University Jena (FSU), 07743 Jena, Germany; Energy Metabolism Laboratory, Swiss Federal Institute of Technology (ETH) Zürich, 8003 Zürich, Switzerland
| | - Kathrin Schmeißer
- Department of Human Nutrition, Friedrich Schiller-University Jena (FSU), 07743 Jena, Germany
| | - Silvio Waschina
- Research Group Theoretical Systems Biology, Friedrich Schiller-University (FSU) Jena, 07745 Jena, Germany; Research Group Medical Systems Biology, Christian-Albrechts-University Kiel, 24105 Kiel, Germany
| | - Susanne Brandes
- Department of Bioinformatics, Friedrich Schiller-University (FSU) Jena, 07743 Jena, Germany; Applied Systems Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745Jena, Germany
| | - Lukas Klimmasch
- Department of Bioinformatics, Friedrich Schiller-University (FSU) Jena, 07743 Jena, Germany
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland
| | - Kim Zarse
- Department of Human Nutrition, Friedrich Schiller-University Jena (FSU), 07743 Jena, Germany; Energy Metabolism Laboratory, Swiss Federal Institute of Technology (ETH) Zürich, 8003 Zürich, Switzerland
| | - Stefan Schuster
- Department of Bioinformatics, Friedrich Schiller-University (FSU) Jena, 07743 Jena, Germany
| | - Michael Ristow
- Department of Human Nutrition, Friedrich Schiller-University Jena (FSU), 07743 Jena, Germany; Energy Metabolism Laboratory, Swiss Federal Institute of Technology (ETH) Zürich, 8003 Zürich, Switzerland
| | - Sascha Schäuble
- Research Group Theoretical Systems Biology, Friedrich Schiller-University (FSU) Jena, 07745 Jena, Germany; Jena University Language and Information Engineering Lab, Friedrich Schiller-University (FSU) Jena, 07743 Jena, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Christian-Albrechts-University Kiel, 24105 Kiel, Germany; Research Group Theoretical Systems Biology, Friedrich Schiller-University (FSU) Jena, 07745 Jena, Germany.
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46
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Waschina S, D'Souza G, Kost C, Kaleta C. Metabolic network architecture and carbon source determine metabolite production costs. FEBS J 2016; 283:2149-63. [PMID: 27029764 DOI: 10.1111/febs.13727] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 02/04/2016] [Accepted: 03/30/2016] [Indexed: 11/28/2022]
Abstract
Metabolism is essential to organismal life, because it provides energy and building block metabolites. Even though it is known that the biosynthesis of metabolites consumes a significant proportion of the resources available to a cell, the factors that determine their production costs remain less well understood. In this context, it is especially unclear how the nutritional environment affects the costs of metabolite production. Here, we use the amino acid metabolism of Escherichia coli as a model to show that the point at which a carbon source enters central metabolic pathways is a major determinant of individual metabolite production costs. Growth rates of auxotrophic genotypes, which in the presence of the required amino acid save biosynthetic costs, were compared to the growth rates that prototrophic cells achieved under the same conditions. The experimental results showed a strong concordance with computationally estimated biosynthetic costs, which allowed us, for the first time, to systematically quantify carbon source-dependent metabolite production costs. Thus, we demonstrate that the nutritional environment in combination with network architecture is an important but hitherto underestimated factor influencing biosynthetic costs and thus microbial growth. Our observations are highly relevant for the optimization of biotechnological processes as well as for understanding the ecology of microorganisms in their natural environments.
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Affiliation(s)
- Silvio Waschina
- Research Group Theoretical Systems Biology, Friedrich Schiller University Jena, Jena, Germany.,Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany.,Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Glen D'Souza
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Christian Kost
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Christoph Kaleta
- Research Group Theoretical Systems Biology, Friedrich Schiller University Jena, Jena, Germany.,Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
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47
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Mansfeld J, Urban N, Priebe S, Groth M, Frahm C, Hartmann N, Gebauer J, Ravichandran M, Dommaschk A, Schmeisser S, Kuhlow D, Monajembashi S, Bremer-Streck S, Hemmerich P, Kiehntopf M, Zamboni N, Englert C, Guthke R, Kaleta C, Platzer M, Sühnel J, Witte OW, Zarse K, Ristow M. Branched-chain amino acid catabolism is a conserved regulator of physiological ageing. Nat Commun 2015; 6:10043. [PMID: 26620638 PMCID: PMC4686672 DOI: 10.1038/ncomms10043] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 10/29/2015] [Indexed: 01/08/2023] Open
Abstract
Ageing has been defined as a global decline in physiological function depending on both environmental and genetic factors. Here we identify gene transcripts that are similarly regulated during physiological ageing in nematodes, zebrafish and mice. We observe the strongest extension of lifespan when impairing expression of the branched-chain amino acid transferase-1 (bcat-1) gene in C. elegans, which leads to excessive levels of branched-chain amino acids (BCAAs). We further show that BCAAs reduce a LET-363/mTOR-dependent neuro-endocrine signal, which we identify as DAF-7/TGFβ, and that impacts lifespan depending on its related receptors, DAF-1 and DAF-4, as well as ultimately on DAF-16/FoxO and HSF-1 in a cell-non-autonomous manner. The transcription factor HLH-15 controls and epistatically synergizes with BCAT-1 to modulate physiological ageing. Lastly and consistent with previous findings in rodents, nutritional supplementation of BCAAs extends nematodal lifespan. Taken together, BCAAs act as periphery-derived metabokines that induce a central neuro-endocrine response, culminating in extended healthspan.
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Affiliation(s)
- Johannes Mansfeld
- Energy Metabolism Laboratory, Swiss Federal Institute of Technology (ETH) Zurich, CH-8603 Zurich, Switzerland
- DFG Graduate School of Adaptive Stress Response #1715, D-07745 Jena, Germany
- Department of Human Nutrition, Institute of Nutrition, Friedrich-Schiller-University Jena, D-07743 Jena, Germany
- GerontoSysJenAge Consortium, BMBF 0315581, D-07745 Jena, Germany
| | - Nadine Urban
- Department of Human Nutrition, Institute of Nutrition, Friedrich-Schiller-University Jena, D-07743 Jena, Germany
| | - Steffen Priebe
- GerontoSysJenAge Consortium, BMBF 0315581, D-07745 Jena, Germany
- Biocomputing Group, Leibniz Institute on Aging—Fritz Lipmann Institute, D-07745 Jena, Germany
- Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, D-07745 Jena, Germany
| | - Marco Groth
- GerontoSysJenAge Consortium, BMBF 0315581, D-07745 Jena, Germany
- Genome Analysis, Leibniz Institute on Aging—Fritz Lipmann Institute, D-07745 Jena, Germany
| | - Christiane Frahm
- GerontoSysJenAge Consortium, BMBF 0315581, D-07745 Jena, Germany
- Hans Berger Department of Neurology, Jena University Hospital, D-07747 Jena, Germany
| | - Nils Hartmann
- GerontoSysJenAge Consortium, BMBF 0315581, D-07745 Jena, Germany
- Molecular Genetics, Leibniz Institute on Aging—Fritz Lipmann Institute, D-07745 Jena, Germany
| | - Juliane Gebauer
- GerontoSysJenAge Consortium, BMBF 0315581, D-07745 Jena, Germany
- Research Group Theoretical Systems Biology, Friedrich-Schiller-University Jena, D-07743 Jena, Germany
| | - Meenakshi Ravichandran
- Energy Metabolism Laboratory, Swiss Federal Institute of Technology (ETH) Zurich, CH-8603 Zurich, Switzerland
| | - Anne Dommaschk
- Department of Human Nutrition, Institute of Nutrition, Friedrich-Schiller-University Jena, D-07743 Jena, Germany
| | - Sebastian Schmeisser
- Department of Human Nutrition, Institute of Nutrition, Friedrich-Schiller-University Jena, D-07743 Jena, Germany
| | - Doreen Kuhlow
- Department of Human Nutrition, Institute of Nutrition, Friedrich-Schiller-University Jena, D-07743 Jena, Germany
- GerontoSysJenAge Consortium, BMBF 0315581, D-07745 Jena, Germany
- German Institute of Human Nutrition Potsdam-Rehbrücke, D-14558 Nuthetal, Germany
| | - Shamci Monajembashi
- Imaging Facility, Leibniz Institute on Aging—Fritz Lipmann Institute, D-07745 Jena, Germany
| | - Sibylle Bremer-Streck
- Institute of Clinical Chemistry and Laboratory Medicine, University of Jena, D-07743 Jena, Germany
| | - Peter Hemmerich
- GerontoSysJenAge Consortium, BMBF 0315581, D-07745 Jena, Germany
- Imaging Facility, Leibniz Institute on Aging—Fritz Lipmann Institute, D-07745 Jena, Germany
| | - Michael Kiehntopf
- Institute of Clinical Chemistry and Laboratory Medicine, University of Jena, D-07743 Jena, Germany
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, CH-8093 Zürich, Switzerland
| | - Christoph Englert
- GerontoSysJenAge Consortium, BMBF 0315581, D-07745 Jena, Germany
- Molecular Genetics, Leibniz Institute on Aging—Fritz Lipmann Institute, D-07745 Jena, Germany
- Faculty of Biology and Pharmacy, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Reinhard Guthke
- GerontoSysJenAge Consortium, BMBF 0315581, D-07745 Jena, Germany
- Systems Biology and Bioinformatics Group, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, D-07745 Jena, Germany
| | - Christoph Kaleta
- GerontoSysJenAge Consortium, BMBF 0315581, D-07745 Jena, Germany
- Research Group Theoretical Systems Biology, Friedrich-Schiller-University Jena, D-07743 Jena, Germany
- Faculty of Biology and Pharmacy, Friedrich-Schiller-University Jena, 07743 Jena, Germany
| | - Matthias Platzer
- GerontoSysJenAge Consortium, BMBF 0315581, D-07745 Jena, Germany
- Genome Analysis, Leibniz Institute on Aging—Fritz Lipmann Institute, D-07745 Jena, Germany
| | - Jürgen Sühnel
- GerontoSysJenAge Consortium, BMBF 0315581, D-07745 Jena, Germany
- Biocomputing Group, Leibniz Institute on Aging—Fritz Lipmann Institute, D-07745 Jena, Germany
| | - Otto W. Witte
- GerontoSysJenAge Consortium, BMBF 0315581, D-07745 Jena, Germany
- Hans Berger Department of Neurology, Jena University Hospital, D-07747 Jena, Germany
| | - Kim Zarse
- Energy Metabolism Laboratory, Swiss Federal Institute of Technology (ETH) Zurich, CH-8603 Zurich, Switzerland
- Department of Human Nutrition, Institute of Nutrition, Friedrich-Schiller-University Jena, D-07743 Jena, Germany
- GerontoSysJenAge Consortium, BMBF 0315581, D-07745 Jena, Germany
| | - Michael Ristow
- Energy Metabolism Laboratory, Swiss Federal Institute of Technology (ETH) Zurich, CH-8603 Zurich, Switzerland
- DFG Graduate School of Adaptive Stress Response #1715, D-07745 Jena, Germany
- Department of Human Nutrition, Institute of Nutrition, Friedrich-Schiller-University Jena, D-07743 Jena, Germany
- GerontoSysJenAge Consortium, BMBF 0315581, D-07745 Jena, Germany
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de Hijas-Liste GM, Balsa-Canto E, Ewald J, Bartl M, Li P, Banga JR, Kaleta C. Optimal programs of pathway control: dissecting the influence of pathway topology and feedback inhibition on pathway regulation. BMC Bioinformatics 2015; 16:163. [PMID: 25982966 PMCID: PMC4433072 DOI: 10.1186/s12859-015-0587-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/22/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Adjusting the capacity of metabolic pathways in response to rapidly changing environmental conditions is an important component of microbial adaptation strategies to stochastic environments. In this work, we use advanced dynamic optimization techniques combined with theoretical models to study which reactions in pathways are optimally targeted by regulatory interactions in order to minimize the regulatory effort that is required to adjust the flux through a complex metabolic network. Moreover, we analyze how constraints in the speed at which an organism can respond on a proteomic level influences these optimal targets of pathway control. RESULTS We find that limitations in protein biosynthetic rates have a strong influence. With increasing protein biosynthetic rates the regulatory effort targeting the initial enzyme in a pathway is reduced while the regulatory effort in the terminal enzyme is increased. Studying the impact of allosteric regulation for different pathway topologies, we find that the presence of feedback inhibition by products of metabolic pathways allows organisms to reduce the regulatory effort that is required to control a metabolic pathway in all cases. In a linear pathway this even leads to the case where the sole transcriptional regulatory control of the terminal enzyme is sufficient to control flux through the entire pathway. We confirm the utilization of these pathway regulation strategies through the large-scale analysis of transcriptional regulation in several hundred prokaryotes. CONCLUSIONS This work expands our knowledge about optimal programs of pathway control. Optimal targets of pathway control strongly depend on the speed at which proteins can be synthesized. Moreover, post-translational regulation such as allosteric regulation allows to strongly reduce the number of transcriptional regulatory interactions required to control a metabolic pathway across different pathway topologies.
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Affiliation(s)
- Gundián M de Hijas-Liste
- Bioprocess Engineering Group, Spanish National Research Council, IIM-CSIC, C/Eduardo Cabello 6, Vigo, 36208, Spain.
| | - Eva Balsa-Canto
- Bioprocess Engineering Group, Spanish National Research Council, IIM-CSIC, C/Eduardo Cabello 6, Vigo, 36208, Spain.
| | - Jan Ewald
- esearch Group Theoretical Systems Biology, Friedrich Schiller University Jena, Leutragraben 1,, Jena, 07743, Germany.
| | - Martin Bartl
- esearch Group Theoretical Systems Biology, Friedrich Schiller University Jena, Leutragraben 1,, Jena, 07743, Germany.
| | - Pu Li
- Simulation and Optimal Processes Group, Ilmenau University of Technology, P.O.Box 100565, Ilmenau, 98684, Germany.
| | - Julio R Banga
- Bioprocess Engineering Group, Spanish National Research Council, IIM-CSIC, C/Eduardo Cabello 6, Vigo, 36208, Spain.
| | - Christoph Kaleta
- esearch Group Theoretical Systems Biology, Friedrich Schiller University Jena, Leutragraben 1,, Jena, 07743, Germany. .,Research Group Medical Systems Biology, Christian-Albrechts-University Kiel, Brunswiker Straße 10, Kiel, 24105, Germany.
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Ewald J, Kötzing M, Bartl M, Kaleta C. Footprints of optimal protein assembly strategies in the operonic structure of prokaryotes. Metabolites 2015; 5:252-69. [PMID: 25927816 PMCID: PMC4495372 DOI: 10.3390/metabo5020252] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/27/2015] [Accepted: 04/24/2015] [Indexed: 11/23/2022] Open
Abstract
In this work, we investigate optimality principles behind synthesis strategies for protein complexes using a dynamic optimization approach. We show that the cellular capacity of protein synthesis has a strong influence on optimal synthesis strategies reaching from a simultaneous to a sequential synthesis of the subunits of a protein complex. Sequential synthesis is preferred if protein synthesis is strongly limited, whereas a simultaneous synthesis is optimal in situations with a high protein synthesis capacity. We confirm the predictions of our optimization approach through the analysis of the operonic organization of protein complexes in several hundred prokaryotes. Thereby, we are able to show that cellular protein synthesis capacity is a driving force in the dissolution of operons comprising the subunits of a protein complex. Thus, we also provide a tested hypothesis explaining why the subunits of many prokaryotic protein complexes are distributed across several operons despite the presumably less precise co-regulation.
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Affiliation(s)
- Jan Ewald
- Research Group Theoretical Systems Biology, Friedrich-Schiller-Universität Jena, Leutragraben 1, 07743 Jena, Germany.
| | - Martin Kötzing
- Research Group Theoretical Systems Biology, Friedrich-Schiller-Universität Jena, Leutragraben 1, 07743 Jena, Germany.
| | - Martin Bartl
- Research Group Theoretical Systems Biology, Friedrich-Schiller-Universität Jena, Leutragraben 1, 07743 Jena, Germany.
| | - Christoph Kaleta
- Research Group Theoretical Systems Biology, Friedrich-Schiller-Universität Jena, Leutragraben 1, 07743 Jena, Germany.
- Research Group Medical Systems Biology, Christian-Albrechts-Universität Kiel, Brunswiker Straße 10, 24105 Kiel, Germany.
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D'Souza G, Waschina S, Kaleta C, Kost C. Plasticity and epistasis strongly affect bacterial fitness after losing multiple metabolic genes. Evolution 2015; 69:1244-54. [DOI: 10.1111/evo.12640] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 02/27/2015] [Indexed: 01/28/2023]
Affiliation(s)
- Glen D'Souza
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry; Max Planck Institute for Chemical Ecology; 07745 Jena Germany
| | - Silvio Waschina
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry; Max Planck Institute for Chemical Ecology; 07745 Jena Germany
- Research Group Theoretical Systems Biology, Friedrich Schiller University of Jena; 07743 Jena Germany
| | - Christoph Kaleta
- Research Group Theoretical Systems Biology, Friedrich Schiller University of Jena; 07743 Jena Germany
- Research Group Medical Systems Biology, Institute for Experimental Medicine; Christian-Albrechts-University Kiel; 24105 Kiel Germany
| | - Christian Kost
- Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry; Max Planck Institute for Chemical Ecology; 07745 Jena Germany
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