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Bruse N, Jansen A, Gerretsen J, Rijbroek D, Wienholts K, Arron M, van Goor H, Ederveen THA, Pickkers P, Kox M. The gut microbiota composition has no predictive value for the endotoxin-induced immune response or development of endotoxin tolerance in humans invivo. Microbes Infect 2023; 25:105174. [PMID: 37348752 DOI: 10.1016/j.micinf.2023.105174] [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: 03/02/2023] [Revised: 05/23/2023] [Accepted: 06/16/2023] [Indexed: 06/24/2023]
Abstract
BACKGROUND It is largely unknown whether the gut microbiome regulates immune responses in humans. We determined relationships between the microbiota composition and immunological phenotypes in 108 healthy volunteers, using 16S sequencing, an ex vivo monocyte challenge model, and an in vivo challenge model of systemic inflammation induced by lipopolysaccharide (LPS). RESULTS Significant associations were observed between the microbiota composition and ex vivo monocytic cytokine responses induced by several stimuli, most notably IL-10 production induced by Pam3Cys, Pseudomonas aeruginosa and Candida albicans, although the explained variance was rather low (0.3-4.8%). Furthermore, a number of pairwise correlations between Blautia, Bacteroides and Prevotella genera and cytokine production induced by these stimuli were identified. LPS administration induced a profound transient in vivo inflammatory response. A second LPS challenge one week after the first resulted in a severely blunted response, reflecting endotoxin tolerance. However, no significant relationships between microbiota composition and in vivo parameters of inflammation or tolerance were found (explained variance ranging from 0.4 to 1.5%, ns). CONCLUSIONS The gut microbiota composition explains a limited degree of variance in ex vivo monocytic cytokine responses to several pathogenic stimuli, but no relationships with the LPS-induced in vivo immune response or tolerance was observed.
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Affiliation(s)
- Niklas Bruse
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Department of Intensive Care Medicine, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands; Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Aron Jansen
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Department of Intensive Care Medicine, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands; Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Jelle Gerretsen
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Department of Intensive Care Medicine, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands; Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Danielle Rijbroek
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Department of Intensive Care Medicine, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands; Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Kiedo Wienholts
- Department of Surgery, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands; Amsterdam UMC Location University of Amsterdam, Surgery, Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Therapy, De Boelelaan 1118, 1081 HV Amsterdam, the Netherlands
| | - Melissa Arron
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Department of Intensive Care Medicine, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands; Department of Surgery, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Harry van Goor
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Department of Intensive Care Medicine, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands; Department of Surgery, Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Thomas H A Ederveen
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Peter Pickkers
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Department of Intensive Care Medicine, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands; Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
| | - Matthijs Kox
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Department of Intensive Care Medicine, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands; Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands.
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Brix LM, Monleon D, Collado MC, Ederveen THA, Toksöz I, Bordes J, van Doeselaar L, Engelhardt C, Mitra S, Narayan S, Schmidt MV. Metabolic effects of early life stress and pre-pregnancy obesity are long-lasting and sex-specific in mice. Eur J Neurosci 2023. [PMID: 37203224 DOI: 10.1111/ejn.16047] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/12/2023] [Accepted: 05/17/2023] [Indexed: 05/20/2023]
Abstract
Early life stress (ELS) is associated with metabolic-, cognitive-, and psychiatric diseases and has a very high prevalence, highlighting the urgent need for a better understanding of the versatile physiological changes and identification of predictive biomarkers. In addition to programming the hypothalamic-pituitary-axis (HPA), ELS may also affect the gut microbiota and metabolome, opening up a promising research direction for identifying early biomarkers of ELS-induced (mal)adaptation. Other factors affecting these parameters include maternal metabolic status and diet, with maternal obesity shown to predispose offspring to later metabolic disease. The aim of the present study was to investigate the long-term effects of ELS and maternal obesity on the metabolic- and stress phenotype of rodent offspring. To this end, offspring of both sexes were subjected to an adverse early-life experience, and their metabolic and stress phenotypes were examined. In addition, we assessed whether a prenatal maternal and an adult high-fat diet (HFD) stressor further shape observed ELS-induced phenotypes. We show that ELS has long-term effects on male body weight (BW) across the lifespan, whereas females more successfully counteract ELS-induced weight loss, possibly by adapting their microbiota, thereby stabilizing a balanced metabolome. Furthermore, the metabolic effects of a maternal HFD on BW are exclusively triggered by a dietary challenge in adult offspring and are more pronounced in males than in females. Overall, our study suggests that the female microbiota protects against an ELS challenge, rendering them more resilient to additional maternal- and adult nutritional stressors than males.
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Affiliation(s)
- Lea M Brix
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS- TP), Munich, Germany
| | - Daniel Monleon
- Department of Pathology, Medicine and Odontology Faculty, University of Valencia, Valencia, Spain
- Health Research Institute INCLIVA/CIBERFES, Valencia, Spain
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National ResearchCouncil (IATA-CSIC), Valencia, Spain
| | - Thomas H A Ederveen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen Medical Center (Radboudumc), Nijmegen, The Netherlands
| | - Irmak Toksöz
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, Munich, Germany
| | - Joeri Bordes
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, Munich, Germany
| | - Lotte van Doeselaar
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS- TP), Munich, Germany
| | - Clara Engelhardt
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, Munich, Germany
| | - Shiladitya Mitra
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, Munich, Germany
| | - Sowmya Narayan
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry (IMPRS- TP), Munich, Germany
| | - Mathias V Schmidt
- Research Group Neurobiology of Stress Resilience, Max Planck Institute of Psychiatry, Munich, Germany
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3
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Agamah FE, Bayjanov JR, Niehues A, Njoku KF, Skelton M, Mazandu GK, Ederveen THA, Mulder N, Chimusa ER, 't Hoen PAC. Computational approaches for network-based integrative multi-omics analysis. Front Mol Biosci 2022; 9:967205. [PMID: 36452456 PMCID: PMC9703081 DOI: 10.3389/fmolb.2022.967205] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 06/12/2022] [Accepted: 10/20/2022] [Indexed: 08/27/2023] Open
Abstract
Advances in omics technologies allow for holistic studies into biological systems. These studies rely on integrative data analysis techniques to obtain a comprehensive view of the dynamics of cellular processes, and molecular mechanisms. Network-based integrative approaches have revolutionized multi-omics analysis by providing the framework to represent interactions between multiple different omics-layers in a graph, which may faithfully reflect the molecular wiring in a cell. Here we review network-based multi-omics/multi-modal integrative analytical approaches. We classify these approaches according to the type of omics data supported, the methods and/or algorithms implemented, their node and/or edge weighting components, and their ability to identify key nodes and subnetworks. We show how these approaches can be used to identify biomarkers, disease subtypes, crosstalk, causality, and molecular drivers of physiological and pathological mechanisms. We provide insight into the most appropriate methods and tools for research questions as showcased around the aetiology and treatment of COVID-19 that can be informed by multi-omics data integration. We conclude with an overview of challenges associated with multi-omics network-based analysis, such as reproducibility, heterogeneity, (biological) interpretability of the results, and we highlight some future directions for network-based integration.
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Affiliation(s)
- Francis E. Agamah
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI-Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jumamurat R. Bayjanov
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Anna Niehues
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Kelechi F. Njoku
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Michelle Skelton
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI-Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gaston K. Mazandu
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI-Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- African Institute for Mathematical Sciences, Cape Town, South Africa
| | - Thomas H. A. Ederveen
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI-Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Emile R. Chimusa
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, United Kingdom
| | - Peter A. C. 't Hoen
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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4
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Guzzardi MA, Ederveen THA, Rizzo F, Weisz A, Collado MC, Muratori F, Gross G, Alkema W, Iozzo P. Maternal pre-pregnancy overweight and neonatal gut bacterial colonization are associated with cognitive development and gut microbiota composition in pre-school-age offspring. Brain Behav Immun 2022; 100:311-320. [PMID: 34920092 DOI: 10.1016/j.bbi.2021.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 06/10/2021] [Revised: 11/03/2021] [Accepted: 12/11/2021] [Indexed: 12/17/2022] Open
Abstract
Maternal gestational obesity is a risk factor for offspring's neurodevelopment and later neuro-cognitive disorders. Altered gut microbiota composition has been found in patients with neurocognitive disorders, and in relation to maternal metabolic health. We explored the associations between gut microbiota and cognitive development during infancy, and their link with maternal obesity. In groups of children from the Pisa birth Cohort (PISAC), we analysed faecal microbiota composition by 16S rRNA marker gene sequencing of first-pass meconium samples and of faecal samples collected at age 3, 6, 12, 24, 36 months, and its relationship with maternal gestational obesity or diabetes, and with cognitive development, as measured from 6 to 60 months of age by the Griffith's Mental Development Scales. Gut microbiota composition in the first phases of life is dominated by Bifidobacteria (Actinobacteria phylum), with contribution of Escherichia/Shigella and Klebsiella genera (Proteobacteria phylum), whereas Firmicutes become more dominant at 36 months of age. Maternal overweight leads to lower abundance of Bifidobacterium, Blautia and Ruminococcus, and lower practical reasoning scores in the offspring at the age of 36 months. In the whole population, microbiota in the first-pass meconium samples shows much higher alpha diversity compared to later samples, and its composition, particularly Bifidobacterium and Veillonella abundances, correlates with practical reasoning scores at 60 months of age. Maternal overweight correlates with bacterial colonization and with the development of reasoning skills at pre-school age. Associations between neonatal gut colonization and later cognitive function provide new perspectives of primary (antenatal) prevention of neurodevelopmental disorders.
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Affiliation(s)
- Maria Angela Guzzardi
- Institute of Clinical Physiology (IFC), National Research Council (CNR), Pisa, Italy.
| | - Thomas H A Ederveen
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), Nijmegen, the Netherlands.
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana, University of Salerno, Baronissi, SA, Italy; Genome Research Center for Health (CRGS), Baronissi, SA, Italy.
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana, University of Salerno, Baronissi, SA, Italy; Genome Research Center for Health (CRGS), Baronissi, SA, Italy.
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology, National Research Council (IATA-CSIC), Valencia, Spain.
| | | | - Gabriele Gross
- Medical and Scientific Affairs, Nutrition, RB Mead Johnson Nutrition Institute, Nijmegen, the Netherlands.
| | - Wynand Alkema
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), Nijmegen, the Netherlands.
| | - Patricia Iozzo
- Institute of Clinical Physiology (IFC), National Research Council (CNR), Pisa, Italy.
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5
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Niehues H, van der Krieken DA, Ederveen THA, Jansen PAM, van Niftrik L, Mesman R, Netea MG, Smits JPH, Schalkwijk J, van den Bogaard EH, Zeeuwen PLJM. Antimicrobial late cornified envelope (LCE) proteins: the psoriasis risk factor LCE3B/C-del affects microbiota composition. J Invest Dermatol 2021; 142:1947-1955.e6. [PMID: 34942199 DOI: 10.1016/j.jid.2021.11.036] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 11/03/2021] [Accepted: 11/22/2021] [Indexed: 12/20/2022]
Abstract
Late cornified envelope (LCE) proteins are predominantly expressed in the skin and other cornified epithelia. Based on sequence similarity, this eighteen-member homologous gene family has been subdivided into six groups. The LCE3 proteins have been the focus of dermatological research, as the combined deletion of LCE3B and LCE3C genes (LCE3B/C-del) is a risk factor for psoriasis. We previously reported that LCE3B/C-del increases expression of the LCE3A gene and that LCE3 proteins exert antibacterial activity. In the current study we analyzed the antimicrobial properties of other family members and the role of LCE3B/C-del in modulation of microbiota composition of the skin and oral cavity. Differences in killing efficiency and specificity between the LCE proteins and their target microbes were found, and the amino acid content, rather than the order, of the well-conserved central domain of the LCE3A protein was found responsible for its antibacterial activity. In vivo, LCE3B/C-del correlated with a higher beta-diversity in the skin and oral microbiota. From these results we conclude that all LCE proteins possess antimicrobial activity. Tissue-specific and genotype-dependent antimicrobial protein profiles impact skin and oral microbiota composition, which could direct towards LCE3B/C-del associated dysbiosis and a possible role for microbiota in the pathophysiology of psoriasis.
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Affiliation(s)
- Hanna Niehues
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen Medical Center (Radboudumc), Nijmegen, The Netherlands
| | - Danique A van der Krieken
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen Medical Center (Radboudumc), Nijmegen, The Netherlands
| | - Thomas H A Ederveen
- Center for Molecular and Biomolecular Informatics, RIMLS, Radboudumc, Nijmegen, The Netherlands
| | - Patrick A M Jansen
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen Medical Center (Radboudumc), Nijmegen, The Netherlands
| | - Laura van Niftrik
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Rob Mesman
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine, RIMLS, Radboudumc, Nijmegen, The Netherlands; Department of Immunology and Metabolism, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Jos P H Smits
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen Medical Center (Radboudumc), Nijmegen, The Netherlands
| | - Joost Schalkwijk
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen Medical Center (Radboudumc), Nijmegen, The Netherlands
| | - Ellen H van den Bogaard
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen Medical Center (Radboudumc), Nijmegen, The Netherlands
| | - Patrick L J M Zeeuwen
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen Medical Center (Radboudumc), Nijmegen, The Netherlands.
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6
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Andralojc KM, Molina MA, Qiu M, Spruijtenburg B, Rasing M, Pater B, Huynen MA, Dutilh BE, Ederveen THA, Elmelik D, Siebers AG, Loopik D, Bekkers RLM, Leenders WPJ, Melchers WJG. Novel high-resolution targeted sequencing of the cervicovaginal microbiome. BMC Biol 2021; 19:267. [PMID: 34915863 PMCID: PMC8680041 DOI: 10.1186/s12915-021-01204-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 06/01/2021] [Accepted: 12/02/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The cervicovaginal microbiome (CVM) plays a significant role in women's cervical health and disease. Microbial alterations at the species level and characteristic community state types (CST) have been associated with acquisition and persistence of high-risk human papillomavirus (hrHPV) infections that may result in progression of cervical lesions to malignancy. Current sequencing methods, especially most commonly used multiplex 16S rRNA gene sequencing, struggle to fully clarify these changes because they generally fail to provide sufficient taxonomic resolution to adequately perform species-level associative studies. To improve CVM species designation, we designed a novel sequencing tool targeting microbes at the species taxonomic rank and examined its potential for profiling the CVM. RESULTS We introduce an accessible and practical circular probe-based RNA sequencing (CiRNAseq) technology with the potential to profile and quantify the CVM. In vitro and in silico validations demonstrate that CiRNAseq can distinctively detect species in a mock mixed microbial environment, with the output data reflecting its ability to estimate microbes' abundance. Moreover, compared to 16S rRNA gene sequencing, CiRNAseq provides equivalent results but with improved sequencing sensitivity. Analyses of a cohort of cervical smears from hrHPV-negative women versus hrHPV-positive women with high-grade cervical intraepithelial neoplasia confirmed known differences in CST occurring in the CVM of women with hrHPV-induced lesions. The technique also revealed variations in microbial diversity and abundance in the CVM of hrHPV-positive women when compared to hrHPV-negative women. CONCLUSIONS CiRNAseq is a promising tool for studying the interplay between the CVM and hrHPV in cervical carcinogenesis. This technology could provide a better understanding of cervicovaginal CST and microbial species during health and disease, prompting the discovery of biomarkers, additional to hrHPV, that can help detect high-grade cervical lesions.
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Affiliation(s)
- Karolina M. Andralojc
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Mariano A. Molina
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mengjie Qiu
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Bram Spruijtenburg
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Menno Rasing
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Bernard Pater
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Martijn A. Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Bas E. Dutilh
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Thomas H. A. Ederveen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Duaa Elmelik
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
| | - Albert G. Siebers
- Department of Pathology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Diede Loopik
- Department of Obstetrics and Gynecology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Ruud L. M. Bekkers
- Department of Obstetrics and Gynecology, Catharina Hospital, 5602 ZA Eindhoven, The Netherlands
- GROW, School for Oncology & Developmental Biology, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
| | - William P. J. Leenders
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, 6525 GA Nijmegen, The Netherlands
- Predica Diagnostics, Toernooiveld 1, 6525 GA Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
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7
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Hartog GD, Ederveen THA, Venkatasubramanian PB, Ferwerda G, van den Kieboom CH, van der Gaast-de Jongh CE, Vissers M, Zoll J, Melchers WJG, Huynen MA, Rots N, Rahamat-Langendoen J, de Jonge MI. Chemokine profiling in children and adults with symptomatic and asymptomatic respiratory viral infections. J Infect 2021; 83:709-737. [PMID: 34715239 DOI: 10.1016/j.jinf.2021.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 10/20/2022]
Abstract
Molecular diagnosis; Viral infection; Chemokines; Disease prognosis; CXCL10; CXCL11; CCL3; CCL4; CCL5; Random forest.
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Affiliation(s)
- G Den Hartog
- Centre for Immunology of Infectious Diseases and Vaccination, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, the Netherlands.
| | - T H A Ederveen
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - P B Venkatasubramanian
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - G Ferwerda
- Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - C H van den Kieboom
- Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - C E van der Gaast-de Jongh
- Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - M Vissers
- Centre for Immunology of Infectious Diseases and Vaccination, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, the Netherlands
| | - J Zoll
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands; Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - W J G Melchers
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands; Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - M A Huynen
- Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - N Rots
- Centre for Immunology of Infectious Diseases and Vaccination, National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, Bilthoven 3721 MA, the Netherlands
| | - J Rahamat-Langendoen
- Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands; Department of Medical Microbiology, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
| | - M I de Jonge
- Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands; Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein Zuid 10, Nijmegen 6525 GA, the Netherlands
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8
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van Beek LF, Surmann K, van den Berg van Saparoea HB, Houben D, Jong WSP, Hentschker C, Ederveen THA, Mitsi E, Ferreira DM, van Opzeeland F, van der Gaast-de Jongh CE, Joosten I, Völker U, Schmidt F, Luirink J, Diavatopoulos DA, de Jonge MI. Exploring metal availability in the natural niche of Streptococcus pneumoniae to discover potential vaccine antigens. Virulence 2021; 11:1310-1328. [PMID: 33017224 PMCID: PMC7550026 DOI: 10.1080/21505594.2020.1825908] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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] [Indexed: 11/30/2022] Open
Abstract
Nasopharyngeal colonization by Streptococcus pneumoniae is a prerequisite for pneumococcal transmission and disease. Current vaccines protect only against disease and colonization caused by a limited number of serotypes, consequently allowing serotype replacement and transmission. Therefore, the development of a broadly protective vaccine against colonization, transmission and disease is desired but requires a better understanding of pneumococcal adaptation to its natural niche. Hence, we measured the levels of free and protein-bound transition metals in human nasal fluid, to determine the effect of metal concentrations on the growth and proteome of S. pneumoniae. Pneumococci cultured in medium containing metal levels comparable to nasal fluid showed a highly distinct proteomic profile compared to standard culture conditions, including the increased abundance of nine conserved, putative surface-exposed proteins. AliA, an oligopeptide binding protein, was identified as the strongest protective antigen, demonstrated by the significantly reduced bacterial load in a murine colonization and a lethal mouse pneumonia model, highlighting its potential as vaccine antigen.
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Affiliation(s)
- Lucille F van Beek
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences , Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases , Nijmegen, The Netherlands
| | - Kristin Surmann
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald , Greifswald, Germany
| | | | | | | | - Christian Hentschker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald , Greifswald, Germany
| | - Thomas H A Ederveen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center , Nijmegen, The Netherlands
| | - Elena Mitsi
- Liverpool School of Tropical medicine, Respiratory Infection Group , Liverpool, United Kingdom of Great Britain and Northern Ireland
| | - Daniela M Ferreira
- Liverpool School of Tropical medicine, Respiratory Infection Group , Liverpool, United Kingdom of Great Britain and Northern Ireland
| | - Fred van Opzeeland
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences , Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases , Nijmegen, The Netherlands
| | - Christa E van der Gaast-de Jongh
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences , Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases , Nijmegen, The Netherlands
| | - Irma Joosten
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences , Nijmegen, The Netherlands
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald , Greifswald, Germany
| | - Frank Schmidt
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald , Greifswald, Germany.,Proteomics Core, Weill Cornell Medicine-Qatar , Doha, Qatar
| | - Joen Luirink
- Abera Bioscience AB , Solna, Sweden.,Department of Molecular Microbiology, Faculty of Science, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam , Amsterdam, The Netherlands
| | - Dimitri A Diavatopoulos
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences , Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases , Nijmegen, The Netherlands
| | - Marien I de Jonge
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences , Nijmegen, The Netherlands.,Radboud Center for Infectious Diseases , Nijmegen, The Netherlands
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9
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Voorberg AN, Niehues H, Oosterhaven JAF, Romeijn GLE, van Vlijmen-Willems IMJJ, van Erp PEJ, Ederveen THA, Zeeuwen PLJM, Schuttelaar MLA. Vesicular hand eczema transcriptome analysis provides insights into its pathophysiology. Exp Dermatol 2021; 30:1775-1786. [PMID: 34252224 PMCID: PMC8596617 DOI: 10.1111/exd.14428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/22/2021] [Revised: 06/18/2021] [Accepted: 07/06/2021] [Indexed: 12/15/2022]
Abstract
Hand eczema is a common inflammatory skin condition of the hands whose pathogenesis is largely unknown. More insight and knowledge of the disease on a more fundamental level might lead to a better understanding of the biological processes involved, which could provide possible new treatment strategies. We aimed to profile the transcriptome of lesional palmar epidermal skin of patients suffering from vesicular hand eczema using RNA‐sequencing. RNA‐sequencing was performed to identify differentially expressed genes in lesional vs. non‐lesional palmar epidermal skin from a group of patients with vesicular hand eczema compared to healthy controls. Comprehensive real‐time quantitative PCR analyses and immunohistochemistry were used for validation of candidate genes and protein profiles for vesicular hand eczema. Overall, a significant and high expression of genes/proteins involved in keratinocyte host defense and inflammation was found in lesional skin. Furthermore, we detected several molecules, both up or downregulated in lesional skin, which are involved in epidermal differentiation. Immune signalling genes were found to be upregulated in lesional skin, albeit with relatively low expression levels. Non‐lesional patient skin showed no significant differences compared to healthy control skin. Lesional vesicular hand eczema skin shows a distinct expression profile compared to non‐lesional skin and healthy control skin. Notably, the overall results indicate a large overlap between vesicular hand eczema and earlier reported atopic dermatitis lesional transcriptome profiles, which suggests that treatments for atopic dermatitis could also be effective in (vesicular) hand eczema.
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Affiliation(s)
- Angelique N Voorberg
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hanna Niehues
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen Medical Center (Radboudumc), Nijmegen, The Netherlands
| | - Jart A F Oosterhaven
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Geertruida L E Romeijn
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ivonne M J J van Vlijmen-Willems
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen Medical Center (Radboudumc), Nijmegen, The Netherlands
| | - Piet E J van Erp
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen Medical Center (Radboudumc), Nijmegen, The Netherlands
| | - Thomas H A Ederveen
- Center for Molecular and Biomolecular Informatics, RIMLS, Radboudumc, Nijmegen, The Netherlands
| | - Patrick L J M Zeeuwen
- Department of Dermatology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Nijmegen Medical Center (Radboudumc), Nijmegen, The Netherlands
| | - Marie L A Schuttelaar
- Department of Dermatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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10
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Ederveen THA, Smits JPH, Boekhorst J, Schalkwijk J, van den Bogaard EH, Zeeuwen PLJM. Skin microbiota in health and disease: From sequencing to biology. J Dermatol 2020; 47:1110-1118. [PMID: 32804417 PMCID: PMC7589227 DOI: 10.1111/1346-8138.15536] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 03/02/2020] [Accepted: 07/06/2020] [Indexed: 01/24/2023]
Abstract
Microbiota live in a closely regulated interaction with their environment, and vice versa. The presence and absence of microbial entities is greatly influenced by features of the niche in which they thrive. Characteristic of this phenomenon is that different human skin sites harbor niche‐specific communities of microbes. Microbial diversity is considerable, and the current challenge lies in determining which microbes and (corresponding) functionality are of importance to a given ecological niche. Furthermore, as there is increasing evidence of microbial involvement in health and disease, the need arises to fundamentally understand microbiome processes for application in health care, nutrition and personal care products (e.g. diet, cosmetics, probiotics). This review provides a current overview of state‐of‐the‐art sequencing‐based techniques and corresponding data analysis methodology for profiling of complex microbial communities. Furthermore, we also summarize the existing knowledge regarding cutaneous microbiota and their human host for a wide range of skin diseases.
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Affiliation(s)
- Thomas H A Ederveen
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands.,Department of Dermatology, RIMLS, Radboudumc, Nijmegen, The Netherlands
| | - Jos P H Smits
- Department of Dermatology, RIMLS, Radboudumc, Nijmegen, The Netherlands
| | - Jos Boekhorst
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands.,NIZO, Ede, The Netherlands
| | - Joost Schalkwijk
- Department of Dermatology, RIMLS, Radboudumc, Nijmegen, The Netherlands
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11
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Voß F, van Beek LF, Schwudke D, Ederveen THA, van Opzeeland FJ, Thalheim D, Werner S, de Jonge MI, Hammerschmidt S. Lipidation of Pneumococcal Antigens Leads to Improved Immunogenicity and Protection. Vaccines (Basel) 2020; 8:vaccines8020310. [PMID: 32560374 PMCID: PMC7350230 DOI: 10.3390/vaccines8020310] [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: 04/09/2020] [Revised: 05/04/2020] [Accepted: 06/11/2020] [Indexed: 12/20/2022] Open
Abstract
Streptococcus pneumoniae infections lead to high morbidity and mortality rates worldwide. Pneumococcal polysaccharide conjugate vaccines significantly reduce the burden of disease but have a limited range of protection, which encourages the development of a broadly protective protein-based alternative. We and others have shown that immunization with pneumococcal lipoproteins that lack the lipid anchor protects against colonization. Since immunity against S. pneumoniae is mediated through Toll-like receptor 2 signaling induced by lipidated proteins, we investigated the effects of a lipid modification on the induced immune responses in either intranasally or subcutaneously vaccinated mice. Here, we demonstrate that lipidation of recombinant lipoproteins DacB and PnrA strongly improves their immunogenicity. Mice immunized with lipidated proteins showed enhanced antibody concentrations and different induction kinetics. The induced humoral immune response was modulated by lipidation, indicated by increased IgG2/IgG1 subclass ratios related to Th1-type immunity. In a mouse model of colonization, immunization with lipidated antigens led to a moderate but consistent reduction of pneumococcal colonization as compared to the non-lipidated proteins, indicating that protein lipidation can improve the protective capacity of the coupled antigen. Thus, protein lipidation represents a promising approach for the development of a serotype-independent pneumococcal vaccine.
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Affiliation(s)
- Franziska Voß
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute of Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany; (F.V.); (D.T.); (S.W.)
| | - Lucille F. van Beek
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboudumc, 6525 GA Nijmegen, The Netherlands; (L.F.v.B.); (F.J.v.O.); (M.I.d.J.)
- Radboud Center for Infectious Diseases, Radboudumc, 6525 GA Nijmegen, The Netherlands
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Priority Area Infection, Research Center Borstel, Leibniz Center for Medicine and Bioscience, 23845 Borstel, Germany;
- German Center for Infection Research (DZIF), 38124 Braunschweig, Germany
- Airway Research Center North Member of the German Center for Lung Research (DZL), 22927 Großhansdorf, Germany
| | - Thomas H. A. Ederveen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands;
| | - Fred J. van Opzeeland
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboudumc, 6525 GA Nijmegen, The Netherlands; (L.F.v.B.); (F.J.v.O.); (M.I.d.J.)
- Radboud Center for Infectious Diseases, Radboudumc, 6525 GA Nijmegen, The Netherlands
| | - Daniela Thalheim
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute of Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany; (F.V.); (D.T.); (S.W.)
| | - Sidney Werner
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute of Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany; (F.V.); (D.T.); (S.W.)
| | - Marien I. de Jonge
- Section Pediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboudumc, 6525 GA Nijmegen, The Netherlands; (L.F.v.B.); (F.J.v.O.); (M.I.d.J.)
- Radboud Center for Infectious Diseases, Radboudumc, 6525 GA Nijmegen, The Netherlands
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Interfaculty Institute of Genetics and Functional Genomics, Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany; (F.V.); (D.T.); (S.W.)
- Correspondence: ; Tel.: +49-383-4420-5700; Fax: +49-3834-4205-709
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12
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Rogier R, Ederveen THA, Wopereis H, Hartog A, Boekhorst J, van Hijum SAFT, Knol J, Garssen J, Walgreen B, Helsen MM, van der Kraan PM, van Lent PLEM, van de Loo FAJ, Abdollahi-Roodsaz S, Koenders MI. Correction: Supplementation of diet with non-digestible oligosaccharides alters the intestinal microbiota, but not arthritis development, in IL-1 receptor antagonist deficient mice. PLoS One 2019; 14:e0227517. [PMID: 31891648 PMCID: PMC6938321 DOI: 10.1371/journal.pone.0227517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0219366.].
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13
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Gommers LMM, Ederveen THA, van der Wijst J, Overmars-Bos C, Kortman GAM, Boekhorst J, Bindels RJM, de Baaij JHF, Hoenderop JGJ. Low gut microbiota diversity and dietary magnesium intake are associated with the development of PPI-induced hypomagnesemia. FASEB J 2019; 33:11235-11246. [PMID: 31299175 DOI: 10.1096/fj.201900839r] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proton pump inhibitors (PPIs) are used by millions of patients for the treatment of stomach acid-reflux diseases. Although PPIs are generally considered safe, about 13% of the users develop hypomagnesemia. Despite rising attention for this issue, the underlying mechanism is still unknown. Here, we examine whether the gut microbiome is involved in the development of PPI-induced hypomagnesemia in wild-type C57BL/6J mice. After 4 wk of treatment under normal or low dietary Mg2+ availability, omeprazole significantly reduced serum Mg2+ levels only in mice on a low-Mg2+ diet without affecting the mRNA expression of colonic or renal Mg2+ transporters. Overall, 16S rRNA gene sequencing revealed a lower gut microbial diversity in omeprazole-treated mice. Omeprazole induced a shift in microbial composition, which was associated with a 3- and 2-fold increase in the abundance of Lactobacillus and Bifidobacterium, respectively. To examine the metabolic consequences of these microbial alterations, the colonic composition of organic acids was evaluated. Low dietary Mg2+ intake, independent of omeprazole treatment, resulted in a 10-fold increase in formate levels. Together, these results imply that both omeprazole treatment and low dietary Mg2+ intake disturb the gut internal milieu and may pose a risk for the malabsorption of Mg2+ in the colon.-Gommers, L. M. M., Ederveen, T. H. A., van der Wijst, J., Overmars-Bos, C., Kortman, G. A. M., Boekhorst, J., Bindels, R. J. M., de Baaij, J. H. F., Hoenderop, J. G. J. Low gut microbiota diversity and dietary magnesium intake are associated with the development of PPI-induced hypomagnesemia.
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Affiliation(s)
- Lisanne M M Gommers
- Department of Physiology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (RADBOUDUMC), Nijmegen, The Netherlands
| | - Thomas H A Ederveen
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands.,NIZO Food Research, Ede, The Netherlands
| | - Jenny van der Wijst
- Department of Physiology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (RADBOUDUMC), Nijmegen, The Netherlands
| | - Caro Overmars-Bos
- Department of Physiology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (RADBOUDUMC), Nijmegen, The Netherlands
| | | | - Jos Boekhorst
- Center for Molecular and Biomolecular Informatics (CMBI), Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (Radboudumc), Nijmegen, The Netherlands.,NIZO Food Research, Ede, The Netherlands
| | - René J M Bindels
- Department of Physiology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (RADBOUDUMC), Nijmegen, The Netherlands
| | - Jeroen H F de Baaij
- Department of Physiology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (RADBOUDUMC), Nijmegen, The Netherlands
| | - Joost G J Hoenderop
- Department of Physiology, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center (RADBOUDUMC), Nijmegen, The Netherlands
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14
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Rogier R, Ederveen THA, Wopereis H, Hartog A, Boekhorst J, van Hijum SAFT, Knol J, Garssen J, Walgreen B, Helsen MM, van der Kraan PM, van Lent PLEM, van de Loo FAJ, Abdollahi-Roodsaz S, Koenders MI. Supplementation of diet with non-digestible oligosaccharides alters the intestinal microbiota, but not arthritis development, in IL-1 receptor antagonist deficient mice. PLoS One 2019; 14:e0219366. [PMID: 31283798 PMCID: PMC6613703 DOI: 10.1371/journal.pone.0219366] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 12/14/2018] [Accepted: 06/22/2019] [Indexed: 02/07/2023] Open
Abstract
The intestinal microbiome is perturbed in patients with new-onset and chronic autoimmune inflammatory arthritis. Recent studies in mouse models suggest that development and progression of autoimmune arthritis is highly affected by the intestinal microbiome. This makes modulation of the intestinal microbiota an interesting novel approach to suppress inflammatory arthritis. Prebiotics, defined as non-digestible carbohydrates that selectively stimulate the growth and activity of beneficial microorganisms, provide a relatively non-invasive approach to modulate the intestinal microbiota. The aim of this study was to assess the therapeutic potential of dietary supplementation with a prebiotic mixture of 90% short-chain galacto-oligosaccharides and 10% long-chain fructo-oligosaccharides (scGOS/lcFOS) in experimental arthritis in mice. We here show that dietary supplementation with scGOS/lcFOS has a pronounced effect on the composition of the fecal microbiota. Interestingly, the genera Enterococcus and Clostridium were markedly decreased by scGOS/lcFOS dietary supplementation. In contrast, the family Lachnospiraceae and the genus Lactobacillus, both associated with healthy microbiota, increased in mice receiving scGOS/lcFOS diet. However, the scGOS/lcFOS induced alterations of the intestinal microbiota did not induce significant effects on the intestinal and systemic T helper cell subsets and were not sufficient to reproducibly suppress arthritis in mice. As expected, we did observe a significant increase in the bone mineral density in mice upon dietary supplementation with scGOS/lcFOS for 8 weeks. Altogether, this study suggests that dietary scGOS/lcFOS supplementation is able to promote presumably healthy gut microbiota and improve bone mineral density, but not inflammation, in arthritis-prone mice.
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Affiliation(s)
- Rebecca Rogier
- Experimental Rheumatology, Radboudumc, Nijmegen, The Netherlands
| | - Thomas H. A. Ederveen
- Centre for Molecular and Biomolecular Informatics, Radboudumc, Nijmegen, The Netherlands
| | - Harm Wopereis
- Danone Nutricia Research, Utrecht, The Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Anita Hartog
- Danone Nutricia Research, Utrecht, The Netherlands
- NIZO food research, Ede, The Netherlands
| | - Jos Boekhorst
- Centre for Molecular and Biomolecular Informatics, Radboudumc, Nijmegen, The Netherlands
- NIZO food research, Ede, The Netherlands
| | | | - Jan Knol
- Danone Nutricia Research, Utrecht, The Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Johan Garssen
- Danone Nutricia Research, Utrecht, The Netherlands
- Division of Pharmacology, Utrecht institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | | | | | | | | | | | | | - Marije I. Koenders
- Experimental Rheumatology, Radboudumc, Nijmegen, The Netherlands
- * E-mail:
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15
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Chermprapai S, Ederveen THA, Broere F, Broens EM, Schlotter YM, van Schalkwijk S, Boekhorst J, van Hijum SAFT, Rutten VPMG. The bacterial and fungal microbiome of the skin of healthy dogs and dogs with atopic dermatitis and the impact of topical antimicrobial therapy, an exploratory study. Vet Microbiol 2018; 229:90-99. [PMID: 30642603 DOI: 10.1016/j.vetmic.2018.12.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 10/27/2022]
Abstract
Canine atopic dermatitis is a genetically predisposed inflammatory and pruritic allergic skin disease that is often complicated by (secondary) bacterial and fungal (yeast) infections. High-throughput DNA sequencing was used to characterize the composition of the microbiome (bacteria and fungi) inhabiting specific sites of skin in healthy dogs and dogs with atopic dermatitis (AD) before and after topical antimicrobial treatment. Skin microbiome samples were collected from six healthy control dogs and three dogs spontaneously affected by AD by swabbing at (non-) predilection sites before, during and after treatment. Bacteria and fungi were profiled by Illumina sequencing of the 16S ribosomal RNA gene of bacteria (16S) and the internally transcribed spacer of the ribosomal gene cassette in fungi (ITS). The total cohort of dogs showed a high diversity of microbes on skin with a strong individual variability of both 16S and ITS profiles. The genera of Staphylococcus and Porphyromonas were dominantly present both on atopic and healthy skin and across all skin sites studied. In addition, bacterial and fungal alpha diversity were similar at the different skin sites. The topical antimicrobial treatment increased the diversity of bacterial and fungal compositions in course of time on both AD and healthy skin.
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Affiliation(s)
- Suttiwee Chermprapai
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL, the Netherlands; Department of Companion Animals Clinical Sciences, Faculty of Veterinary Medicine, Kasetsart University, Bangkok, 10900, Thailand; Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CM, the Netherlands.
| | - Thomas H A Ederveen
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Nijmegen Medical Centre, Nijmegen, 6525 GA, the Netherlands; NIZO, Ede, 6718 ZB, the Netherlands.
| | - Femke Broere
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL, the Netherlands; Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CM, the Netherlands.
| | - Els M Broens
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL, the Netherlands.
| | - Yvette M Schlotter
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CM, the Netherlands.
| | | | - Jos Boekhorst
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Nijmegen Medical Centre, Nijmegen, 6525 GA, the Netherlands; NIZO, Ede, 6718 ZB, the Netherlands.
| | - Sacha A F T van Hijum
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Nijmegen Medical Centre, Nijmegen, 6525 GA, the Netherlands; NIZO, Ede, 6718 ZB, the Netherlands.
| | - Victor P M G Rutten
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, 3584 CL, the Netherlands; Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, 0110, South Africa.
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Ederveen THA, Ferwerda G, Ahout IM, Vissers M, de Groot R, Boekhorst J, Timmerman HM, Huynen MA, van Hijum SAFT, de Jonge MI. Haemophilus is overrepresented in the nasopharynx of infants hospitalized with RSV infection and associated with increased viral load and enhanced mucosal CXCL8 responses. Microbiome 2018; 6:10. [PMID: 29325581 PMCID: PMC5765694 DOI: 10.1186/s40168-017-0395-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [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: 09/01/2017] [Accepted: 12/21/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND While almost all infants are infected with respiratory syncytial virus (RSV) before the age of 2 years, only a small percentage develops severe disease. Previous studies suggest that the nasopharyngeal microbiome affects disease development. We therefore studied the effect of the nasopharyngeal microbiome on viral load and mucosal cytokine responses, two important factors influencing the pathophysiology of RSV disease. To determine the relation between (i) the microbiome of the upper respiratory tract, (ii) viral load, and (iii) host mucosal inflammation during an RSV infection, nasopharyngeal microbiota profiles of RSV infected infants (< 6 months) with different levels of disease severity and age-matched healthy controls were determined by 16S rRNA marker gene sequencing. The viral load was measured using qPCR. Nasopharyngeal CCL5, CXCL10, MMP9, IL6, and CXCL8 levels were determined with ELISA. RESULTS Viral load in nasopharyngeal aspirates of patients associates significantly to total nasopharyngeal microbiota composition. Healthy infants (n = 21) and RSV patients (n = 54) display very distinct microbial patterns, primarily characterized by a loss in commensals like Veillonella and overrepresentation of opportunistic organisms like Haemophilus and Achromobacter in RSV-infected individuals. Furthermore, nasopharyngeal microbiota profiles are significantly different based on CXCL8 levels. CXCL8 is a chemokine that was previously found to be indicative for disease severity and for which we find Haemophilus abundance as the strongest predictor for CXCL8 levels. CONCLUSIONS The nasopharyngeal microbiota in young infants with RSV infection is marked by an overrepresentation of the genus Haemophilus. We present that this bacterium is associated with viral load and mucosal CXCL8 responses, both which are involved in RSV disease pathogenesis.
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Affiliation(s)
- Thomas H A Ederveen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Gerben Ferwerda
- Laboratory of Pediatric Infectious Diseases, Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein-Zuid 10 (Route 412), 6525, GA, Nijmegen, The Netherlands.
| | - Inge M Ahout
- Laboratory of Pediatric Infectious Diseases, Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein-Zuid 10 (Route 412), 6525, GA, Nijmegen, The Netherlands
| | - Marloes Vissers
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Ronald de Groot
- Laboratory of Pediatric Infectious Diseases, Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein-Zuid 10 (Route 412), 6525, GA, Nijmegen, The Netherlands
| | - Jos Boekhorst
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- NIZO, Ede, The Netherlands
| | | | - Martijn A Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sacha A F T van Hijum
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- NIZO, Ede, The Netherlands
| | - Marien I de Jonge
- Laboratory of Pediatric Infectious Diseases, Radboud Center for Infectious Diseases, Radboud University Medical Center, Geert Grooteplein-Zuid 10 (Route 412), 6525, GA, Nijmegen, The Netherlands
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Aarts E, Ederveen THA, Naaijen J, Zwiers MP, Boekhorst J, Timmerman HM, Smeekens SP, Netea MG, Buitelaar JK, Franke B, van Hijum SAFT, Arias Vasquez A. Gut microbiome in ADHD and its relation to neural reward anticipation. PLoS One 2017; 12:e0183509. [PMID: 28863139 PMCID: PMC5581161 DOI: 10.1371/journal.pone.0183509] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 08/04/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Microorganisms in the human intestine (i.e. the gut microbiome) have an increasingly recognized impact on human health, including brain functioning. Attention-deficit/hyperactivity disorder (ADHD) is a neurodevelopmental disorder associated with abnormalities in dopamine neurotransmission and deficits in reward processing and its underlying neuro-circuitry including the ventral striatum. The microbiome might contribute to ADHD etiology via the gut-brain axis. In this pilot study, we investigated potential differences in the microbiome between ADHD cases and undiagnosed controls, as well as its relation to neural reward processing. METHODS We used 16S rRNA marker gene sequencing (16S) to identify bacterial taxa and their predicted gene functions in 19 ADHD and 77 control participants. Using functional magnetic resonance imaging (fMRI), we interrogated the effect of observed microbiome differences in neural reward responses in a subset of 28 participants, independent of diagnosis. RESULTS For the first time, we describe gut microbial makeup of adolescents and adults diagnosed with ADHD. We found that the relative abundance of several bacterial taxa differed between cases and controls, albeit marginally significant. A nominal increase in the Bifidobacterium genus was observed in ADHD cases. In a hypothesis-driven approach, we found that the observed increase was linked to significantly enhanced 16S-based predicted bacterial gene functionality encoding cyclohexadienyl dehydratase in cases relative to controls. This enzyme is involved in the synthesis of phenylalanine, a precursor of dopamine. Increased relative abundance of this functionality was significantly associated with decreased ventral striatal fMRI responses during reward anticipation, independent of ADHD diagnosis and age. CONCLUSIONS Our results show increases in gut microbiome predicted function of dopamine precursor synthesis between ADHD cases and controls. This increase in microbiome function relates to decreased neural responses to reward anticipation. Decreased neural reward anticipation constitutes one of the hallmarks of ADHD.
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Affiliation(s)
- Esther Aarts
- Centre for Cognitive Neuroimaging, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- * E-mail:
| | - Thomas H. A. Ederveen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jilly Naaijen
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marcel P. Zwiers
- Centre for Cognitive Neuroimaging, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Jos Boekhorst
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- NIZO, Ede, The Netherlands
| | | | - Sanne P. Smeekens
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jan K. Buitelaar
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Karakter Child and Adolescent Psychiatry University Centre, Nijmegen, The Netherlands
| | - Barbara Franke
- Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sacha A. F. T. van Hijum
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- NIZO, Ede, The Netherlands
| | - Alejandro Arias Vasquez
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Psychiatry, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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Rogier R, Ederveen THA, Boekhorst J, Wopereis H, Scher JU, Manasson J, Frambach SJCM, Knol J, Garssen J, van der Kraan PM, Koenders MI, van den Berg WB, van Hijum SAFT, Abdollahi-Roodsaz S. Aberrant intestinal microbiota due to IL-1 receptor antagonist deficiency promotes IL-17- and TLR4-dependent arthritis. Microbiome 2017; 5:63. [PMID: 28645307 PMCID: PMC5481968 DOI: 10.1186/s40168-017-0278-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [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: 11/03/2016] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Perturbation of commensal intestinal microbiota has been associated with several autoimmune diseases. Mice deficient in interleukin-1 receptor antagonist (Il1rn -/- mice) spontaneously develop autoimmune arthritis and are susceptible to other autoimmune diseases such as psoriasis, diabetes, and encephalomyelitis; however, the mechanisms of increased susceptibility to these autoimmune phenotypes are poorly understood. We investigated the role of interleukin-1 receptor antagonist (IL-1Ra) in regulation of commensal intestinal microbiota, and assessed the involvement of microbiota subsets and innate and adaptive mucosal immune responses that underlie the development of spontaneous arthritis in Il1rn -/- mice. RESULTS Using high-throughput 16S rRNA gene sequencing, we show that IL-1Ra critically maintains the diversity and regulates the composition of intestinal microbiota in mice. IL-1Ra deficiency reduced the intestinal microbial diversity and richness, and caused specific taxonomic alterations characterized by overrepresented Helicobacter and underrepresented Ruminococcus and Prevotella. Notably, the aberrant intestinal microbiota in IL1rn -/- mice specifically potentiated IL-17 production by intestinal lamina propria (LP) lymphocytes and skewed the LP T cell balance in favor of T helper 17 (Th17) cells, an effect transferable to WT mice by fecal microbiota. Importantly, LP Th17 cell expansion and the development of spontaneous autoimmune arthritis in IL1rn -/- mice were attenuated under germ-free condition. Selective antibiotic treatment revealed that tobramycin-induced alterations of commensal intestinal microbiota, i.e., reduced Helicobacter, Flexispira, Clostridium, and Dehalobacterium, suppressed arthritis in IL1rn -/- mice. The arthritis phenotype in IL1rn -/- mice was previously shown to depend on Toll-like receptor 4 (TLR4). Using the ablation of both IL-1Ra and TLR4, we here show that the aberrations in the IL1rn -/- microbiota are partly TLR4-dependent. We further identify a role for TLR4 activation in the intestinal lamina propria production of IL-17 and cytokines involved in Th17 differentiation preceding the onset of arthritis. CONCLUSIONS These findings identify a critical role for IL1Ra in maintaining the natural diversity and composition of intestinal microbiota, and suggest a role for TLR4 in mucosal Th17 cell induction associated with the development of autoimmune disease in mice.
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Affiliation(s)
- Rebecca Rogier
- Experimental Rheumatology (272), Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, The Netherlands
| | - Thomas H. A. Ederveen
- Experimental Rheumatology (272), Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, The Netherlands
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jos Boekhorst
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- NIZO food research, Ede, The Netherlands
| | - Harm Wopereis
- Danone Nutricia Research, Utrecht, The Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Jose U. Scher
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, 301 East 17th Street, Room 1611A, New York, USA
| | - Julia Manasson
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, 301 East 17th Street, Room 1611A, New York, USA
| | - Sanne J. C. M. Frambach
- Experimental Rheumatology (272), Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, The Netherlands
| | - Jan Knol
- Danone Nutricia Research, Utrecht, The Netherlands
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Johan Garssen
- Danone Nutricia Research, Utrecht, The Netherlands
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Peter M. van der Kraan
- Experimental Rheumatology (272), Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, The Netherlands
| | - Marije I. Koenders
- Experimental Rheumatology (272), Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, The Netherlands
| | - Wim B. van den Berg
- Experimental Rheumatology (272), Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, The Netherlands
| | - Sacha A. F. T. van Hijum
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- NIZO food research, Ede, The Netherlands
| | - Shahla Abdollahi-Roodsaz
- Experimental Rheumatology (272), Radboud University Medical Center, PO Box 9101, 6500HB Nijmegen, The Netherlands
- Division of Rheumatology, Department of Medicine, New York University School of Medicine, 301 East 17th Street, Room 1611A, New York, USA
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van der Krieken DA, Ederveen THA, van Hijum SAFT, Jansen PAM, Melchers WJG, Scheepers PTJ, Schalkwijk J, Zeeuwen PLJM. An In vitro Model for Bacterial Growth on Human Stratum Corneum. Acta Derm Venereol 2016; 96:873-879. [PMID: 26976779 DOI: 10.2340/00015555-2401] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The diversity and dynamics of the skin microbiome in health and disease have been studied recently, but adequate model systems to study skin microbiotas in vitro are largely lacking. We developed an in vitro system that mimics human stratum corneum, using human callus as substrate and nutrient source for bacterial growth. The growth of several commensal and pathogenic bacterial strains was measured for up to one week by counting colony-forming units or by quantitative PCR with strain-specific primers. Human skin pathogens were found to survive amidst a minimal microbiome consisting of 2 major skin commensals: Staphylococcus epidermidis and Propionibacterium acnes. In addition, complete microbiomes, taken from the backs of healthy volunteers, were inoculated and maintained using this system. This model may enable the modulation of skin microbiomes in vitro and allow testing of pathogens, biological agents and antibiotics in a medium-throughput format.
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Ederveen THA, Overmars L, van Hijum SAFT. Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction. PLoS One 2013; 8:e63523. [PMID: 23675487 PMCID: PMC3651085 DOI: 10.1371/journal.pone.0063523] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [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: 07/27/2012] [Accepted: 04/05/2013] [Indexed: 12/02/2022] Open
Abstract
Nowadays, prokaryotic genomes are sequenced faster than the capacity to manually curate gene annotations. Automated genome annotation engines provide users a straight-forward and complete solution for predicting ORF coordinates and function. For many labs, the use of AGEs is therefore essential to decrease the time necessary for annotating a given prokaryotic genome. However, it is not uncommon for AGEs to provide different and sometimes conflicting predictions. Combining multiple AGEs might allow for more accurate predictions. Here we analyzed the ab initio open reading frame (ORF) calling performance of different AGEs based on curated genome annotations of eight strains from different bacterial species with GC% ranging from 35–52%. We present a case study which demonstrates a novel way of comparative genome annotation, using combinations of AGEs in a pre-defined order (or path) to predict ORF start codons. The order of AGE combinations is from high to low specificity, where the specificity is based on the eight genome annotations. For each AGE combination we are able to derive a so-called projected confidence value, which is the average specificity of ORF start codon prediction based on the eight genomes. The projected confidence enables estimating likeliness of a correct prediction for a particular ORF start codon by a particular AGE combination, pinpointing ORFs notoriously difficult to predict start codons. We correctly predict start codons for 90.5±4.8% of the genes in a genome (based on the eight genomes) with an accuracy of 81.1±7.6%. Our consensus-path methodology allows a marked improvement over majority voting (9.7±4.4%) and with an optimal path ORF start prediction sensitivity is gained while maintaining a high specificity.
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Affiliation(s)
- Thomas H. A. Ederveen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Lex Overmars
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Netherlands Bioinformatics Centre, Nijmegen, The Netherlands
| | - Sacha A. F. T. van Hijum
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Netherlands Bioinformatics Centre, Nijmegen, The Netherlands
- NIZO Food Research, Kluyver Centre for Genomics of Industrial Fermentation, Ede, The Netherlands
- Top Institute Food and Nutrition, Wageningen, The Netherlands
- * E-mail:
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