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Labenz J, Borkenstein DP, Heil FJ, Madisch A, Tappe U, Schmidt H, Terjung B, Klymiuk I, Horvath A, Gross M, Stadlbauer V. Corrigendum: Application of a multispecies probiotic reduces gastro-intestinal discomfort and induces microbial changes after colonoscopy. Front Oncol 2024; 14:1395635. [PMID: 38601766 PMCID: PMC11005451 DOI: 10.3389/fonc.2024.1395635] [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: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
[This corrects the article DOI: 10.3389/fonc.2022.1078315.].
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Affiliation(s)
- Joachim Labenz
- Department of Internal Medicine, Diakonie Klinikum Jung-Stilling, Siegen, Germany
| | | | | | - Ahmed Madisch
- Department of Internal Medicine I, Hospital Clinic Siloah, Hannover, Germany
- Centrum Gastroenterologie Bethanien, Agaplesion Krankenhaus Bethanien, Frankfurt, Germany
| | - Ulrich Tappe
- Gastropraxis an der St. Barbara Klinik, Hamm, Germany
| | - Harald Schmidt
- Praxis für Innere Medizin und Gastroenterologie Dr. H. Schmidt, Berlin, Germany
| | | | - Ingeborg Klymiuk
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Angela Horvath
- Division for Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Area 3 Microbiome Modulation for Precision Medicine, Center for Biomarker Research in Medicine (CBmed), Graz, Austria
| | - Manfred Gross
- Department of Internal Medicine, Internistisches Klinikum München Süd, Munich, Germany
| | - Vanessa Stadlbauer
- Division for Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Area 3 Microbiome Modulation for Precision Medicine, Center for Biomarker Research in Medicine (CBmed), Graz, Austria
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2
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Nadvornik C, Kallab M, Hommer N, Schlatter A, Stengel T, Garhöfer G, Zeitlinger M, Eberl S, Klymiuk I, Trajanoski S, Nehr M, Makristathis A, Schmidl D, Nussbaumer-Proell A. Effect of Antibiotic Eye Drops on the Nasal Microbiome in Healthy Subjects—A Pilot Study. Antibiotics (Basel) 2023; 12:antibiotics12030517. [PMID: 36978384 PMCID: PMC10044076 DOI: 10.3390/antibiotics12030517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023] Open
Abstract
Background: Antibiotic eye drops are frequently used in clinical practice. Due to the anatomical connection via the nasolacrimal duct, it seems possible that they have an influence on the nasal/pharyngeal microbiome. This was investigated by using two different commonly used antibiotic eye drops. Methods: 20 subjects were randomized to four groups of five subjects receiving eye drops containing gentamicin, ciprofloxacin, or, as controls, unpreserved povidone or benzalkonium chloride-preserved povidone. Nasal and pharyngeal swabs were performed before and after the instillation period. Swabs were analyzed by Illumina next-generation sequencing (NGS)-based 16S rRNA analysis. Bacterial culture was performed on solid media, and bacterial isolates were identified to the species level by MALDI-TOF MS. Species-dependent antimicrobial susceptibility testing was performed using single isolates and pools of isolates. Results: Bacterial richness in the nose increased numerically from 163 ± 30 to 243 ± 100 OTUs (gentamicin) and from 114 ± 17 to 144 ± 45 OTUs (ciprofloxacin). Phylogenetic diversity index (pd) of different bacterial strains in the nasal microbiome increased from 12.4 ± 1.0 to 16.9 ± 5.6 pd (gentamicin) and from 10.2 ± 1.4 to 11.8 ± 3.1 pd (ciprofloxacin). Unpreserved povidone eye drops resulted in minimal changes in bacterial counts. Preservative-containing povidone eye drops resulted in no change. A minor increase (1–2-fold) in the minimal inhibitory concentration (MIC) was observed in single streptococcal isolates. Conclusions: Antibiotic eye drops could affect the nasal microbiome. After an instillation period of seven days, an increase in the diversity and richness of bacterial strains in the nasal microbiome was observed.
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Affiliation(s)
- Clemens Nadvornik
- Department of Clinical Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Martin Kallab
- Department of Clinical Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Nikolaus Hommer
- Department of Clinical Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Andreas Schlatter
- Department of Clinical Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Theresa Stengel
- Department of Clinical Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Gerhard Garhöfer
- Department of Clinical Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Markus Zeitlinger
- Department of Clinical Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Sabine Eberl
- Department of Clinical Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Ingeborg Klymiuk
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, 8036 Graz, Austria
| | - Slave Trajanoski
- Core Facility Computational Bioanalytics, Center for Medical Research, Medical University of Graz, 8036 Graz, Austria
| | - Marion Nehr
- Department of Clinical Microbiology, Clinical Institute of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Athanasios Makristathis
- Department of Clinical Microbiology, Clinical Institute of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Doreen Schmidl
- Department of Clinical Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Alina Nussbaumer-Proell
- Department of Clinical Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
- Correspondence: ; Tel.: +43-(0)1-40400-29810
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3
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Labenz J, Borkenstein DP, Heil FJ, Madisch A, Tappe U, Schmidt H, Terjung B, Klymiuk I, Horvath A, Gross M, Stadlbauer V. Application of a multispecies probiotic reduces gastro-intestinal discomfort and induces microbial changes after colonoscopy. Front Oncol 2023; 12:1078315. [PMID: 36698396 PMCID: PMC9870247 DOI: 10.3389/fonc.2022.1078315] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/02/2022] [Indexed: 01/11/2023] Open
Abstract
Even after decades of research and pharmaceutical development, cancer is still one of the most common causes of death in the western population and the management of cancer will remain a major challenge of medical research. One of the most common types of cancer is colorectal cancer (CRC). Prevention by detection of early-stage precursors is the most reliable method to prevent CRC development. In dependence of age, familial predisposition, and other risk factors the preventative routine screening for CRC by colonoscopy should be performed at least twice in intervals of about ten years. Although colonoscopy is a life-saving clinical examination reducing both incidence and mortality of CRC significantly, it has still a bad reputation in the population as an uncomfortable procedure with unpleasant side effects lasting sometimes over days to weeks. These effects are most likely caused by the bowel preparation before colonoscopy, which is crucial for a successful colonoscopy with high quality. Beside pain, bleeding and other rare but severe complications of colonoscopy, cleaning of the intestinal mucosa alters the gut microbiome significantly and consistently. Abdominal pain, cramps, diarrhea, nausea, bloating, and constipation are common adverse events which can continue to affect patients for days or even weeks after the procedure. In this multicenter, placebo controlled, double blind clinical trial, we investigated the effect of an intervention with a multispecies probiotic formulation for 30 days on the adverse events due to bowel preparation. We show that the treatment of participants with the multispecies probiotic formulation decreases the number of days with constipation significantly, and reduced pain, bloating, diarrhea, and general discomfort. 16S based amplicon analyses reveal recovery of administered probiotic strains from stool samples and differences in alpha diversity dynamics with higher variability in the probiotic group compared to the placebo group. In conclusion, the probiotic ameliorates the side effects after colonoscopy and might be an important supplement to increase acceptance of this life-saving preventative examination. Further, we present here for the first time that probiotic intervention of only 30 days affects alpha diversity parameters in stool samples.
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Affiliation(s)
- Joachim Labenz
- Department of Internal Medicine, Diakonie Klinikum Jung-Stilling, Siegen, Germany
| | | | | | - Ahmed Madisch
- Department of Internal Medicine I, Hospital Clinic Siloah, Hannover, Germany
- Centrum Gastroenterologie Bethanien, Agaplesion Krankenhaus Bethanien, Frankfurt, Germany
| | - Ulrich Tappe
- Gastropraxis an der St. Barbara Klinik, Hamm, Germany
| | - Harald Schmidt
- Praxis für Innere Medizin und Gastroenterologie Dr. H. Schmidt, Berlin, Germany
| | | | - Ingeborg Klymiuk
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Angela Horvath
- Division for Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Area 3 Microbiome Modulation for Precision Medicine, Center for Biomarker Research in Medicine (CBmed), Graz, Austria
| | - Manfred Gross
- Department of Internal medicine, Internistisches Klinikum München Süd, Munich, Germany
| | - Vanessa Stadlbauer
- Division for Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- Area 3 Microbiome Modulation for Precision Medicine, Center for Biomarker Research in Medicine (CBmed), Graz, Austria
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Klymiuk I, Bilgilier C, Mahnert A, Prokesch A, Heininger C, Brandl I, Sahbegovic H, Singer C, Fuereder T, Steininger C. Chemotherapy-associated oral microbiome changes in breast cancer patients. Front Oncol 2022; 12:949071. [PMID: 36016616 PMCID: PMC9396302 DOI: 10.3389/fonc.2022.949071] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/15/2022] [Indexed: 11/17/2022] Open
Abstract
Cytotoxic chemotherapy with or without a combination of humanized monoclonal antibodies is regarded as the gold standard of personalized medicine for the treatment of breast cancer patients. Significant medication-related side effects are common accompanying phenomena for these patients, such as oral discomfort, mucositis, or even osteonecrosis of the jaw. In this study, we analyze the saliva samples of 20 breast cancer patients at three time points throughout their chemotherapy: at the baseline prior to treatment initiation (T1), after four-to-six cycles of chemotherapy (T2), and 1 year after the start of the treatment (T3) to investigate and characterize the long-term effects of chemotherapy on the oral microbiome. We aimed to characterize changes in the oral bacterial microbiome based on 16S rRNA gene amplicon analysis during chemotherapeutic treatment, as a potential target to treat common oral side effects occurring during therapy. The chemotherapeutic drugs used in our study for patient treatment were trastuzumab, docetaxel, pertuzumab, epirubicin, and cyclophosphamide. We find a significant increase in the relative abundance of potentially pathogenic taxa like Escherichia/Shigella and non-significant trends in the relative abundance of, for example, Actinomyces ssp. In conclusion, the role of microbiota in the oral side effects of chemotherapeutic treatment needs to be considered and should be analyzed in more detail using larger patient cohorts. Oral side effects in breast cancer patients undergoing chemotherapy are a common burden and should be treated for a better tolerability of the therapy.
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Affiliation(s)
- Ingeborg Klymiuk
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Ceren Bilgilier
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Alexander Mahnert
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Andreas Prokesch
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Christoph Heininger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Ingeborg Brandl
- Department of Gynecology, Clinical Department of General Gynecology and Gynecological Oncology. Medical University Vienna, Vienna, Austria
| | - Hanka Sahbegovic
- Department of Gynecology, Clinical Department of General Gynecology and Gynecological Oncology. Medical University Vienna, Vienna, Austria
| | - Christian Singer
- Department of Gynecology, Clinical Department of General Gynecology and Gynecological Oncology. Medical University Vienna, Vienna, Austria
| | - Thorsten Fuereder
- Division of Oncology, Department of Medicine I, Medical University Vienna, Vienna, Austria
| | - Christoph Steininger
- Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Medical University Vienna, Vienna, Austria
- Karl Landsteiner Institute for Microbiome Research, St. Pölten, Austria
- *Correspondence: Christoph Steininger,
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5
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Reinisch I, Klymiuk I, Michenthaler H, Moyschewitz E, Galhuber M, Krstic J, Domingo M, Zhang F, Karbiener M, Vujić N, Kratky D, Schreiber R, Schupp M, Lenihan-Geels G, Schulz TJ, Malli R, Madl T, Prokesch A. p53 Regulates a miRNA-Fructose Transporter Axis in Brown Adipose Tissue Under Fasting. Front Genet 2022; 13:913030. [PMID: 35734423 PMCID: PMC9207587 DOI: 10.3389/fgene.2022.913030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/02/2022] [Indexed: 11/25/2022] Open
Abstract
Active thermogenic adipocytes avidly consume energy substrates like fatty acids and glucose to maintain body temperature upon cold exposure. Despite strong evidence for the involvement of brown adipose tissue (BAT) in controlling systemic energy homeostasis upon nutrient excess, it is unclear how the activity of brown adipocytes is regulated in times of nutrient scarcity. Therefore, this study aimed to scrutinize factors that modulate BAT activity to balance thermogenic and energetic needs upon simultaneous fasting and cold stress. For an unbiased view, we performed transcriptomic and miRNA sequencing analyses of BAT from acutely fasted (24 h) mice under mild cold exposure. Combining these data with in-depth bioinformatic analyses and in vitro gain-of-function experiments, we define a previously undescribed axis of p53 inducing miR-92a-1-5p transcription that is highly upregulated by fasting in thermogenic adipocytes. p53, a fasting-responsive transcription factor, was previously shown to control genes involved in the thermogenic program and miR-92a-1-5p was found to negatively correlate with human BAT activity. Here, we identify fructose transporter Slc2a5 as one direct downstream target of this axis and show that fructose can be taken up by and metabolized in brown adipocytes. In sum, this study delineates a fasting-induced pathway involving p53 that transactivates miR-92a-1-5p, which in turn decreases Slc2a5 expression, and suggests fructose as an energy substrate in thermogenic adipocytes.
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Affiliation(s)
- Isabel Reinisch
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Ingeborg Klymiuk
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Helene Michenthaler
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Elisabeth Moyschewitz
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Markus Galhuber
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Jelena Krstic
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Magnus Domingo
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Fangrong Zhang
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
- Key Laboratory of Gastrointestinal Cancer, Ministry of Education, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | | | - Nemanja Vujić
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Dagmar Kratky
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Renate Schreiber
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, Graz, Austria
- BioHealth Graz, Graz, Austria
| | - Michael Schupp
- Cardiovascular Metabolic Renal (CMR)- Research Center, Institute of Pharmacology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt- Universität zu Berlin, Berlin, Germany
| | - Georgia Lenihan-Geels
- Department of Adipocyte Development and Nutrition, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
| | - Tim J. Schulz
- Department of Adipocyte Development and Nutrition, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
| | - Roland Malli
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Andreas Prokesch
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
- *Correspondence: Andreas Prokesch,
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6
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Horstmann H, Anto Michel N, Sheng XS, Hansen S, Lindau A, Klymiuk I, Marchini T, Winkels H, Verheyen N, Gerhardt T, Oswald W, Conhert T, Bode C, Zirlik A, Wolf D. Integrative single cell RNA-sequencing descrambles a substantial divergence of adaptive immune cell identities and transcriptional programs in mouse and human atherosclerosis. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.3411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Aims
The distinct function of immune cells in human atherosclerosis has been mostly defined by preclinical mouse studies. Contrastingly, the immune cell composition of human atherosclerotic plaques and their contribution to disease progression is only poorly understood. It remains uncertain whether genetic animal models allow for valuable translational approaches.
Methods and results
We performed single cell RNA-sequencing (scRNAseq) to define the immune cell landscape in human carotid atherosclerotic plaques. The human immune cell repertoire was dominated by T cells with a considerable inter-patient variability and an unexpected heterogeneity. We performed bioinformatical integration with 7 mouse data sets and discovered a total of 38 cellular identities, of which some were not conserved between species and exclusively found in mice or humans. Locations, frequencies, and transcriptional programs of immune cells in preclinical mouse models did not resemble the immune cell landscape in human atherosclerosis. In contrast to mice, human plaques were not myeloid- and B cell-dominated and instead contained several T cell phenotypes with hallmarks of T cell memory, dysregulation, exhaustion, and activation. Human immune cells were predominantly enriched for transcriptional programs of hypoxia, glucose, and autoimmunity. In a validation cohort of 43 patients activated immune cell subsets defined by multi-colour flow cytometry associated with cerebral ischemia and coronary artery disease.
Conclusion
Here, we uncover yet undefined immune cell types associating with clinical disease. This leukocyte atlas of human atherosclerosis builds the conceptual basis for subsequent identification of cellular targets for clinical immunomodulatory therapies and risk prediction.
Funding Acknowledgement
Type of funding sources: Public grant(s) – National budget only. Main funding source(s): ERC Starting Grant
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Affiliation(s)
- H Horstmann
- University Hospital of Freiburg, Freiburg, Germany
| | - N Anto Michel
- Medical University of Graz, Cardiology, Graz, Austria
| | - X S Sheng
- University Hospital of Freiburg, Freiburg, Germany
| | - S Hansen
- University Hospital of Freiburg, Freiburg, Germany
| | - A Lindau
- University Hospital of Freiburg, Freiburg, Germany
| | - I Klymiuk
- Medical University of Graz, Cardiology, Graz, Austria
| | - T Marchini
- University Hospital of Freiburg, Freiburg, Germany
| | - H Winkels
- University hospital Köln, Cologne, Germany
| | - N Verheyen
- Medical University of Graz, Cardiology, Graz, Austria
| | - T Gerhardt
- Charite - Campus Benjamin Franklin, Berlin, Germany
| | - W Oswald
- Medical University of Graz, Cardiology, Graz, Austria
| | - T Conhert
- Medical University of Graz, Cardiology, Graz, Austria
| | - C Bode
- University Hospital of Freiburg, Freiburg, Germany
| | - A Zirlik
- Medical University of Graz, Cardiology, Graz, Austria
| | - D Wolf
- University Hospital of Freiburg, Freiburg, Germany
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Castellani C, Obermüller B, Kienesberger B, Singer G, Peterbauer C, Grabherr R, Mayrhofer S, Klymiuk I, Horvath A, Stadlbauer V, Russmayer H, Miekisch W, Fuchs P, Till H, Heinl S. Production, Storage Stability, and Susceptibility Testing of Reuterin and Its Impact on the Murine Fecal Microbiome and Volatile Organic Compound Profile. Front Microbiol 2021; 12:699858. [PMID: 34394042 PMCID: PMC8361477 DOI: 10.3389/fmicb.2021.699858] [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] [Received: 04/24/2021] [Accepted: 06/29/2021] [Indexed: 12/18/2022] Open
Abstract
Background: Probiotics are generally considered as safe, but infections may rarely occur in vulnerable patients. Alternatives to live microorganisms to manage dysbiosis may be of interest in these patients. Reuterin is a complex component system exhibiting broad spectrum antimicrobial activity and a possible candidate substance in these cases. Methods: Reuterin supernatant was cultured from Lentilactobacillus diolivorans in a bioreactor in a two-step process. Storage stability at −20°C and effect of repeated freeze-thaw cycles were assessed by high performance liquid chromatography (HPLC). Antimicrobial activity was tested against Clostridium difficile, Listeria monocytogenes, Escherichia coli, Enterococcus faecium, Staphylococcus (S.) aureus, Staphylococcus epidermidis, Streptococcus (S.) agalactiae, Propionibacterium acnes, and Pseudomonas aeruginosae. Male BALBc mice were gavage fed with reuterin supernatant (n = 10) or culture medium (n = 10). Fecal volatile organic compounds (VOC) were assessed by gas chromatography mass spectroscopy; the microbiome was examined by 16S rRNA gene sequencing. Results: The supernatant contained 13.4 g/L reuterin (3-hydroxypropionaldehyde; 3-HPA). 3-HPA content remained stable at −20°C for 35 days followed by a slow decrease of its concentration. Repeated freezing/thawing caused a slow 3-HPA decrease. Antimicrobial activity was encountered against S. aureus, S. epidermidis, and S. agalactiae. Microbiome analysis showed no differences in alpha and beta diversity markers. Linear discriminant effect size (LEfSe) analysis identified Lachnospiraceae_bacterium_COE1 and Ruminoclostridium_5_uncultured_Clostridiales_ bacterium (in the reuterin medium group) and Desulfovibrio_uncultured_ bacterium, Candidatus Arthromitus, Ruminococcae_NK4A214_group, and Eubacterium_xylanophilum_group (in the reuterin group) as markers for group differentiation. VOC analysis showed a significant decrease of heptane and increase of 3-methylbutanal in the reuterin group. Conclusion: The supernatant produced in this study contained acceptable amounts of 3-HPA remaining stable for 35 days at −20°C and exhibiting an antimicrobial effect against S. aureus, S. agalactiae, and S. epidermidis. Under in vivo conditions, the reuterin supernatant caused alterations of the fecal microbiome. In the fecal, VOC analysis decreased heptane and increased 3-methylbutanal were encountered. These findings suggest the high potential of the reuterin system to influence the intestinal microbiome in health and disease, which needs to be examined in detail in future projects.
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Affiliation(s)
- Christoph Castellani
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, Graz, Austria
| | - Beate Obermüller
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, Graz, Austria
| | - Bernhard Kienesberger
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, Graz, Austria
| | - Georg Singer
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, Graz, Austria
| | - Clemens Peterbauer
- Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Reingard Grabherr
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Sigrid Mayrhofer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Ingeborg Klymiuk
- Core Facility of Molecular Biology, Medical University of Graz, Graz, Austria.,Department of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Angela Horvath
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria.,Center of Biomarker Research in Medicine (CBmed), Graz, Austria
| | - Vanessa Stadlbauer
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria.,Center of Biomarker Research in Medicine (CBmed), Graz, Austria
| | - Hannes Russmayer
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria.,CD Laboratory for Biotechnology of Glycerol, Vienna, Austria
| | - Wolfram Miekisch
- Department of Anesthesiology and Intensive Care, Experimental Research Center, University of Rostock, Rostock, Germany
| | - Patricia Fuchs
- Department of Anesthesiology and Intensive Care, Experimental Research Center, University of Rostock, Rostock, Germany
| | - Holger Till
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, Graz, Austria
| | - Stefan Heinl
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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8
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Thannesberger J, Rascovan N, Eisenmann A, Klymiuk I, Zittra C, Fuehrer HP, Scantlebury-Manning T, Gittens-St Hilaire M, Austin S, Landis RC, Steininger C. Viral metagenomics reveals the presence of novel Zika virus variants in Aedes mosquitoes from Barbados. Parasit Vectors 2021; 14:343. [PMID: 34187544 PMCID: PMC8244189 DOI: 10.1186/s13071-021-04840-0] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/11/2021] [Indexed: 01/08/2023] Open
Abstract
Background The Zika virus (ZIKV) epidemic of 2015/2016 spread throughout numerous countries. It emerged in mainland Latin America and spread to neighboring islands, including the Caribbean island of Barbados. Recent studies have indicated that the virus must have already been circulating in local mosquito populations in Brazil for almost 2 years before it was identified by the World Health Organization in 2015. Metagenomic detection assays have the potential to detect emerging pathogens without prior knowledge of their genomic nucleic acid sequence. Yet their applicability as vector surveillance tools has been widely limited by the complexity of DNA populations from field-collected mosquito preparations. The aim of this study was to investigate local vector biology and characterize metagenomic arbovirus diversity in Aedes mosquitoes during the ongoing 2015/2016 ZIKV epidemic. Methods We performed a short-term vector screening study on the island of Barbados during the ongoing 2015/2016 ZIKV epidemic, where we sampled local Aedes mosquitoes. We reanalyzed mosquito viral microbiome data derived from standard Illumina MiSeq sequencing to detect arbovirus sequences. Additionally, we employed deep sequencing techniques (Illumina HiSeq) and designed a novel bait capture enrichment assay to increase sequencing efficiency for arbovirus sequences from complex DNA samples. Results We found that Aedes aegypti seemed to be the most likely vector of ZIKV, although it prevailed at a low density during the observed time period. The number of detected viruses increased with sequencing depth. Arbovirus sequence enrichment of metagenomic DNA preparations allowed the detection of arbovirus sequences of two different ZIKV genotypes, including a novel one. To our knowledge, this is the first report of the S3116W mutation in the NS5 gene region of ZIKV polyprotein. Conclusions The metagenomic arbovirus detection approach presented here may serve as a useful tool for the identification of epidemic-causing arboviruses with the additional benefit of enabling the collection of phylogenetic information on the source. Apart from detecting more than 88 viruses using this approach, we also found evidence of novel ZIKV variants circulating in the local mosquito population during the observed time period. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04840-0.
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Affiliation(s)
- J Thannesberger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
| | - N Rascovan
- Department of Genomes & Genetics, Institut Pasteur, Paris, France
| | - A Eisenmann
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria
| | - I Klymiuk
- Department of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - C Zittra
- Institute of Parasitology, University of Veterinary Medicine, Vienna, Austria
| | - H P Fuehrer
- Institute of Parasitology, University of Veterinary Medicine, Vienna, Austria
| | - T Scantlebury-Manning
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, Bridgetown, Barbados
| | | | - S Austin
- Department of Biological and Chemical Sciences, University of the West Indies, Cave Hill Campus, Cave Hill, Barbados
| | - R C Landis
- Edmund Cohen Laboratory for Vascular Research, George Alleyne Chronic Disease Research Centre, The University of the West Indies, Bridgetown, Barbados
| | - C Steininger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.
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9
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Kienesberger B, Obermüller B, Singer G, Mittl B, Grabherr R, Mayrhofer S, Heinl S, Stadlbauer V, Horvath A, Miekisch W, Fuchs P, Klymiuk I, Till H, Castellani C. (S)-Reutericyclin: Susceptibility Testing and In Vivo Effect on Murine Fecal Microbiome and Volatile Organic Compounds. Int J Mol Sci 2021; 22:6424. [PMID: 34203988 PMCID: PMC8232739 DOI: 10.3390/ijms22126424] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/08/2021] [Accepted: 06/14/2021] [Indexed: 11/17/2022] Open
Abstract
We aimed to assess the in vitro antimicrobial activity and the in vivo effect on the murine fecal microbiome and volatile organic compound (VOC) profile of (S)-reutericyclin. The antimicrobial activity of (S)-reutericyclin was tested against Clostridium difficile, Listeria monocytogenes, Escherichia coli, Enterococcus faecium, Staphylococcus aureus, Staphylococcus (S.) epidermidis, Streptococcus agalactiae, Pseudomonas aeruginosa and Propionibacterium acnes. Reutericyclin or water were gavage fed to male BALBc mice for 7 weeks. Thereafter stool samples underwent 16S based microbiome analysis and VOC analysis by gas chromatography mass spectrometry (GC-MS). (S)-reutericyclin inhibited growth of S. epidermidis only. Oral (S)-reutericyclin treatment caused a trend towards reduced alpha diversity. Beta diversity was significantly influenced by reutericyclin. Linear discriminant analysis Effect Size (LEfSe) analysis showed an increase of Streptococcus and Muribaculum as well as a decrease of butyrate producing Ruminoclostridium, Roseburia and Eubacterium in the reutericyclin group. VOC analysis revealed significant increases of pentane and heptane and decreases of 2,3-butanedione and 2-heptanone in reutericyclin animals. The antimicrobial activity of (S)-reutericyclin differs from reports of (R)-reutericyclin with inhibitory effects on a multitude of Gram-positive bacteria reported in the literature. In vivo (S)-reutericyclin treatment led to a microbiome shift towards dysbiosis and distinct alterations of the fecal VOC profile.
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Affiliation(s)
- Bernhard Kienesberger
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, 8036 Graz, Austria; (B.K.); (G.S.); (B.M.); (H.T.); (C.C.)
| | - Beate Obermüller
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, 8036 Graz, Austria; (B.K.); (G.S.); (B.M.); (H.T.); (C.C.)
| | - Georg Singer
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, 8036 Graz, Austria; (B.K.); (G.S.); (B.M.); (H.T.); (C.C.)
| | - Barbara Mittl
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, 8036 Graz, Austria; (B.K.); (G.S.); (B.M.); (H.T.); (C.C.)
| | - Reingard Grabherr
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria; (R.G.); (S.M.); (S.H.)
| | - Sigrid Mayrhofer
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria; (R.G.); (S.M.); (S.H.)
| | - Stefan Heinl
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, 1190 Vienna, Austria; (R.G.); (S.M.); (S.H.)
| | - Vanessa Stadlbauer
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Graz, 8036 Graz, Austria; (V.S.); (A.H.)
| | - Angela Horvath
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Graz, 8036 Graz, Austria; (V.S.); (A.H.)
- Center of Biomarker Research (CBmed), 8036 Graz, Austria
| | - Wolfram Miekisch
- Experimental Research Center, Department of Anesthesiology and Intensive Care, Rostock University Medical Center, 18057 Rostock, Germany; (W.M.); (P.F.)
| | - Patricia Fuchs
- Experimental Research Center, Department of Anesthesiology and Intensive Care, Rostock University Medical Center, 18057 Rostock, Germany; (W.M.); (P.F.)
| | - Ingeborg Klymiuk
- Gottfried Schatz Research Center, Department of Cell Biology, Histology and Embryology, Medical University of Graz, 8036 Graz, Austria;
| | - Holger Till
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, 8036 Graz, Austria; (B.K.); (G.S.); (B.M.); (H.T.); (C.C.)
| | - Christoph Castellani
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, 8036 Graz, Austria; (B.K.); (G.S.); (B.M.); (H.T.); (C.C.)
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10
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Klymiuk I, Singer G, Castellani C, Trajanoski S, Obermüller B, Till H. Characterization of the Luminal and Mucosa-Associated Microbiome along the Gastrointestinal Tract: Results from Surgically Treated Preterm Infants and a Murine Model. Nutrients 2021; 13:nu13031030. [PMID: 33806771 PMCID: PMC8004827 DOI: 10.3390/nu13031030] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 02/02/2021] [Revised: 03/10/2021] [Accepted: 03/18/2021] [Indexed: 02/07/2023] Open
Abstract
Environmental factors, including nutritional habits or birth mode, are known key determinants for intestinal microbial composition. Investigations of the intestinal microbiome in different species in a multiplicity of studies during recent decades have revealed differential microbial patterns and quantities along the gastrointestinal (GI) tract. Characterization of the microbial pattern in various aspects is a prerequisite for nutritional interventions. In this 16S rRNA amplicon-based approach, we present a characterization of the mucosa-associated microbiome in comparison with the luminal community of four infants at the time of the closure of ileostomies and perform a systematic characterization of the corresponding luminal and mucosal microbiome from jejunal, ileal and colonic regions, as well as collected feces in mice. The most dominant taxa in infant-derived samples altered due to individual differences, and in the mucosa, Enterococcus, Clostridiumsensustricto1, Veillonella, Streptococcus and Staphylococcus were the most abundant. Two less abundant taxa differed significantly between the mucosa and lumen. In murine samples, relative abundances differed significantly, mainly between the intestinal regions. Significant differences between mouse mucosa- and lumen-derived samples could be found in the observed species with a trend to lower estimated diversity in mucosa-derived samples, as well as in the relative abundance of individual taxa. In this study, we examined the difference between the mucosal and luminal bacterial colonization of the gastrointestinal tract in a small sample cohort of preterm infants. Individual differences were characterized and statistical significance was reached in two taxa (Cupriavidus, Ralstonia). The corresponding study on the different murine intestinal regions along the GI tract showed differences all over the intestinal region.
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Affiliation(s)
- Ingeborg Klymiuk
- Center for Medical Research, Medical University of Graz, 8010 Graz, Austria; (I.K.); (S.T.)
| | - Georg Singer
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, 8010 Graz, Austria; (C.C.); (B.O.); (H.T.)
- Correspondence: ; Tel.: +43-316-385-83722
| | - Christoph Castellani
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, 8010 Graz, Austria; (C.C.); (B.O.); (H.T.)
| | - Slave Trajanoski
- Center for Medical Research, Medical University of Graz, 8010 Graz, Austria; (I.K.); (S.T.)
| | - Beate Obermüller
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, 8010 Graz, Austria; (C.C.); (B.O.); (H.T.)
| | - Holger Till
- Department of Paediatric and Adolescent Surgery, Medical University of Graz, 8010 Graz, Austria; (C.C.); (B.O.); (H.T.)
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11
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Warncke G, Singer G, Windhaber J, Schabl L, Friehs E, Miekisch W, Gierschner P, Klymiuk I, Eber E, Zeder K, Pfleger A, Obermüller B, Till H, Castellani C. Volatile Organic Compounds, Bacterial Airway Microbiome, Spirometry and Exercise Performance of Patients after Surgical Repair of Congenital Diaphragmatic Hernia. Molecules 2021; 26:molecules26030645. [PMID: 33530644 PMCID: PMC7865878 DOI: 10.3390/molecules26030645] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 11/16/2022] Open
Abstract
The aim of this study was to analyze the exhaled volatile organic compounds (VOCs) profile, airway microbiome, lung function and exercise performance in congenital diaphragmatic hernia (CDH) patients compared to healthy age and sex-matched controls. A total of nine patients (median age 9 years, range 6-13 years) treated for CDH were included. Exhaled VOCs were measured by GC-MS. Airway microbiome was determined from deep induced sputum by 16S rRNA gene sequencing. Patients underwent conventional spirometry and exhausting bicycle spiroergometry. The exhaled VOC profile showed significantly higher levels of cyclohexane and significantly lower levels of acetone and 2-methylbutane in CDH patients. Microbiome analysis revealed no significant differences for alpha-diversity, beta-diversity and LefSe analysis. CDH patients had significantly lower relative abundances of Pasteurellales and Pasteurellaceae. CDH patients exhibited a significantly reduced Tiffeneau Index. Spiroergometry showed no significant differences. This is the first study to report the VOCs profile and airway microbiome in patients with CDH. Elevations of cyclohexane observed in the CDH group have also been reported in cases of lung cancer and pneumonia. CDH patients had no signs of impaired physical performance capacity, fueling controversial reports in the literature.
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MESH Headings
- Acetone/analysis
- Adolescent
- Bacteria/classification
- Bacteria/genetics
- Bacteria/isolation & purification
- Child
- DNA, Bacterial/genetics
- DNA, Ribosomal/genetics
- Exercise
- Female
- Hernias, Diaphragmatic, Congenital/metabolism
- Hernias, Diaphragmatic, Congenital/physiopathology
- Hernias, Diaphragmatic, Congenital/surgery
- Herniorrhaphy/methods
- Humans
- Male
- Microbiota
- Pentanes/analysis
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- Spirometry
- Vital Capacity
- Volatile Organic Compounds/analysis
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Affiliation(s)
- Gert Warncke
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Georg Singer
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
- Correspondence: ; Tel.: +43-316-385-83722
| | - Jana Windhaber
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Lukas Schabl
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Elena Friehs
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Wolfram Miekisch
- Department of Anesthesiology and Intensive Care Medicine, Rostock Medical Breath Research Analytics and Technologies (ROMBAT), Rostock University Medical Centre, 18057 Rostock, Germany; (W.M.); (P.G.)
| | - Peter Gierschner
- Department of Anesthesiology and Intensive Care Medicine, Rostock Medical Breath Research Analytics and Technologies (ROMBAT), Rostock University Medical Centre, 18057 Rostock, Germany; (W.M.); (P.G.)
| | - Ingeborg Klymiuk
- Core Facility Molecular Biology, Center for Medical Research, Medical University of Graz, 8036 Graz, Austria;
| | - Ernst Eber
- Department of Paediatrics and Adolescent Medicine, Division of Paediatric Pulmonology and Allergology, Medical University of Graz, 8036 Graz, Austria; (E.E.); (K.Z.); (A.P.)
| | - Katarina Zeder
- Department of Paediatrics and Adolescent Medicine, Division of Paediatric Pulmonology and Allergology, Medical University of Graz, 8036 Graz, Austria; (E.E.); (K.Z.); (A.P.)
| | - Andreas Pfleger
- Department of Paediatrics and Adolescent Medicine, Division of Paediatric Pulmonology and Allergology, Medical University of Graz, 8036 Graz, Austria; (E.E.); (K.Z.); (A.P.)
| | - Beate Obermüller
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Holger Till
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
| | - Christoph Castellani
- Department of Paediatric and Adolescent Surgery, Medical University Graz, 8036 Graz, Austria; (G.W.); (J.W.); (L.S.); (E.F.); (B.O.); (H.T.); (C.C.)
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12
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Berg JL, Perfler B, Hatzl S, Mayer MC, Wurm S, Uhl B, Reinisch A, Klymiuk I, Tierling S, Pregartner G, Bachmaier G, Berghold A, Geissler K, Pichler M, Hoefler G, Strobl H, Wölfler A, Sill H, Zebisch A. Micro-RNA-125a mediates the effects of hypomethylating agents in chronic myelomonocytic leukemia. Clin Epigenetics 2021; 13:1. [PMID: 33407852 PMCID: PMC7789782 DOI: 10.1186/s13148-020-00979-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 06/03/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Chronic myelomonocytic leukemia (CMML) is an aggressive hematopoietic malignancy that arises from hematopoietic stem and progenitor cells (HSPCs). Patients with CMML are frequently treated with epigenetic therapeutic approaches, in particular the hypomethylating agents (HMAs), azacitidine (Aza) and decitabine (Dec). Although HMAs are believed to mediate their efficacy via re-expression of hypermethylated tumor suppressors, knowledge about relevant HMA targets is scarce. As silencing of tumor-suppressive micro-RNAs (miRs) by promoter hypermethylation is a crucial step in malignant transformation, we asked for a role of miRs in HMA efficacy in CMML. RESULTS Initially, we performed genome-wide miR-expression profiling in a KrasG12D-induced CMML mouse model. Selected candidates with prominently decreased expression were validated by qPCR in CMML mice and human CMML patients. These experiments revealed the consistent decrease in miR-125a, a miR with previously described tumor-suppressive function in myeloid neoplasias. Furthermore, we show that miR-125a downregulation is caused by hypermethylation of its upstream region and can be reversed by HMA treatment. By employing both lentiviral and CRISPR/Cas9-based miR-125a modification, we demonstrate that HMA-induced miR-125a upregulation indeed contributes to mediating the anti-leukemic effects of these drugs. These data were validated in a clinical context, as miR-125a expression increased after HMA treatment in CMML patients, a phenomenon that was particularly pronounced in cases showing clinical response to these drugs. CONCLUSIONS Taken together, we report decreased expression of miR-125a in CMML and delineate its relevance as mediator of HMA efficacy within this neoplasia.
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Affiliation(s)
- Johannes Lorenz Berg
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Bianca Perfler
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Stefan Hatzl
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Marie-Christina Mayer
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Sonja Wurm
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Barbara Uhl
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Andreas Reinisch
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Ingeborg Klymiuk
- Core Facility Molecular Biology, Medical University of Graz, Graz, Austria
| | - Sascha Tierling
- Department of Genetics, University of Saarland, Saarbrücken, Germany
| | - Gudrun Pregartner
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Gerhard Bachmaier
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Andrea Berghold
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Graz, Austria
| | - Klaus Geissler
- 5th Medical Department with Hematology, Oncology and Palliative Medicine, Hospital Hietzing, Vienna, Austria.,Sigmund Freud University, Vienna, Austria
| | - Martin Pichler
- Division of Oncology, Medical University of Graz, Graz, Austria.,Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Centre, Houston, TX, USA
| | - Gerald Hoefler
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Herbert Strobl
- Otto Loewi Research Centre, Immunology and Pathophysiology, Medical University of Graz, Graz, Austria
| | - Albert Wölfler
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Heinz Sill
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria
| | - Armin Zebisch
- Division of Hematology, Medical University of Graz, Auenbruggerplatz 38, 8036, Graz, Austria. .,Otto-Loewi Research Centre for Vascular Biology, Immunology and Inflammation, Division of Pharmacology, Medical University of Graz, Universitätsplatz 4, 8010, Graz, Austria.
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13
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Thannesberger J, Rascovan N, Eisenmann A, Klymiuk I, Zittra C, Fuehrer HP, Scantlebury-Manning T, Gittens-St.Hilaire M, Austin S, Landis RC, Steininger C. Highly Sensitive Virome Characterization of Aedes aegypti and Culex pipiens Complex from Central Europe and the Caribbean Reveals Potential for Interspecies Viral Transmission. Pathogens 2020; 9:E686. [PMID: 32839419 PMCID: PMC7559857 DOI: 10.3390/pathogens9090686] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 07/16/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 12/31/2022] Open
Abstract
Mosquitoes are the most important vectors for arthropod-borne viral diseases. Mixed viral infections of mosquitoes allow genetic recombination or reassortment of diverse viruses, turning mosquitoes into potential virologic mixing bowls. In this study, we field-collected mosquitoes of different species (Aedes aegypti and Culex pipiens complex), from different geographic locations and environments (central Europe and the Caribbean) for highly sensitive next-generation sequencing-based virome characterization. We found a rich virus community associated with a great diversity of host species. Among those, we detected a large diversity of novel virus sequences that we could predominately assign to circular Rep-encoding single-stranded (CRESS) DNA viruses, including the full-length genome of a yet undescribed Gemykrogvirus species. Moreover, we report for the first time the detection of a potentially zoonotic CRESS-DNA virus (Cyclovirus VN) in mosquito vectors. This study expands the knowledge on virus diversity in medically important mosquito vectors, especially for CRESS-DNA viruses that have previously been shown to easily recombine and jump the species barrier.
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Affiliation(s)
- Jakob Thannesberger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, 1090 Vienna, Austria; (J.T.); (A.E.)
| | - Nicolas Rascovan
- Department of Genomes & Genetics, Institut Pasteur, 75015 Paris, France;
| | - Anna Eisenmann
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, 1090 Vienna, Austria; (J.T.); (A.E.)
| | - Ingeborg Klymiuk
- Center for Medical Research, Core Facility Molecular Biology, Medical University of Graz, 8036 Graz, Austria;
| | - Carina Zittra
- Institute of Parasitology, University of Veterinary Medicine, 1210 Vienna, Austria; (C.Z.); (H.-P.F.)
- Unit Limnology, Department of Functional and Evolutionary Ecology, University of Vienna, 1010 Vienna, Austria
| | - Hans-Peter Fuehrer
- Institute of Parasitology, University of Veterinary Medicine, 1210 Vienna, Austria; (C.Z.); (H.-P.F.)
| | - Thea Scantlebury-Manning
- Department of Biological and Chemical Sciences, Faculty of Science and Technology, Cave Hill Campus, The University of the West Indies, Bridgetown BB11000, Barbados; (T.S.-M.); (S.A.)
| | - Marquita Gittens-St.Hilaire
- Faculty of Medical Sciences, University of the West Indies, Queen Elizabeth Hospital, St. Michael BB14004, Barbados;
| | - Shane Austin
- Department of Biological and Chemical Sciences, Faculty of Science and Technology, Cave Hill Campus, The University of the West Indies, Bridgetown BB11000, Barbados; (T.S.-M.); (S.A.)
| | - Robert Clive Landis
- Edmund Cohen Laboratory for Vascular Research, George Alleyne Chronic Disease Research Centre, The University of the West Indies, Bridgetown BB11115, Barbados;
| | - Christoph Steininger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, 1090 Vienna, Austria; (J.T.); (A.E.)
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14
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Zollner-Schwetz I, Scarpatetti M, Pichler G, Pux C, Klymiuk I, Trajanoski S, Krause R. Effect of a Multispecies Probiotic on Intestinal and Skin Colonization by Multidrug-Resistant Gram-Negative Bacteria in Patients in a Long-Term Care Facility: A Pilot Study. Nutrients 2020; 12:nu12061586. [PMID: 32481668 PMCID: PMC7352861 DOI: 10.3390/nu12061586] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/20/2020] [Accepted: 05/27/2020] [Indexed: 01/02/2023] Open
Abstract
Residents in long-term care facilities (LTCFs) are frequently colonized by multidrug-resistant Gram-negative bacteria, putting them at risk for subsequent infections. We aimed to evaluate the effect of the multispecies probiotic Omnibiotic10AAD® on the intestinal and inguinal skin colonization of patients by multidrug-resistant Gram-negative bacteria in LTCFs. Patients colonized by multidrug-resistant Gram-negative bacteria received a 12 week oral course of Omnibiotic10AAD®. Inguinal swabs and stool samples were collected during and after treatment for microbiological and microbiome analysis. The median age of patients was 76 years. Twelve patients completed the pilot study. Intestinal colonization was reduced to 42% of patients 8 weeks after the end of treatment, but increased to 66% 24 weeks after the end of probiotic treatment. Colonization of inguinal skin was lowest during probiotic treatment and increased thereafter. Fecal microbiome analysis revealed statistically significant increases of the genus Enterococcus comparing start and end of probiotic treatment. In conclusion, a 12 week course of a multispecies probiotic led to a transient reduction of intestinal colonization 8 weeks after the end of treatment. The findings of our pilot study warrant further research in the area of probiotics and intestinal colonization by multidrug-resistant bacteria.
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Affiliation(s)
- Ines Zollner-Schwetz
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria;
- Correspondence:
| | - Monika Scarpatetti
- Geriatric Health Centres of the City of Graz, Albert-Schweitzer-Gasse 36, 8020 Graz, Austria; (M.S.); (G.P.); (C.P.)
| | - Gerald Pichler
- Geriatric Health Centres of the City of Graz, Albert-Schweitzer-Gasse 36, 8020 Graz, Austria; (M.S.); (G.P.); (C.P.)
| | - Christian Pux
- Geriatric Health Centres of the City of Graz, Albert-Schweitzer-Gasse 36, 8020 Graz, Austria; (M.S.); (G.P.); (C.P.)
| | - Ingeborg Klymiuk
- Core Facility Molecular Biology, Centre for Medical Research, Medical University of Graz, Stiftingtalstraße 24/1, 8010 Graz, Austria; (I.K.); (S.T.)
| | - Slave Trajanoski
- Core Facility Molecular Biology, Centre for Medical Research, Medical University of Graz, Stiftingtalstraße 24/1, 8010 Graz, Austria; (I.K.); (S.T.)
| | - Robert Krause
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria;
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15
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Stadlbauer V, Komarova I, Klymiuk I, Durdevic M, Reisinger A, Blesl A, Rainer F, Horvath A. Disease severity and proton pump inhibitor use impact strongest on faecal microbiome composition in liver cirrhosis. Liver Int 2020; 40:866-877. [PMID: 31943691 PMCID: PMC7187411 DOI: 10.1111/liv.14382] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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] [Received: 10/07/2019] [Revised: 12/13/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Compositional changes of the faecal microbiome in cirrhosis are well described and have been associated with complications and prognosis. However, it is less well known, which disease or treatment-related factors affect microbiome composition most distinctively. METHODS 16S rDNA sequencing data of 88 cirrhotic outpatients were investigated. Factors influencing microbiome composition were analysed by univariate and multivariate redundancy analysis. The association of the identified factors with changes in diversity and taxonomic composition was studied in depth using analysis of composition of microbiome, LDA-effect size and least absolute shrinkage and selection operator regularized regression. RESULTS Disease severity and aetiology, proton pump inhibitor (PPI) use, nutritional status, age and C-reactive protein are significant explanatory variables for faecal microbiome composition in liver cirrhosis. Despite some taxonomic overlaps especially between disease severity and PPI use, we could show that the effects of disease severity, aetiology, PPI use and age are independent factors influencing microbiome composition also in subgroup analyses. CONCLUSION Our cross sectional system biology study identifies disease severity, aetiology, PPI use and age as independent factors that influence microbiome composition in liver cirrhosis. In chronic diseases with high morbidity, such as liver cirrhosis, precise patient metadata documentation is of utmost importance in microbiome analysis. Further studies with a higher sample size are necessary to validate this finding. TRIAL REGISTRATION NUMBER NCT01607528.
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Affiliation(s)
- Vanessa Stadlbauer
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineMedical University of GrazGrazAustria,Center for Biomarker Research in Medicine (CBmed)GrazAustria
| | - Irina Komarova
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineMedical University of GrazGrazAustria
| | - Ingeborg Klymiuk
- Center for Medical ResearchMedical University of GrazGrazAustria
| | - Marija Durdevic
- Center for Medical ResearchMedical University of GrazGrazAustria,Institute of PathologyMedical University of GrazGrazAustria
| | - Alexander Reisinger
- Intensive Care UnitDepartment of Internal MedicineMedical University of GrazGrazAustria
| | - Andreas Blesl
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineMedical University of GrazGrazAustria
| | - Florian Rainer
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineMedical University of GrazGrazAustria
| | - Angela Horvath
- Division of Gastroenterology and HepatologyDepartment of Internal MedicineMedical University of GrazGrazAustria,Center for Biomarker Research in Medicine (CBmed)GrazAustria
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16
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Horvath A, Rainer F, Bashir M, Leber B, Schmerboeck B, Klymiuk I, Groselj-Strele A, Durdevic M, Freedberg DE, Abrams JA, Fickert P, Stiegler P, Stadlbauer V. Biomarkers for oralization during long-term proton pump inhibitor therapy predict survival in cirrhosis. Sci Rep 2019; 9:12000. [PMID: 31427714 PMCID: PMC6700098 DOI: 10.1038/s41598-019-48352-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [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: 02/06/2019] [Accepted: 07/31/2019] [Indexed: 02/07/2023] Open
Abstract
Proton pump inhibitors (PPI) are an invaluable therapy option for acid related diseases; however, PPI therapy is also linked to a series of side effects in cirrhosis, such as microbiome alterations, spontaneous bacterial peritonitis and hepatic encephalopathy. Decision tools to balance benefits and risks of PPI therapy are largely missing. In this study, we tested gut-derived biomarkers to identify PPI-associated dysbiosis, its association with gut barrier function and liver-related mortality. In this observational study, faecal microbiome composition data obtained from 16S rDNA sequencing of 90 cirrhotic patients with and without long-term PPI use and additional potential biomarkers identified from the literature were evaluated for their predictive value regarding PPI-associated dysbiosis and liver-related three-year mortality. In addition, faecal calprotectin, faecal zonulin and serum lipopolysaccharides were assessed as markers for intestinal inflammation, gut permeability and bacterial translocation. Streptococcus salivarius, Veillonella parvula and the genus Streptococcus were significantly increased in patients with long-term PPI therapy and performed well as biomarkers for PPI-associated dysbiosis (accuracy: 74%, 72% and 74%, respectively). The abundance of Streptococcus salivarius was linked to intestinal inflammation and gut barrier dysfunction, whereas the abundance of Veillonella parvula showed associations with liver disease severity; both were independent predictors for liver-related three-year mortality. Gut-derived biomarkers of PPI-associated dysbiosis are linked to worse outcome and a potential option to evaluate the risks of adverse events during long-term PPI therapy.
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Affiliation(s)
- Angela Horvath
- Department of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria. .,Center for Biomarker Research in Medicine (CBmed), Graz, Austria.
| | - Florian Rainer
- Department of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| | - Mina Bashir
- Department of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
| | - Bettina Leber
- Department of Transplantation Surgery, Medical University of Graz, Graz, Austria
| | - Bianca Schmerboeck
- Department of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria.,Center for Biomarker Research in Medicine (CBmed), Graz, Austria
| | - Ingeborg Klymiuk
- Center for Medical Research, Core Facility Molecular Biology, Medical University of Graz, Graz, Austria
| | - Andrea Groselj-Strele
- Center for Medical Research, Core Facility Computational Bioanalytics, Medical University of Graz, Graz, Austria
| | - Marija Durdevic
- Center for Medical Research, Core Facility Computational Bioanalytics, Medical University of Graz, Graz, Austria
| | - Daniel E Freedberg
- Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, USA
| | - Julian A Abrams
- Division of Digestive and Liver Diseases, Columbia University Medical Center, New York, USA
| | - Peter Fickert
- Department of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| | - Philipp Stiegler
- Department of Transplantation Surgery, Medical University of Graz, Graz, Austria
| | - Vanessa Stadlbauer
- Department of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
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17
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Stadlbauer V, Horvath A, Komarova I, Schmerboeck B, Feldbacher N, Wurm S, Klymiuk I, Durdevic M, Rainer F, Blesl A, Stryeck S, Madl T, Stiegler P, Leber B. A single alcohol binge impacts on neutrophil function without changes in gut barrier function and gut microbiome composition in healthy volunteers. PLoS One 2019; 14:e0211703. [PMID: 30707717 PMCID: PMC6358085 DOI: 10.1371/journal.pone.0211703] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 08/14/2018] [Accepted: 01/15/2019] [Indexed: 12/31/2022] Open
Abstract
Alcohol binge drinking is a dangerous drinking habit, associated with neurological problems and inflammation. The impact of a single alcohol binge on innate immunity, gut barrier and gut microbiome was studied. In this cohort study 15 healthy volunteers received 2 ml vodka 40% v/v ethanol/kg body weight. Neutrophil function was studied by flow cytometry; markers of gut permeability and inflammation (lactulose/mannitol/sucrose test, zonulin, calprotectin, diamino-oxidase) were studied with NMR spectroscopy and enzyme-linked immunosorbent assay in urine, stool and serum respectively. Bacterial products in serum were quantified using different reporter cell lines. Gut microbiome composition was studied by 16S rDNA sequencing and bioinformatics analysis. After a single alcohol binge, neutrophils were transiently primed and the response to E.coli stimulation with reactive oxygen species (ROS) production was transiently increased, on the other hand the percentage of neutrophils that did not perform phagocytosis increased. No changes in gut permeability, inflammatory biomarker, bacterial translocation and microbiome composition could be detected up to 4 hours after a single alcohol binge or on the next day. A single alcohol binge in young, healthy volunteers transiently impacts on neutrophil function. Although the exact biological consequence of this finding is not clear yet, we believe that this strengthens the importance to avoid any alcohol binge drinking, even in young, otherwise healthy persons.
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Affiliation(s)
- Vanessa Stadlbauer
- Department of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
- * E-mail:
| | - Angela Horvath
- Department of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
- Center for Biomarker Research in Medicine (CBmed), Graz, Austria
| | - Irina Komarova
- Department of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| | - Bianca Schmerboeck
- Department of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
- Center for Biomarker Research in Medicine (CBmed), Graz, Austria
| | - Nicole Feldbacher
- Department of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| | - Sonja Wurm
- Department of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| | - Ingeborg Klymiuk
- Center for Medical Research, Core Facility Molecular Biology, Medical University of Graz, Graz, Austria
| | - Marija Durdevic
- Core Facility Computational Bioanalytics, Medical University of Graz, Graz, Austria
| | - Florian Rainer
- Department of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| | - Andreas Blesl
- Department of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| | - Sarah Stryeck
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Graz, Austria
- BioTechMed, Graz, Austria
| | - Philipp Stiegler
- Department of Transplantation Surgery, Medical University of Graz, Graz, Austria
| | - Bettina Leber
- Center for Biomarker Research in Medicine (CBmed), Graz, Austria
- Department of Transplantation Surgery, Medical University of Graz, Graz, Austria
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18
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Kispal ZF, Vajda P, Kardos D, Klymiuk I, Moissl-Eichinger C, Castellani C, Singer G, Till H. The local microbiome after pediatric bladder augmentation: intestinal segments and the native urinary bladder host similar mucosal microbiota. J Pediatr Urol 2019; 15:30.e1-30.e7. [PMID: 30206025 DOI: 10.1016/j.jpurol.2018.07.028] [Citation(s) in RCA: 5] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/26/2018] [Indexed: 01/26/2023]
Abstract
INTRODUCTION Next-generation sequencing (NGS) techniques have provided novel insights into the microbiome of the urinary bladder (UB). In children after bladder augmentation using either ileum (ileocystoplasty, ICP) or colon (colocystoplasty, CCP), the fate of the mucosal microbiome introduced into the urinary tract remains unknown. OBJECTIVE The aim was to compare the mucosal microbiome of the native UB vs the augmented intestinal segment (IS) using NGS. STUDY DESIGN Twelve children after bladder augmentation (ICP n = 6, CCP n = 6) were included. Biopsies were taken during routine postoperative cystoscopy from the native UB and the IS. Specimens underwent whole-genome DNA extraction, 16S rRNA gene amplification, NGS, and Quantitative Insights Into Microbial Ecology (QIIME) data analysis. Downstream statistical data analyses were performed in Calypso. RESULTS Patients' median age at the time of surgery was 11 years (6-17 years), and the median interval between augmentation and sampling was 7 years (4-13 years). α-Diversity (Shannon diversity index) was not significantly different between IS vs UB, ICP vs CCP, and male vs female. No general differences in the overall bacterial pattern (β-diversity) were found between IS, UB, ICP, and CCP groups. The groups overlapped in principal coordinate analysis (PCoA) and non-metric multidimensional scaling (NMDS) analysis (Figure). Age at sampling had a statistically significant influence on β-diversity at the genus level. Corynebacterium, Pseudoxanthomonas, Lactobacillus, Flavobacterium, and Micrococcus were the most dominating taxa detected over all samples. There was an obvious dominance of the genus Corynebacterium in the samples taken from the UB and IS in both ICP and CCP patients. Limitations of this study include the relatively small number of patients. CONCLUSION After bladder augmentation, the native UB and augmented ISs (ICP and CCP) host similar microbiota despite their distinct differences of originating mucosal anatomy.
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Affiliation(s)
- Z F Kispal
- Department of Pediatric and Adolescent Surgery, Medical University of Graz, Auenbruggerplatz 34, 8036 Graz, Austria
| | - P Vajda
- Department of Pediatrics, Surgical Division, University of Pecs, József A Str 7, 7623 Pecs, Hungary
| | - D Kardos
- Department of Pediatrics, Surgical Division, University of Pecs, József A Str 7, 7623 Pecs, Hungary
| | - I Klymiuk
- Center for Medical Research, Core Facility Molecular Biology, Medical University of Graz, Stiftingtalstraße 24, 8036 Graz, Austria
| | - C Moissl-Eichinger
- Department of Internal Medicine, Joint Facilities, Medical University of Graz, Stiftingtalstraße 24, 8036 Graz, Austria; BioTechMed, Mozartgasse 12/II, 8010 Graz, Austria
| | - C Castellani
- Department of Pediatric and Adolescent Surgery, Medical University of Graz, Auenbruggerplatz 34, 8036 Graz, Austria
| | - G Singer
- Department of Pediatric and Adolescent Surgery, Medical University of Graz, Auenbruggerplatz 34, 8036 Graz, Austria.
| | - H Till
- Department of Pediatric and Adolescent Surgery, Medical University of Graz, Auenbruggerplatz 34, 8036 Graz, Austria
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19
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Stadlbauer V, Horvath A, Komarova I, Schmerboeck B, Feldbacher N, Klymiuk I, Durdevic M, Rainer F, Blesl A, Stiegler P, Leber B. Dysbiosis in early sepsis can be modulated by a multispecies probiotic: a randomised controlled pilot trial. Benef Microbes 2019; 10:265-278. [PMID: 30694100 DOI: 10.3920/bm2018.0067] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 02/06/2023]
Abstract
The gut is hypothesised to play an important role in the development and progression of sepsis. It is however unknown whether the gut microbiome and the gut barrier function is already altered early in sepsis development and whether it is possible to modulate the microbiome in early sepsis. Therefore, a randomised, double blind, placebo-controlled pilot study to examine the alterations of the microbiome and the gut barrier in early sepsis and the influence of a concomitant probiotic intervention on dysbiosis at this early stage of the disease was conducted. Patients with early sepsis, defined as fulfilling the sepsis definition from the 2012 Surviving Sepsis Campaign guidelines but without signs of organ failure, received multispecies probiotic (Winclove 607 based on Omnibiotic® 10 AAD) for 28 days. Gut microbiome composition, function, gut barrier and bacterial translocation were studied. Patients with early sepsis had a significantly lower structural and functional alpha diversity, clustered differently and showed structural alterations on all taxonomic levels. Gut permeability was unaltered but endotoxin, endotoxin binding proteins and peptidoglycans were elevated in early sepsis patients compared to controls. Probiotic intervention successfully increased probiotic strains in stool and led to an improvement of functional diversity. Microbiome composition and function are altered in early sepsis. Probiotic intervention successfully modulates the microbiome and is therefore a promising tool for early intervention in sepsis.
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Affiliation(s)
- V Stadlbauer
- 1 Department of Gastroenterology and Hepatology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - A Horvath
- 1 Department of Gastroenterology and Hepatology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria.,2 Center for Biomarker Research in Medicine (CBmed), Stiftingtalstrasse 5, 8010 Graz, Austria
| | - I Komarova
- 1 Department of Gastroenterology and Hepatology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - B Schmerboeck
- 1 Department of Gastroenterology and Hepatology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria.,2 Center for Biomarker Research in Medicine (CBmed), Stiftingtalstrasse 5, 8010 Graz, Austria
| | - N Feldbacher
- 1 Department of Gastroenterology and Hepatology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - I Klymiuk
- 3 Center for Medical Research, Core Facility Molecular Biology, Medical University of Graz, Graz, Austria
| | - M Durdevic
- 4 Core Facility Computational Bioanalytics, Medical University of Graz, Graz, Austria
| | - F Rainer
- 1 Department of Gastroenterology and Hepatology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - A Blesl
- 1 Department of Gastroenterology and Hepatology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - P Stiegler
- 5 Department of Transplantation Surgery, Medical University Graz, Auenbruggerplatz 29/E, 8036 Graz, Austria
| | - B Leber
- 2 Center for Biomarker Research in Medicine (CBmed), Stiftingtalstrasse 5, 8010 Graz, Austria.,5 Department of Transplantation Surgery, Medical University Graz, Auenbruggerplatz 29/E, 8036 Graz, Austria
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20
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Hirschmugl B, Crozier S, Matthews N, Kitzinger E, Klymiuk I, Inskip HM, Harvey NC, Cooper C, Sibley CP, Glazier J, Wadsack C, Godfrey KM, Desoye G, Lewis RM. Relation of placental alkaline phosphatase expression in human term placenta with maternal and offspring fat mass. Int J Obes (Lond) 2018; 42:1202-1210. [PMID: 29899523 PMCID: PMC6173293 DOI: 10.1038/s41366-018-0136-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 04/24/2018] [Accepted: 05/09/2018] [Indexed: 11/09/2022]
Abstract
INTRODUCTION Alkaline phosphatase is implicated in intestinal lipid transport and in the development of obesity. Placental alkaline phosphatase is localised to the microvillous plasma membrane of the placental syncytiotrophoblast at the maternal-fetal interface, but its role is unclear. We investigated the relations of placental alkaline phosphatase activity and mRNA expression with maternal body composition and offspring fat mass in humans. METHODS Term human placentas from the UK Birthright cohort (n = 52) and the Southampton Women's Survey (SWS) (n = 95) were studied. In the Birthright cohort, alkaline phosphatase activity was measured in placental microvillous plasma membrane vesicles. In the SWS, alkaline phosphatase mRNA was measured using Nanostring. Alkaline phosphatase gene expression was compared to other lipid-related genes. RESULTS In Birthright samples placental microvillous plasma membrane alkaline phosphatase activity was positively associated with maternal triceps skinfold thickness and BMI (β = 0.04 (95% CI: 0.01-0.06) and β = 0.02 (0.00-0.03) µmol/mg protein/min per SD, P = 0.002 and P = 0.05, respectively) after adjusting for potential confounders. In SWS samples placental alkaline phosphatase mRNA expression in term placenta was positively associated with maternal triceps skinfold (β = 0.24 (0.04, 0.44) SD/SD, P = 0.02), had no association with neonatal %fat mass (β = 0.01 (-0.20 to 0.21) SD/SD, P = 0.93) and was negatively correlated with %fat mass at ages 4 (β = -0.28 (-0.52 to -0.04) SD/SD, P = 0.02), 6-7 (β = -0.25 (-0.49 to -0.02) SD/SD, P = 0.03) years. When compared with placental expression of other genes, alkaline phosphatase expression was positively related to genes including the lysophosphatidylcholine transporter MFSD2A (major facilitator superfamily domain containing 2A, P < 0.001) and negatively related to genes including the fatty acid transport proteins 2 and 3 (P = 0.001, P < 0.001). CONCLUSIONS Our findings suggest relationships between placental alkaline phosphatase and both maternal and childhood adiposity. The inverse relationship between placental alkaline phosphatase gene expression and childhood %fat mass suggests that placental alkaline phosphatase may help to protect the foetus from the adverse effects of maternal obesity.
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Affiliation(s)
- Birgit Hirschmugl
- Department of Obstetrics and Gynaecology, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Sarah Crozier
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Nina Matthews
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Eva Kitzinger
- Department of Obstetrics and Gynaecology, Medical University of Graz, Graz, Austria
| | - Ingeborg Klymiuk
- Core Facility Molecular Biology, Centre for Medical Research, Medical University of Graz, Graz, Austria
| | - Hazel M Inskip
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Nicholas C Harvey
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Colin P Sibley
- Maternal and Fetal Health Research Centre, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
| | - Jocelyn Glazier
- Maternal and Fetal Health Research Centre, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9WL, UK
| | - Christian Wadsack
- Department of Obstetrics and Gynaecology, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Faculty of Medicine, University of Southampton, Southampton, UK
| | - Gernot Desoye
- Department of Obstetrics and Gynaecology, Medical University of Graz, Graz, Austria
| | - Rohan M Lewis
- Faculty of Medicine, University of Southampton, Southampton, UK.
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21
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Klymiuk I, Bilgilier C, Stadlmann A, Thannesberger J, Kastner MT, Högenauer C, Püspök A, Biowski-Frotz S, Schrutka-Kölbl C, Thallinger GG, Steininger C. The Human Gastric Microbiome Is Predicated upon Infection with Helicobacter pylori. Front Microbiol 2017; 8:2508. [PMID: 29312210 PMCID: PMC5735373 DOI: 10.3389/fmicb.2017.02508] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [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: 08/01/2017] [Accepted: 12/01/2017] [Indexed: 12/18/2022] Open
Abstract
The human gastric lumen is one of the most hostile environments of the human body suspected to be sterile until the discovery of Helicobacter pylori (H.p.). State of the art next generation sequencing technologies multiply the knowledge on H.p. functional genomics as well as on the colonization of supposed sterile human environments like the gastric habitat. Here we studied in a prospective, multicenter, clinical trial the 16S rRNA gene amplicon based bacterial microbiome in a total of 30 homogenized and frozen gastric biopsy samples from eight geographic locations. The evaluation of the samples for H.p. infection status was done by histopathology and a specific PCR assay. CagA status was determined by a CagA-specific PCR assay. Patients were grouped accordingly as H.p.-negative, H.p.-positive but CagA-negative and H.p.-positive and CagA-positive (n = 10, respectively). Here we show that H.p. infection of the gastric habitat dominates the gastric microbiota in most patients and is associated with a significant decrease of the microbial alpha diversity from H.p. negative to H.p. positive with CagA as a considerable factor. The genera Actinomyces, Granulicatella, Veillonella, Fusobacterium, Neisseria, Helicobacter, Streptococcus, and Prevotella are significantly different between the H.p.-positive and H.p.-negative sample groups. Differences in microbiota found between CagA-positive and CagA-negative patients were not statistically significant and need to be re-evaluated in larger sample cohorts. In conclusion, H.p. infection dominates the gastric microbiome in a multicentre cohort of patients with varying diagnoses.
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Affiliation(s)
- Ingeborg Klymiuk
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Ceren Bilgilier
- Division of Infectious Diseases, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Alexander Stadlmann
- Division of Infectious Diseases, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Jakob Thannesberger
- Division of Infectious Diseases, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Marie-Theres Kastner
- Division of Infectious Diseases, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Christoph Högenauer
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Andreas Püspök
- Department of Internal Medicine II, St. John's Hospital Eisenstadt, Eisenstadt, Austria
| | - Susanne Biowski-Frotz
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University Vienna, Vienna, Austria
| | - Christiane Schrutka-Kölbl
- Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University Vienna, Vienna, Austria
| | - Gerhard G. Thallinger
- Institute of Computational Biotechnology, Graz University of Technology, Graz, Austria
- BioTechMed OMICS Center Graz, Graz, Austria
| | - Christoph Steininger
- Division of Infectious Diseases, Department of Medicine I, Medical University of Vienna, Vienna, Austria
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22
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Costea PI, Zeller G, Sunagawa S, Pelletier E, Alberti A, Levenez F, Tramontano M, Driessen M, Hercog R, Jung FE, Kultima JR, Hayward MR, Coelho LP, Allen-Vercoe E, Bertrand L, Blaut M, Brown JRM, Carton T, Cools-Portier S, Daigneault M, Derrien M, Druesne A, de Vos WM, Finlay BB, Flint HJ, Guarner F, Hattori M, Heilig H, Luna RA, van Hylckama Vlieg J, Junick J, Klymiuk I, Langella P, Le Chatelier E, Mai V, Manichanh C, Martin JC, Mery C, Morita H, O'Toole PW, Orvain C, Patil KR, Penders J, Persson S, Pons N, Popova M, Salonen A, Saulnier D, Scott KP, Singh B, Slezak K, Veiga P, Versalovic J, Zhao L, Zoetendal EG, Ehrlich SD, Dore J, Bork P. Towards standards for human fecal sample processing in metagenomic studies. Nat Biotechnol 2017; 35:1069-1076. [PMID: 28967887 DOI: 10.1038/nbt.3960] [Citation(s) in RCA: 455] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/11/2017] [Indexed: 12/30/2022]
Abstract
Technical variation in metagenomic analysis must be minimized to confidently assess the contributions of microbiota to human health. Here we tested 21 representative DNA extraction protocols on the same fecal samples and quantified differences in observed microbial community composition. We compared them with differences due to library preparation and sample storage, which we contrasted with observed biological variation within the same specimen or within an individual over time. We found that DNA extraction had the largest effect on the outcome of metagenomic analysis. To rank DNA extraction protocols, we considered resulting DNA quantity and quality, and we ascertained biases in estimates of community diversity and the ratio between Gram-positive and Gram-negative bacteria. We recommend a standardized DNA extraction method for human fecal samples, for which transferability across labs was established and which was further benchmarked using a mock community of known composition. Its adoption will improve comparability of human gut microbiome studies and facilitate meta-analyses.
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Affiliation(s)
- Paul I Costea
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Georg Zeller
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Shinichi Sunagawa
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Eric Pelletier
- CEA - Institut François Jacob - Genoscope, Evry, France.,CNRS UMR-8030, Evry, France.,Université Evry Val d'Essonne, Evry, France
| | | | - Florence Levenez
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Melanie Tramontano
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Marja Driessen
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rajna Hercog
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ferris-Elias Jung
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jens Roat Kultima
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Matthew R Hayward
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Luis Pedro Coelho
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, The University of Guelph, Guelph, Ontario, Canada
| | | | - Michael Blaut
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Jillian R M Brown
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | | | | | - Michelle Daigneault
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | | | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands.,Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - B Brett Finlay
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Harry J Flint
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Francisco Guarner
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Masahira Hattori
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hans Heilig
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - Ruth Ann Luna
- Texas Children's Hospital, Feigin Center, Houston, Texas, USA
| | | | - Jana Junick
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Ingeborg Klymiuk
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Philippe Langella
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | - Volker Mai
- Department of Epidemiology, College of Public Health and Health Professions and College of Medicine, Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Chaysavanh Manichanh
- Digestive System Research Unit, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Jennifer C Martin
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | | | - Hidetoshi Morita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Paul W O'Toole
- School of Microbiology & APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Céline Orvain
- CEA - Institut François Jacob - Genoscope, Evry, France
| | - Kiran Raosaheb Patil
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
| | - John Penders
- School of Nutrition and Translational Research in Metabolism (NUTRIM) and Care and Public Health Research Institute (Caphri), Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Søren Persson
- Unit of Foodborne Infections, Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Nicolas Pons
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | | | - Anne Salonen
- Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Delphine Saulnier
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Karen P Scott
- Rowett Institute of Nutrition and Health, University of Aberdeen, Aberdeen, UK
| | - Bhagirath Singh
- Centre for Human Immunology, Department of Microbiology & Immunology and Robarts Research Institute, University of Western Ontario, London, Ontario, Canada
| | - Kathleen Slezak
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | | | | | - Liping Zhao
- Ministry of Education Key Laboratory for Systems Biomedicine, Shanghai Centre for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, PR China
| | - Erwin G Zoetendal
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | - S Dusko Ehrlich
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France.,King's College London, Centre for Host-Microbiome Interactions, Dental Institute Central Office, Guy's Hospital, London, UK
| | - Joel Dore
- Metagenopolis, Institut National de la Recherche Agronomique, Jouy en Josas, France
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.,Molecular Medicine Partnership Unit, Heidelberg, Germany.,Max-Delbrück-Centre for Molecular Medicine, Berlin, Germany
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23
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Thannesberger J, Hellinger HJ, Klymiuk I, Kastner MT, Rieder FJJ, Schneider M, Fister S, Lion T, Kosulin K, Laengle J, Bergmann M, Rattei T, Steininger C. Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples. FASEB J 2017; 31:1987-2000. [PMID: 28179422 DOI: 10.1096/fj.201601168r] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/09/2017] [Indexed: 01/09/2023]
Abstract
Viruses shape a diversity of ecosystems by modulating their microbial, eukaryotic, or plant host metabolism. The complexity of virus-host interaction networks is progressively fathomed by novel metagenomic approaches. By using a novel metagenomic method, we explored the virome in mammalian cell cultures and clinical samples to identify an extensive pool of mobile genetic elements in all of these ecosystems. Despite aseptic treatment, cell cultures harbored extensive and diverse phage populations with a high abundance of as yet unknown and uncharacterized viruses (viral dark matter). Unknown phages also predominated in the oropharynx and urine of healthy individuals and patients infected with cytomegalovirus despite demonstration of active cytomegalovirus replication. The novelty of viral sequences correlated primarily with the individual evaluated, whereas relative abundance of encoded protein functions was associated with the ecologic niches probed. Together, these observations demonstrate the extensive presence of viral dark matter in human and artificial ecosystems.-Thannesberger, J., Hellinger, H.-J., Klymiuk, I., Kastner, M.-T., Rieder, F. J. J., Schneider, M., Fister, S., Lion, T., Kosulin, K., Laengle, J., Bergmann, M., Rattei, T., Steininger, C. Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples.
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Affiliation(s)
- Jakob Thannesberger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - Hans-Joerg Hellinger
- CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Ingeborg Klymiuk
- Center for Medical Research, Core Facility Molecular Biology, Medical University of Graz, Graz, Austria
| | - Marie-Theres Kastner
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - Franz J J Rieder
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - Martina Schneider
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria
| | - Susanne Fister
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, University of Veterinary Medicine, Vienna, Austria
| | - Thomas Lion
- Children's Cancer Research Institute, Vienna, Austria
| | - Karin Kosulin
- Children's Cancer Research Institute, Vienna, Austria
| | - Johannes Laengle
- Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Michael Bergmann
- Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Thomas Rattei
- CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Christoph Steininger
- Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria;
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24
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Klymiuk I, Bambach I, Patra V, Trajanoski S, Wolf P. 16S Based Microbiome Analysis from Healthy Subjects' Skin Swabs Stored for Different Storage Periods Reveal Phylum to Genus Level Changes. Front Microbiol 2016; 7:2012. [PMID: 28066342 PMCID: PMC5167739 DOI: 10.3389/fmicb.2016.02012] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [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: 05/03/2016] [Accepted: 11/30/2016] [Indexed: 12/14/2022] Open
Abstract
Microbiome research and improvements in high throughput sequencing technologies revolutionize our current scientific viewpoint. The human associated microbiome is a prominent focus of clinical research. Large cohort studies are often required to investigate the human microbiome composition and its changes in a multitude of human diseases. Reproducible analyses of large cohort samples require standardized protocols in study design, sampling, storage, processing, and data analysis. In particular, the effect of sample storage on actual results is critical for reproducibility. So far, the effect of storage conditions on the results of microbial analysis has been examined for only a few human biological materials (e.g., stool samples). There is a lack of data and information on appropriate storage conditions on other human derived samples, such as skin. Here, we analyzed skin swab samples collected from three different body locations (forearm, V of the chest and back) of eight healthy volunteers. The skin swabs were soaked in sterile buffer and total DNA was isolated after freezing at -80°C for 24 h, 90 or 365 days. Hypervariable regions V1-2 were amplified from total DNA and libraries were sequenced on an Illumina MiSeq desktop sequencer in paired end mode. Data were analyzed using Qiime 1.9.1. Summarizing all body locations per time point, we found no significant differences in alpha diversity and multivariate community analysis among the three time points. Considering body locations separately significant differences in the richness of forearm samples were found between d0 vs. d90 and d90 vs. d365. Significant differences in the relative abundance of major skin genera (Propionibacterium, Streptococcus, Bacteroides, Corynebacterium, and Staphylococcus) were detected in our samples in Bacteroides only among all time points in forearm samples and between d0 vs. d90 and d90 vs. d365 in V of the chest and back samples. Accordingly, significant differences were detected in the ratios of the main phyla Actinobacteria, Firmicutes, and Bacteroidetes: Actinobacteria vs. Bacteroidetes at d0 vs. d90 (p-value = 0.0234), at d0 vs. d365 (p-value = 0.0234) and d90 vs. d365 (p-value = 0.0234) in forearm samples and at d90 vs. d365 in V of the chest (p-value = 0.0234) and back samples (p-value = 0.0234). The ratios of Firmicutes vs. Bacteroidetes showed no significant changes in any of the body locations as well as the ratios of Actinobacteria vs. Firmicutes at any time point. Studies with larger sample sizes are required to verify our results and determine long term storage effects with regard to specific biological questions.
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Affiliation(s)
- Ingeborg Klymiuk
- Center for Medical Research, Medical University of Graz Graz, Austria
| | - Isabella Bambach
- Research Unit for Photodermatology, Department of Dermatology, Medical University of Graz Graz, Austria
| | - Vijaykumar Patra
- Research Unit for Photodermatology, Department of Dermatology, Medical University of Graz Graz, Austria
| | - Slave Trajanoski
- Center for Medical Research, Medical University of Graz Graz, Austria
| | - Peter Wolf
- Research Unit for Photodermatology, Department of Dermatology, Medical University of Graz Graz, Austria
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25
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Krause R, Halwachs B, Thallinger GG, Klymiuk I, Gorkiewicz G, Hoenigl M, Prattes J, Valentin T, Heidrich K, Buzina W, Salzer HJF, Rabensteiner J, Prüller F, Raggam RB, Meinitzer A, Moissl-Eichinger C, Högenauer C, Quehenberger F, Kashofer K, Zollner-Schwetz I. Characterisation of Candida within the Mycobiome/Microbiome of the Lower Respiratory Tract of ICU Patients. PLoS One 2016; 11:e0155033. [PMID: 27206014 PMCID: PMC4874575 DOI: 10.1371/journal.pone.0155033] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [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: 03/06/2016] [Accepted: 04/22/2016] [Indexed: 02/06/2023] Open
Abstract
Whether the presence of Candida spp. in lower respiratory tract (LRT) secretions is a marker of underlying disease, intensive care unit (ICU) treatment and antibiotic therapy or contributes to poor clinical outcome is unclear. We investigated healthy controls, patients with proposed risk factors for Candida growth in LRT (antibiotic therapy, ICU treatment with and without antibiotic therapy), ICU patients with pneumonia and antibiotic therapy and candidemic patients (for comparison of truly invasive and colonizing Candida spp.). Fungal patterns were determined by conventional culture based microbiology combined with molecular approaches (next generation sequencing, multilocus sequence typing) for description of fungal and concommitant bacterial microbiota in LRT, and host and fungal biomarkes were investigated. Admission to and treatment on ICUs shifted LRT fungal microbiota to Candida spp. dominated fungal profiles but antibiotic therapy did not. Compared to controls, Candida was part of fungal microbiota in LRT of ICU patients without pneumonia with and without antibiotic therapy (63% and 50% of total fungal genera) and of ICU patients with pneumonia with antibiotic therapy (73%) (p<0.05). No case of invasive candidiasis originating from Candida in the LRT was detected. There was no common bacterial microbiota profile associated or dissociated with Candida spp. in LRT. Colonizing and invasive Candida strains (from candidemic patients) did not match to certain clades withdrawing the presence of a particular pathogenic and invasive clade. The presence of Candida spp. in the LRT rather reflected rapidly occurring LRT dysbiosis driven by ICU related factors than was associated with invasive candidiasis.
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Affiliation(s)
- Robert Krause
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- * E-mail:
| | - Bettina Halwachs
- Bioinformatics, Institute for Knowledge Discovery, University of Technology, Graz, Austria and OMICS Center Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | | | - Ingeborg Klymiuk
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | | | - Martin Hoenigl
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Jürgen Prattes
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Thomas Valentin
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Katharina Heidrich
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
- Department of Medicine I, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Walter Buzina
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Helmut J. F. Salzer
- Division of Clinical Infectious Diseases, Research Center Borstel, Leibnitz Center for Medicine and Biosciences, Borstel, Germany
| | - Jasmin Rabensteiner
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Florian Prüller
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Reinhard B. Raggam
- Division of Angiology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Andreas Meinitzer
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | - Christine Moissl-Eichinger
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Christoph Högenauer
- Theodor Escherich Laboratory for Microbiome Research, Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Franz Quehenberger
- Institute for Medical Informatics, Statistics, and Documentation, Medical University of Graz, Graz, Austria
| | - Karl Kashofer
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Ines Zollner-Schwetz
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
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26
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Weiß S, Somitsch W, Klymiuk I, Trajanoski S, Guebitz GM. Comparison of biogas sludge and raw crop material as source of hydrolytic cultures for anaerobic digestion. Bioresour Technol 2016; 207:244-251. [PMID: 26894564 DOI: 10.1016/j.biortech.2016.01.137] [Citation(s) in RCA: 10] [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] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 01/29/2016] [Accepted: 01/31/2016] [Indexed: 06/05/2023]
Abstract
Mixed fermentative/hydrolytic bacteria were enriched on lignocellulose substrates in minimal medium under semi-anaerobic mesophilic conditions in the presence or absence of natural zeolite as growth supporter to ultimately bioaugment non-adapted sludge and thereby enhance the overall anaerobic digestion (AD) of recalcitrant plant material. Desired enzyme activities, i.e. xylanases and cellulase were monitored during subsequent cultivation cycles. Furthermore, enriched microbial communities were characterized by 16S rRNA-based 454-Pyrosequencing, revealing Firmicutes, Bacteriodetes, Proteobacteria and Spirochaetes to be the predominant bacterial groups in cultures derived from anaerobic sludge and raw crop material, i.e. maple green cut and wheat straw as well. Enriched populations relevant for biopolymer hydrolysis were then compared in biological methane potential tests to demonstrate positive effects on the biogasification of renewable plant substrate material. A significant impact on methane productivity was observed with adapted mixed cultures when used in combination with clinoptilolite to augment and supplement non-adapted bioreactor sludge.
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Affiliation(s)
- Stefan Weiß
- Austrian Centre of Industrial Biotechnology, Petersgasse 14/5, A-8010 Graz, Austria.
| | - Walter Somitsch
- Engineering Consultant, Wiedner Hauptstrasse 90/2/19, A-1050 Vienna, Austria; IPUS Mineral- und Umwelttechnologie GmbH, Werksgasse 281, A-8786 Rottenmann, Austria
| | - Ingeborg Klymiuk
- Medical University of Graz, Centre for Medical Research, Core Facility Molecular Biology, Stiftingtalstraße 24, A-8010 Graz, Austria
| | - Slave Trajanoski
- Medical University of Graz, Centre for Medical Research, Core Facility Computational Bioanalytics, Bioinformatics, Stiftingtalstraße 24, A-8010 Graz, Austria
| | - Georg M Guebitz
- Austrian Centre of Industrial Biotechnology, Petersgasse 14/5, A-8010 Graz, Austria; University of Natural Resources and Life Sciences, Institute of Environmental Biotechnology, Konrad Lorenz Strasse 20, A-3430 Tulln, Austria
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27
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Stadlbauer V, Leber B, Lemesch S, Trajanoski S, Bashir M, Horvath A, Tawdrous M, Stojakovic T, Fauler G, Fickert P, Högenauer C, Klymiuk I, Stiegler P, Lamprecht M, Pieber TR, Tripolt NJ, Sourij H. Lactobacillus casei Shirota Supplementation Does Not Restore Gut Microbiota Composition and Gut Barrier in Metabolic Syndrome: A Randomized Pilot Study. PLoS One 2015; 10:e0141399. [PMID: 26509793 PMCID: PMC4625062 DOI: 10.1371/journal.pone.0141399] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [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: 08/06/2015] [Accepted: 10/05/2015] [Indexed: 12/19/2022] Open
Abstract
UNLABELLED Metabolic syndrome is associated with disturbances in gut microbiota composition. We aimed to investigate the effect of Lactobacillus casei Shirota (LcS) on gut microbiota composition, gut barrier integrity, intestinal inflammation and serum bile acid profile in metabolic syndrome. In a single-centre, prospective, randomised controlled pilot study, 28 subjects with metabolic syndrome received either LcS for 12 weeks (n = 13) or no LcS (n = 15). Data were compared to healthy controls (n = 16). Gut microbiota composition was characterised from stool using 454 pyrosequencing of 16S rRNA genes. Serum bile acids were quantified by tandem mass spectrometry. Zonulin and calprotectin were measured in serum and stool by ELISA. Bacteroidetes/Firmicutes ratio was significantly higher in healthy controls compared to metabolic syndrome but was not influenced by LcS. LcS supplementation led to enrichment of Parabacteroides. Zonulin and calprotectin were increased in metabolic syndrome stool samples but not influenced by LcS supplementation. Serum bile acids were similar to controls and not influenced by LcS supplementation. Metabolic syndrome is associated with a higher Bacteroidetes/Firmicutes ratio and gut barrier dysfunction but LcS was not able to change this. LcS administration was associated with subtle microbiota changes at genus level. TRIAL REGISTRATION ClinicalTrials.gov NCT01182844.
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Affiliation(s)
- Vanessa Stadlbauer
- Medical University of Graz, Division of Gastroenterology and Hepatology, Graz, Austria
| | - Bettina Leber
- Medical University of Graz, Division of Transplantation Surgery, Graz, Austria
| | - Sandra Lemesch
- Medical University of Graz, Division of Gastroenterology and Hepatology, Graz, Austria
| | | | - Mina Bashir
- Medical University of Graz, Division of Endocrinology and Metabolism, Graz, Austria
| | - Angela Horvath
- Medical University of Graz, Division of Gastroenterology and Hepatology, Graz, Austria
| | - Monika Tawdrous
- Medical University of Graz, Division of Gastroenterology and Hepatology, Graz, Austria
| | - Tatjana Stojakovic
- Medical University of Graz, Clinical Institute of Medical and Chemical Laboratory Diagnostics, Graz, Austria
| | - Günter Fauler
- Medical University of Graz, Clinical Institute of Medical and Chemical Laboratory Diagnostics, Graz, Austria
| | - Peter Fickert
- Medical University of Graz, Division of Gastroenterology and Hepatology, Graz, Austria
| | - Christoph Högenauer
- Medical University of Graz, Division of Gastroenterology and Hepatology, Graz, Austria
| | | | - Philipp Stiegler
- Medical University of Graz, Division of Transplantation Surgery, Graz, Austria
| | - Manfred Lamprecht
- Medical University of Graz, Institute of Physiological Chemistry, Centre for Physiological Medicine, Graz, Austria
| | - Thomas R. Pieber
- Medical University of Graz, Division of Endocrinology and Metabolism, Graz, Austria
- Centre for Biomarker Research in Medicine (CBmed), Graz, Austria
| | - Norbert J. Tripolt
- Medical University of Graz, Division of Endocrinology and Metabolism, Graz, Austria
| | - Harald Sourij
- Medical University of Graz, Division of Endocrinology and Metabolism, Graz, Austria
- Centre for Biomarker Research in Medicine (CBmed), Graz, Austria
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28
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Kirsch AH, Kirsch A, Artinger K, Schabhüttl C, Goessler W, Klymiuk I, Gülly C, Fritz GA, Frank S, Wimmer R, Brodmann M, Anders HJ, Pramstaller PP, Rosenkranz AR, Eller K, Eller P. Heterogeneous susceptibility for uraemic media calcification and concomitant inflammation within the arterial tree. Nephrol Dial Transplant 2015; 30:1995-2005. [PMID: 26185049 PMCID: PMC4656037 DOI: 10.1093/ndt/gfv265] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 06/01/2015] [Indexed: 12/27/2022] Open
Abstract
Background End-stage renal disease (ESRD) is strongly associated with arterial calcification of the tunica media, decreased vascular compliance and sudden cardiac death. Here, we analysed the distribution pattern of uraemic media calcification and concomitant inflammation in mice and men. Methods Uraemia was induced in DBA/2 mice with high-phosphate diet. Subsequently, we analysed arterial medial calcification using histology, mass spectrometry, and wire myography. Gene expression was quantified using a whole transcriptome array and quantitative PCR. In a cohort of 36 consecutive patients with CKD stage 4–5, we measured the calcium score of the coronary arteries, the ascending thoracic aorta and the infrarenal abdominal aorta using computed tomography scans. Results Uraemic DBA/2 mice showed only minor calcifications in thoracic aortas, whereas there was overt media calcification in abdominal aortas. The transcriptional profile and immunohistochemistry revealed induction of Vcam1 expression by vascular smooth muscle cells in uraemic abdominal aortas. Macrophages infiltrated the tunica media of the abdominal aorta. Anti-inflammatory treatment did not improve uraemic media calcification in our animal model. Arterial calcifications in ESRD patients showed a similar distribution pattern in computed tomography scans, with higher calcium scores of the abdominal aorta when compared with the thoracic aorta. Conclusion Taken together, there was a similar heterogeneous pattern of calcification in both mice and humans, where the abdominal aorta was more prone to media calcification when compared with the thoracic aorta. In uraemia, smooth muscle cells of the abdominal aorta showed a phenotypic switch to an inflammatory and osteoblastic phenotype.
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Affiliation(s)
- Alexander H Kirsch
- Department of Internal Medicine, Clinical Division of Nephrology, Medical University of Graz, Graz, Austria
| | - Andrijana Kirsch
- Center of Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Katharina Artinger
- Department of Internal Medicine, Clinical Division of Nephrology, Medical University of Graz, Graz, Austria
| | - Corinna Schabhüttl
- Department of Internal Medicine, Division of Angiology, Medical University of Graz, Graz, Austria
| | - Walter Goessler
- Institute of Chemistry-Analytical Chemistry, Karl-Franzens University of Graz, Graz, Austria
| | - Ingeborg Klymiuk
- Center for Medical Research, Core Facility Molecular Biology, Medical University of Graz, Graz, Austria
| | - Christian Gülly
- Center for Medical Research, Core Facility Molecular Biology, Medical University of Graz, Graz, Austria
| | - Gerald A Fritz
- Department of Radiology, Medical University of Graz, Graz, Austria
| | - Saša Frank
- Center of Molecular Medicine, Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Roxana Wimmer
- Department of Internal Medicine, Clinical Division of Nephrology, Medical University of Graz, Graz, Austria
| | - Marianne Brodmann
- Department of Internal Medicine, Division of Angiology, Medical University of Graz, Graz, Austria
| | - Hans-Joachim Anders
- Renal Division, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München-Innenstadt, Munich, Germany
| | | | - Alexander R Rosenkranz
- Department of Internal Medicine, Clinical Division of Nephrology, Medical University of Graz, Graz, Austria
| | - Kathrin Eller
- Department of Internal Medicine, Clinical Division of Nephrology, Medical University of Graz, Graz, Austria
| | - Philipp Eller
- Department of Internal Medicine, Division of Angiology, Medical University of Graz, Graz, Austria Department of Internal Medicine, Intensive Care Unit, Medical University of Graz, Graz, Austria
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29
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Abstract
Christoph Steininger and colleagues explore how multiple infectious, autoimmune, metabolic, and neoplastic diseases have been associated with changes in the intestinal microbiome, although a cause-effect relationship is often difficult to establish. Integration of metagenomics into clinical medicine is a challenge, and the authors highlight clinical approaches that are of high priority for the useful medical application of metagenomics. Please see later in the article for the Editors' Summary.
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Affiliation(s)
- Ingeborg Klymiuk
- Core Facility Molecular Biology, Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Christoph Högenauer
- Department of Gastroenterology and Hepatology, Medical University of Graz, Graz, Austria
| | - Bettina Halwachs
- Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
- Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Gerhard G. Thallinger
- Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
- Core Facility Bioinformatics, Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - W. Florian Fricke
- Department of Microbiology and Immunology, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Christoph Steininger
- Division of Infectious Diseases, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- * E-mail:
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30
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Klymiuk I, Kenner L, Adler T, Busch DH, Boersma A, Irmler M, Gailus-Durner V, Fuchs H, Leitner N, Müller M, Kühn R, Schlederer M, Treise I, de Angelis MH, Beckers J. In vivo functional requirement of the mouse Ifitm1 gene for germ cell development, interferon mediated immune response and somitogenesis. PLoS One 2012; 7:e44609. [PMID: 23115618 PMCID: PMC3480353 DOI: 10.1371/journal.pone.0044609] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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: 05/16/2012] [Accepted: 08/03/2012] [Indexed: 01/19/2023] Open
Abstract
The mammalian Interferon induced transmembrane protein 1 (Ifitm1) gene was originally identified as a member of a gene family highly inducible by type I and type II interferons. Based on expression analyses, it was suggested to be required for normal primordial germ cell migration. The knockdown of Ifitm1 in mouse embryos provided evidence for a role in somitogenesis. We generated the first targeted knockin allele of the Ifitm1 gene to systematically reassess all inferred functions. Sperm motility and the fertility of male and female mutant mice are as in wild type littermates. Embryonic somites and the adult vertebral column appear normal in homozygous Ifitm1 knockout mice, demonstrating that Ifitm1 is not essential for normal segmentation of the paraxial mesoderm. Proportions of leucocyte subsets, including granulocytes, monocytes, B-cells, T-cells, NK-cells, and NKT-cells, are unchanged in mutant mice. Based on a normal immune response to Listeria monocytogenes infection, there is no evidence for a dysfunction in downstream IFNγ signaling in Ifitm1 mutant mice. Expression from the Ifitm1 locus from E8.5 to E14.5 is highly dynamic. In contrast, in adult mice, Ifitm1 expression is highly restricted and strong in the bronchial epithelium. Intriguingly, IFITM1 is highly overexpressed in tumor epithelia cells of human squamous cell carcinomas and in adenocarcinomas of NSCLC patients. These analyses underline the general importance of targeted in vivo studies for the functional annotation of the mammalian genome. The first comprehensive description of the Ifitm1 expression pattern provides a rational basis for the further examination of Ifitm1 gene functions. Based on our data, the fact that IFITM1 can function as a negative regulator of cell proliferation, and because the gene maps to chromosome band 11p15.5, previously associated with NSCLC, it is likely that IFITM1 in man has a key role in tumor formation.
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Affiliation(s)
- Ingeborg Klymiuk
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH, Neuherberg, Germany
- * E-mail: (IK); (JB)
| | - Lukas Kenner
- Ludwig Boltzmann Institute for Cancer Research and Institute for Clinical Pathology, Medical University Vienna, Vienna, Austria
| | - Thure Adler
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH, Neuherberg, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
| | - Dirk H. Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Munich, Germany
| | - Auke Boersma
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH, Neuherberg, Germany
- Institute of Laboratory Animal Science and Biomodels Austria, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Martin Irmler
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH, Neuherberg, Germany
| | - Valérie Gailus-Durner
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH, Neuherberg, Germany
| | - Helmut Fuchs
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH, Neuherberg, Germany
| | - Nicole Leitner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Ralf Kühn
- Institute of Developmental Genetics, Helmholtz Zentrum München GmbH, Neuherberg, Germany
| | - Michaela Schlederer
- Ludwig Boltzmann Institute for Cancer Research, Ludwig Boltzmann Gesellschaft, Vienna, Austria
| | - Irina Treise
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH, Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH, Neuherberg, Germany
- Experimental Genetics, Technische Universität München, Freising-Weihenstephan, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics and German Mouse Clinic, Helmholtz Zentrum München GmbH, Neuherberg, Germany
- Experimental Genetics, Technische Universität München, Freising-Weihenstephan, Germany
- * E-mail: (IK); (JB)
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