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Bingöl M, Cardilli A, Bingöl AC, Löber U, Bang C, Franke A, Bartzela T, Beblo S, Mönch E, Stolz S, Schaefer AS, Forslund SK, Richter GM. Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study. J Clin Periodontol 2024. [PMID: 38745393 DOI: 10.1111/jcpe.13998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 03/19/2024] [Accepted: 04/25/2024] [Indexed: 05/16/2024]
Abstract
AIM The oral microenvironment contributes to microbial composition and immune equilibrium. It is considered to be influenced by dietary habits. Phenylketonuria (PKU) patients, who follow a lifelong low-protein diet, exhibit higher prevalence of oral diseases such as periodontitis, offering a suitable model to explore the interplay between diet, oral microbiota and oral health. MATERIALS AND METHODS We conducted 16S rDNA sequencing on saliva and subgingival plaque from 109 PKU patients (ages 6-68 years) and 114 age-matched controls and correlated oral microbial composition and dental health. RESULTS PKU patients exhibited worse dental health, reduced oral microbial diversity and a difference in the abundance of specific taxa, especially Actinobacteriota species, compared to controls. PKU patients with poor periodontal health exhibited higher alpha diversity than the orally healthy ones, marked by high abundance of the genus Tannerella. Notably, the observed taxonomic differences in PKU patients with normal indices of decayed/missing/filled teeth, plaque control record, gingival bleeding index and periodontal screening and recording index generally differed from microbial signatures of periodontitis. CONCLUSIONS PKU patients' reduced microbial diversity may be due to their diet's metabolic challenges disrupting microbial and immune balance, thus increasing oral inflammation. Higher alpha diversity in PKU patients with oral inflammation is likely related to expanded microbial niches.
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Affiliation(s)
- Memduh Bingöl
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Alessio Cardilli
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Experimental and Clinical Research Center, a Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Anne Carolin Bingöl
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Ulrike Löber
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Experimental and Clinical Research Center, a Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Berlin, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Theodosia Bartzela
- Department of Orthodontics, Technische Universität Dresden, Dresden, Germany
| | - Skadi Beblo
- Department of Women and Child Health, Hospital for Children and Adolescents, Centre for Pediatric Research Leipzig, University of Leipzig, Leipzig, Germany
| | - Eberhard Mönch
- Campus Virchow-Klinikum, Interdisciplinary Metabolism Centre, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Simone Stolz
- Department of Pediatric and Adolescent Medicine, Carl-Thiem-Klinikum Cottbus, Cottbus, Germany
| | - Arne S Schaefer
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Sofia Kirke Forslund
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Experimental and Clinical Research Center, a Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Berlin, Germany
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Gesa M Richter
- Department of Periodontology, Oral Medicine and Oral Surgery, Institute for Dental and Craniofacial Sciences, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
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2
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Dörner PJ, Anandakumar H, Röwekamp I, Fiocca Vernengo F, Millet Pascual-Leone B, Krzanowski M, Sellmaier J, Brüning U, Fritsche-Guenther R, Pfannkuch L, Kurth F, Milek M, Igbokwe V, Löber U, Gutbier B, Holstein M, Heinz GA, Mashreghi MF, Schulte LN, Klatt AB, Caesar S, Wienhold SM, Offermanns S, Mack M, Witzenrath M, Jordan S, Beule D, Kirwan JA, Forslund SK, Wilck N, Bartolomaeus H, Heimesaat MM, Opitz B. Clinically used broad-spectrum antibiotics compromise inflammatory monocyte-dependent antibacterial defense in the lung. Nat Commun 2024; 15:2788. [PMID: 38555356 PMCID: PMC10981692 DOI: 10.1038/s41467-024-47149-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 03/20/2024] [Indexed: 04/02/2024] Open
Abstract
Hospital-acquired pneumonia (HAP) is associated with high mortality and costs, and frequently caused by multidrug-resistant (MDR) bacteria. Although prior antimicrobial therapy is a major risk factor for HAP, the underlying mechanism remains incompletely understood. Here, we demonstrate that antibiotic therapy in hospitalized patients is associated with decreased diversity of the gut microbiome and depletion of short-chain fatty acid (SCFA) producers. Infection experiments with mice transplanted with patient fecal material reveal that these antibiotic-induced microbiota perturbations impair pulmonary defense against MDR Klebsiella pneumoniae. This is dependent on inflammatory monocytes (IMs), whose fatty acid receptor (FFAR)2/3-controlled and phagolysosome-dependent antibacterial activity is compromized in mice transplanted with antibiotic-associated patient microbiota. Collectively, we characterize how clinically relevant antibiotics affect antimicrobial defense in the context of human microbiota, and reveal a critical impairment of IM´s antimicrobial activity. Our study provides additional arguments for the rational use of antibiotics and offers mechanistic insights for the development of novel prophylactic strategies to protect high-risk patients from HAP.
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Affiliation(s)
- Patrick J Dörner
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Harithaa Anandakumar
- Experimental and Clinical Research Center, a cooperation of Charité - Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Department of Nephrology and Internal Intensive Care Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ivo Röwekamp
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Facundo Fiocca Vernengo
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Belén Millet Pascual-Leone
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Marta Krzanowski
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Josua Sellmaier
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ulrike Brüning
- Metabolomics Platform, Berlin Institute of Health at Charité, Berlin, Germany
| | | | - Lennart Pfannkuch
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Miha Milek
- Core Unit Bioinformatics, Berlin Institute of Health at Charité, Berlin, Germany
| | - Vanessa Igbokwe
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center, a cooperation of Charité - Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Birgitt Gutbier
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Markus Holstein
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gitta Anne Heinz
- German Rheumatism Research Center, a Leibniz Institute, Berlin, Germany
| | | | - Leon N Schulte
- Department of Medicine, Institute for Lung Research, Philipps University Marburg, Marburg, Germany
- German center for lung research (DZL), Marburg, Germany
| | - Ann-Brit Klatt
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sandra Caesar
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sandra-Maria Wienhold
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Offermanns
- Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Matthias Mack
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Martin Witzenrath
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German center for lung research (DZL), Berlin, Germany
| | - Stefan Jordan
- Institute of Microbiology, Infectious Diseases and Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health at Charité, Berlin, Germany
| | - Jennifer A Kirwan
- Metabolomics Platform, Berlin Institute of Health at Charité, Berlin, Germany
| | - Sofia K Forslund
- Experimental and Clinical Research Center, a cooperation of Charité - Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Nicola Wilck
- Experimental and Clinical Research Center, a cooperation of Charité - Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Department of Nephrology and Internal Intensive Care Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Hendrik Bartolomaeus
- Experimental and Clinical Research Center, a cooperation of Charité - Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Department of Nephrology and Internal Intensive Care Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Markus M Heimesaat
- Institute of Microbiology, Infectious Diseases and Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Bastian Opitz
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- German center for lung research (DZL), Berlin, Germany.
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3
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Cuthbertson L, Löber U, Ish-Horowicz JS, McBrien CN, Churchward C, Parker JC, Olanipekun MT, Burke C, McGowan A, Davies GA, Lewis KE, Hopkin JM, Chung KF, O'Carroll O, Faul J, Creaser-Thomas J, Andrews M, Ghosal R, Piatek S, Willis-Owen SAG, Bartolomaeus TUP, Birkner T, Dwyer S, Kumar N, Turek EM, William Musk A, Hui J, Hunter M, James A, Dumas ME, Filippi S, Cox MJ, Lawley TD, Forslund SK, Moffatt MF, Cookson WOC. Genomic attributes of airway commensal bacteria and mucosa. Commun Biol 2024; 7:171. [PMID: 38347162 PMCID: PMC10861553 DOI: 10.1038/s42003-024-05840-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 01/22/2024] [Indexed: 02/15/2024] Open
Abstract
Microbial communities at the airway mucosal barrier are conserved and highly ordered, in likelihood reflecting co-evolution with human host factors. Freed of selection to digest nutrients, the airway microbiome underpins cognate management of mucosal immunity and pathogen resistance. We show here the initial results of systematic culture and whole-genome sequencing of the thoracic airway bacteria, identifying 52 novel species amongst 126 organisms that constitute 75% of commensals typically present in heathy individuals. Clinically relevant genes encode antimicrobial synthesis, adhesion and biofilm formation, immune modulation, iron utilisation, nitrous oxide (NO) metabolism and sphingolipid signalling. Using whole-genome content we identify dysbiotic features that may influence asthma and chronic obstructive pulmonary disease. We match isolate gene content to transcripts and metabolites expressed late in airway epithelial differentiation, identifying pathways to sustain host interactions with microbiota. Our results provide a systematic basis for decrypting interactions between commensals, pathogens, and mucosa in lung diseases of global significance.
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Affiliation(s)
- Leah Cuthbertson
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Ulrike Löber
- Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site, 10785, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Jonathan S Ish-Horowicz
- National Heart and Lung Institute, Imperial College London, London, UK
- Department of Mathematics, Imperial College London, London, UK
| | - Claire N McBrien
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Colin Churchward
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Jeremy C Parker
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Conor Burke
- Department of Respiratory Medicine, Connolly Hospital, Dublin, Ireland
| | - Aisling McGowan
- Department of Respiratory Medicine, Connolly Hospital, Dublin, Ireland
| | - Gwyneth A Davies
- Population Data Science and Health Data Research UK BREATHE Hub, Swansea University Medical School, Swansea University, Swansea, UK
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
| | - Keir E Lewis
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
- Respiratory Medicine, Hywel Dda University Health Board, Llanelli, UK
| | - Julian M Hopkin
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Orla O'Carroll
- Department of Respiratory Medicine, Connolly Hospital, Dublin, Ireland
| | - John Faul
- Department of Respiratory Medicine, Connolly Hospital, Dublin, Ireland
| | - Joy Creaser-Thomas
- College of Medicine, Institute of Life Science, Swansea University, Swansea, UK
| | - Mark Andrews
- Respiratory Medicine, Hywel Dda University Health Board, Llanelli, UK
| | - Robin Ghosal
- Respiratory Medicine, Hywel Dda University Health Board, Llanelli, UK
| | - Stefan Piatek
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Theda U P Bartolomaeus
- Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site, 10785, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Till Birkner
- Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Sarah Dwyer
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Nitin Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Elena M Turek
- National Heart and Lung Institute, Imperial College London, London, UK
| | - A William Musk
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Perth, WA, Australia
- Department of Respiratory Medicine Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Jennie Hui
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Michael Hunter
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Alan James
- School of Population and Global Health, The University of Western Australia, Perth, WA, Australia
- Department of Respiratory Medicine Sir Charles Gairdner Hospital, Perth, WA, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Perth, WA, Australia
| | - Marc-Emmanuel Dumas
- National Heart and Lung Institute, Imperial College London, London, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- U1283 INSERM / UMR8199 CNRS, Institut Pasteur de Lille, Lille University Hospital, European Genomic Institute for Diabetes, University of Lille, Lille, France
- McGill Genome Centre, McGill University, Montréal, QC, Canada
| | - Sarah Filippi
- Department of Mathematics, Imperial College London, London, UK
| | - Michael J Cox
- University of Birmingham College of Medical and Dental Sciences, 150183, Institute of Microbiology and Infection, Birmingham, UK
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Sofia K Forslund
- Max Delbrück Center for Molecular Medicine (MDC), 13125, Berlin, Germany.
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site, 10785, Berlin, Germany.
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117, Berlin, Germany.
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany.
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College London, London, UK.
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Mottaghinia S, Stenzel S, Tsangaras K, Nikolaidis N, Laue M, Müller K, Hölscher H, Löber U, McEwen GK, Donnellan SC, Rowe KC, Aplin KP, Goffinet C, Greenwood AD. A recent gibbon ape leukemia virus germline integration in a rodent from New Guinea. Proc Natl Acad Sci U S A 2024; 121:e2220392121. [PMID: 38305758 PMCID: PMC10861895 DOI: 10.1073/pnas.2220392121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 11/30/2023] [Indexed: 02/03/2024] Open
Abstract
Germline colonization by retroviruses results in the formation of endogenous retroviruses (ERVs). Most colonization's occurred millions of years ago. However, in the Australo-Papuan region (Australia and New Guinea), several recent germline colonization events have been discovered. The Wallace Line separates much of Southeast Asia from the Australo-Papuan region restricting faunal and pathogen dispersion. West of the Wallace Line, gibbon ape leukemia viruses (GALVs) have been isolated from captive gibbons. Two microbat species from China appear to have been infected naturally. East of Wallace's Line, the woolly monkey virus (a GALV) and the closely related koala retrovirus (KoRV) have been detected in eutherians and marsupials in the Australo-Papuan region, often vertically transmitted. The detected vertically transmitted GALV-like viruses in Australo-Papuan fauna compared to sporadic horizontal transmission in Southeast Asia and China suggest the GALV-KoRV clade originates in the former region and further models of early-stage genome colonization may be found. We screened 278 samples, seven bat and one rodent family endemic to the Australo-Papuan region and bat and rodent species found on both sides of the Wallace Line. We identified two rodents (Melomys) from Australia and Papua New Guinea and no bat species harboring GALV-like retroviruses. Melomys leucogaster from New Guinea harbored a genomically complete replication-competent retrovirus with a shared integration site among individuals. The integration was only present in some individuals of the species indicating this retrovirus is at the earliest stages of germline colonization of the Melomys genome, providing a new small wild mammal model of early-stage genome colonization.
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Affiliation(s)
- Saba Mottaghinia
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin10315, Germany
- Centre International de Recherche en Infectiologie, Université de Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Nationale Supérieure de Lyon, LyonF-69007, France
| | - Saskia Stenzel
- Institute of Virology Charité–Universitätsmedizin Berlin, BerlinD-10117, Germany
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, LiverpoolL3 5QA, United Kingdom
| | - Kyriakos Tsangaras
- Department of Life and Health Sciences, University of Nicosia, NicosiaCY-2417, Cyprus
| | - Nikolas Nikolaidis
- Department of Biological Science, Center for Applied Biotechnology Studies, and Center for Computational and Applied Mathematics, College of Natural Sciences and Mathematics, California State University Fullerton, Fullerton, CA92834-6850
| | - Michael Laue
- Advanced Light and Electron Microscopy (ZBS 4), Centre for Biological Threats and Special Pathogens, Robert Koch Institute, BerlinD-13353, Germany
| | - Karin Müller
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin10315, Germany
| | - Henriette Hölscher
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin10315, Germany
| | - Ulrike Löber
- Max-Delbrük Center for Molecular Medicine Helmholtz Association, Berlin13125, Germany
| | - Gayle K. McEwen
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin10315, Germany
| | | | - Kevin C. Rowe
- Sciences Department, Museums Victoria, Melbourne, VIC3001, Australia
| | - Ken P. Aplin
- South Australian Museum, North Terrace, Adelaide SA5000, Australia
| | - Christine Goffinet
- Institute of Virology Charité–Universitätsmedizin Berlin, BerlinD-10117, Germany
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, LiverpoolL3 5QA, United Kingdom
| | - Alex D. Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin10315, Germany
- School of Veterinary Medicine, Freie Universität Berlin, Berlin14163, Germany
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5
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Essex M, Rios Rodriguez V, Rademacher J, Proft F, Löber U, Markó L, Pleyer U, Strowig T, Marchand J, Kirwan JA, Siegmund B, Forslund SK, Poddubnyy D. Shared and Distinct Gut Microbiota in Spondyloarthritis, Acute Anterior Uveitis, and Crohn's Disease. Arthritis Rheumatol 2024; 76:48-58. [PMID: 37471465 DOI: 10.1002/art.42658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 06/26/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023]
Abstract
OBJECTIVE Spondyloarthritis (SpA) is a group of immune-mediated diseases highly concomitant with nonmusculoskeletal inflammatory disorders, such as acute anterior uveitis (AAU) and Crohn's disease (CD). The gut microbiome represents a promising avenue to elucidate shared and distinct underlying pathophysiology. METHODS We performed 16S ribosomal RNA sequencing on stool samples of 277 patients (72 CD, 103 AAU, and 102 SpA) included in the German Spondyloarthritis Inception Cohort and 62 back pain controls without any inflammatory disorder. Discriminatory statistical methods were used to disentangle microbial disease signals from one another and a wide range of potential confounders. Patients were naive to or had not received treatment with biological disease-modifying antirheumatic drugs (DMARDs) for >3 months before enrollment, providing a better approximation of a true baseline disease signal. RESULTS We identified a shared, immune-mediated disease signal represented by low abundances of Lachnospiraceae taxa relative to controls, most notably Fusicatenibacter, which was most abundant in controls receiving nonsteroidal antiinflammatory drug monotherapy and implied to partially mediate higher serum C-reactive protein. Patients with SpA showed an enrichment of Collinsella, whereas human leukocyte antigen (HLA)-B27+ individuals displayed enriched Faecalibacterium. CD patients had higher abundances of a Ruminococcus taxon, and previous conventional/synthetic DMARD therapy was associated with increased Akkermansia. CONCLUSION Our work supports the existence of a common gut dysbiosis in SpA and related inflammatory pathologies. We reveal shared and disease-specific microbial associations and suggest potential mediators of disease activity. Validation studies are needed to clarify the role of Fusicatenibacter in gut-joint inflammation, and metagenomic resolution is needed to understand the relationship between Faecalibacterium commensals and HLA-B27.
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Affiliation(s)
- Morgan Essex
- Experimental and Clinical Research Center (ECRC; a cooperation of the Max Delbrück Center and Charité-Universitätsmedizin), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), and Charité-Universitätsmedizin Berlin (a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin), Berlin, Germany
| | - Valeria Rios Rodriguez
- Medical Department of Gastroenterology, Infectiology and Rheumatology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Judith Rademacher
- Medical Department of Gastroenterology, Infectiology and Rheumatology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, and Berlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Fabian Proft
- Medical Department of Gastroenterology, Infectiology and Rheumatology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ulrike Löber
- ECRC, MDC, Charité-Universitätsmedizin Berlin and German Center for Cardiovascular Research (DZHK), Berlin, Germany
| | - Lajos Markó
- ECRC, MDC, Charité-Universitätsmedizin Berlin and German Center for Cardiovascular Research (DZHK), Berlin, Germany
| | - Uwe Pleyer
- Department of Ophthalmology, Campus Virchow, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Till Strowig
- Helmholtz Center for Infection Research, Braunschweig, Germany, and Cluster of Excellence RESIST (EXC 2155), Hannover Medical School and Center for Individualized Infection Medicine (CiiM; a joint venture between the Helmholtz Center for Infection Research and the Hannover Medical School), Hannover, Germany
| | - Jérémy Marchand
- MDC and BIH Metabolomics Platform at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jennifer A Kirwan
- MDC and BIH Metabolomics Platform at Charité-Universitätsmedizin Berlin, Berlin, Germany, and University of Nottingham School of Veterinary Medicine and Science, Loughborough, UK
| | - Britta Siegmund
- Medical Department of Gastroenterology, Infectiology and Rheumatology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sofia K Forslund
- ECRC, MDC, Charité-Universitätsmedizin Berlin, and DZHK, Berlin, and Structural and Computational Biology Unit, EMBL, Heidelberg, Germany
| | - Denis Poddubnyy
- Department of Gastroentergology, Infectiology and Rheumatology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin and German Rheumatism Research Center (DRFZ), Berlin, Germany
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Bengtsson-Palme J, Abramova A, Berendonk TU, Coelho LP, Forslund SK, Gschwind R, Heikinheimo A, Jarquín-Díaz VH, Khan AA, Klümper U, Löber U, Nekoro M, Osińska AD, Ugarcina Perovic S, Pitkänen T, Rødland EK, Ruppé E, Wasteson Y, Wester AL, Zahra R. Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs? Environ Int 2023; 178:108089. [PMID: 37441817 DOI: 10.1016/j.envint.2023.108089] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 04/25/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
Antimicrobial resistance (AMR) is a global threat to human and animal health and well-being. To understand AMR dynamics, it is important to monitor resistant bacteria and resistance genes in all relevant settings. However, while monitoring of AMR has been implemented in clinical and veterinary settings, comprehensive monitoring of AMR in the environment is almost completely lacking. Yet, the environmental dimension of AMR is critical for understanding the dissemination routes and selection of resistant microorganisms, as well as the human health risks related to environmental AMR. Here, we outline important knowledge gaps that impede implementation of environmental AMR monitoring. These include lack of knowledge of the 'normal' background levels of environmental AMR, definition of high-risk environments for transmission, and a poor understanding of the concentrations of antibiotics and other chemical agents that promote resistance selection. Furthermore, there is a lack of methods to detect resistance genes that are not already circulating among pathogens. We conclude that these knowledge gaps need to be addressed before routine monitoring for AMR in the environment can be implemented on a large scale. Yet, AMR monitoring data bridging different sectors is needed in order to fill these knowledge gaps, which means that some level of national, regional and global AMR surveillance in the environment must happen even without all scientific questions answered. With the possibilities opened up by rapidly advancing technologies, it is time to fill these knowledge gaps. Doing so will allow for specific actions against environmental AMR development and spread to pathogens and thereby safeguard the health and wellbeing of humans and animals.
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Affiliation(s)
- Johan Bengtsson-Palme
- Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) in Gothenburg, Sweden.
| | - Anna Abramova
- Division of Systems and Synthetic Biology, Department of Life Sciences, SciLifeLab, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden; Centre for Antibiotic Resistance Research (CARe) in Gothenburg, Sweden
| | - Thomas U Berendonk
- Institute of Hydrobiology, Technische Universität Dresden, Zellescher Weg 40, 01217 Dresden, Germany
| | - Luis Pedro Coelho
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Sofia K Forslund
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rémi Gschwind
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME F-75018 Paris, France
| | - Annamari Heikinheimo
- University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O.Box 66, FI-00014, Finland; Finnish Food Authority, P.O.Box 100, 00027 Seinäjoki, Finland
| | - Víctor Hugo Jarquín-Díaz
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Ayaz Ali Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan; Department of Biotechnology, University of Malakand, Chakdara, Dir (Lower), Khyber Pakhtunkhwa, Pakistan
| | - Uli Klümper
- Institute of Hydrobiology, Technische Universität Dresden, Zellescher Weg 40, 01217 Dresden, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité - Universitätsmedizin Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Experimental and Clinical Research Center, Lindenberger Weg 80, 13125 Berlin, Germany; Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Marmar Nekoro
- Swedish Knowledge Centre on Pharmaceuticals in the Environment, Swedish Medical Products Agency, P.O Box 26, 751 03 Uppsala, Sweden
| | - Adriana D Osińska
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Paraclinical Sciences, P.O.Box 5003 NMBU, N-1432 Ås, Norway
| | - Svetlana Ugarcina Perovic
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China; MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Tarja Pitkänen
- University of Helsinki, Faculty of Veterinary Medicine, Department of Food Hygiene and Environmental Health, P.O.Box 66, FI-00014, Finland; Finnish Institute for Health and Welfare, Expert Microbiology Unit, P.O.Box 95, FI-70701 Kuopio, Finland
| | | | - Etienne Ruppé
- Université Paris Cité and Université Sorbonne Paris Nord, Inserm, IAME F-75018 Paris, France
| | - Yngvild Wasteson
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Paraclinical Sciences, P.O.Box 5003 NMBU, N-1432 Ås, Norway
| | | | - Rabaab Zahra
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
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Chen CY, Löber U, Forslund SK. LongDat: an R package for covariate-sensitive longitudinal analysis of high-dimensional data. Bioinform Adv 2023; 3:vbad063. [PMID: 37359720 PMCID: PMC10284677 DOI: 10.1093/bioadv/vbad063] [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] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 04/15/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023]
Abstract
Summary We introduce LongDat, an R package that analyzes longitudinal multivariable (cohort) data while simultaneously accounting for a potentially large number of covariates. The primary use case is to differentiate direct from indirect effects of an intervention (or treatment) and to identify covariates (potential mechanistic intermediates) in longitudinal data. LongDat focuses on analyzing longitudinal microbiome data, but its usage can be expanded to other data types, such as binary, categorical and continuous data. We tested and compared LongDat with other tools (i.e. MaAsLin2, ANCOM, lgpr and ZIBR) on both simulated and real data. We showed that LongDat outperformed these tools in accuracy, runtime and memory cost, especially when there were multiple covariates. The results indicate that the LongDat R package is a computationally efficient and low-memory-cost tool for longitudinal data with multiple covariates and facilitates robust biomarker searches in high-dimensional datasets. Availability and implementation The R package LongDat is available on CRAN (https://cran.r-project.org/web/packages/LongDat/) and GitHub (https://github.com/CCY-dev/LongDat). Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | - Ulrike Löber
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin 13125, Germany
- Experimental and Clinical Research Center, A Cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité – Universitätsmedizin Berlin, Berlin 13125, Germany
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin 10117, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin 10785, Germany
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8
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Kayongo A, Bartolomaeus TUP, Birkner T, Markó L, Löber U, Kigozi E, Atugonza C, Munana R, Mawanda D, Sekibira R, Uwimaana E, Alupo P, Kalyesubula R, Knauf F, Siddharthan T, Bagaya BS, Kateete DP, Joloba ML, Sewankambo NK, Jjingo D, Kirenga B, Checkley W, Forslund SK. Sputum Microbiome and Chronic Obstructive Pulmonary Disease in a Rural Ugandan Cohort of Well-Controlled HIV Infection. Microbiol Spectr 2023; 11:e0213921. [PMID: 36790203 PMCID: PMC10100697 DOI: 10.1128/spectrum.02139-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
Sub-Saharan Africa has increased morbidity and mortality related to chronic obstructive pulmonary disease (COPD). COPD among people living with HIV (PLWH) has not been well studied in this region, where HIV/AIDS is endemic. Increasing evidence suggests that respiratory microbial composition plays a role in COPD severity. Therefore, we aimed to investigate microbiome patterns and associations among PLWH with COPD in Sub-Saharan Africa. We conducted a cross-sectional study of 200 adults stratified by HIV and COPD in rural Uganda. Induced sputum samples were collected as an easy-to-obtain proxy for the lower respiratory tract microbiota. We performed 16S rRNA gene sequencing and used PICRUSt2 (version 2.2.3) to infer the functional profiles of the microbial community. We used a statistical tool to detect changes in specific taxa that searches and adjusts for confounding factors such as antiretroviral therapy (ART), age, sex, and other participant characteristics. We could cluster the microbial community into three community types whose distribution was shown to be significantly impacted by HIV. Some genera, e.g., Veillonella, Actinomyces, Atopobium, and Filifactor, were significantly enriched in HIV-infected individuals, while the COPD status was significantly associated with Gammaproteobacteria and Selenomonas abundance. Furthermore, reduced bacterial richness and significant enrichment in Campylobacter were associated with HIV-COPD comorbidity. Functional prediction using PICRUSt2 revealed a significant depletion in glutamate degradation capacity pathways in HIV-positive patients. A comparison of our findings with an HIV cohort from the United Kingdom revealed significant differences in the sputum microbiome composition, irrespective of viral suppression. IMPORTANCE Even with ART available, HIV-infected individuals are at high risk of suffering comorbidities, as shown by the high prevalence of noninfectious lung diseases in the HIV population. Recent studies have suggested a role for the respiratory microbiota in driving chronic lung inflammation. The respiratory microbiota was significantly altered among PLWH, with disease persisting up to 3 years post-ART initiation and HIV suppression. The community structure and diversity of the sputum microbiota in COPD are associated with disease severity and clinical outcomes, both in stable COPD and during exacerbations. Therefore, a better understanding of the sputum microbiome among PLWH could improve COPD prognostic and risk stratification strategies. In this study, we observed that in a virologically suppressed HIV cohort in rural Uganda, we could show differences in sputum microbiota stratified by HIV and COPD, reduced bacterial richness, and significant enrichment in Campylobacter associated with HIV-COPD comorbidity.
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Affiliation(s)
- Alex Kayongo
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Theda Ulrike Patricia Bartolomaeus
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Till Birkner
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Lajos Markó
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Ulrike Löber
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
| | - Edgar Kigozi
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Carolyne Atugonza
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Richard Munana
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Denis Mawanda
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Rogers Sekibira
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Esther Uwimaana
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Patricia Alupo
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Robert Kalyesubula
- African Community Center for Social Sustainability (ACCESS), Department of Research, Nakaseke, Uganda
- Makerere University, College of Health Sciences, Department of Medicine, Kampala, Uganda
| | - Felix Knauf
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Trishul Siddharthan
- University of Miami, School of Medicine, Division of pulmonary and critical care medicine, Miami, Florida, USA
| | - Bernard S. Bagaya
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - David P. Kateete
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Moses L. Joloba
- Makerere University, College of Health Sciences, Department of Immunology and Molecular Biology, Kampala, Uganda
| | - Nelson K. Sewankambo
- Makerere University, College of Health Sciences, Department of Medicine, Kampala, Uganda
| | - Daudi Jjingo
- Makerere University, College of Computing and Information Sciences, Department of Computer Science, Kampala, Uganda
- African Center of Excellence in Bioinformatics and Data Science, Infectious Diseases Institute, Kampala, Uganda
| | - Bruce Kirenga
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
- Makerere University, College of Health Sciences, Department of Medicine, Kampala, Uganda
| | - William Checkley
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University, Baltimore, Maryland, USA
- Center for Global Non-Communicable Disease Research and Training, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sofia K. Forslund
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- German Centre for Cardiovascular Research, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
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9
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Noormohammadi M, Ghorbani Z, Löber U, Mahdavi-Roshan M, Bartolomaeus TUP, Kazemi A, Shoaibinobarian N, Forslund SK. The effect of probiotic and synbiotic supplementation on appetite-regulating hormones and desire to eat: A systematic review and meta-analysis of clinical trials. Pharmacol Res 2023; 187:106614. [PMID: 36538981 DOI: 10.1016/j.phrs.2022.106614] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 09/21/2022] [Revised: 12/11/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Recent studies have demonstrated the effect of probiotics, prebiotics, and synbiotics on adiponectin and leptin levels; however, those findings remain contested. The present study aimed to explore the impact of probiotics/synbiotics on appetite-regulating hormones and the desire to eat. METHODS A systematic review was conducted by searching the Medline (PubMed) and Scopus databases from inception to December 2021, using relevant keywords and MeSH terms, and appropriate randomized controlled trials (RCTs) were extracted. The standardized mean differences (SMD) and 95% confidence intervals (95%CIs) were calculated as part of the meta-analysis using a random-effect model to determine the mean effect sizes. Analysis of Galbraith plots and the Cochrane Chi-squared test were conducted to examine heterogeneity. RESULTS Meta-analysis of data from a total of 26 RCTs (n = 1536) showed a significant decrease in serum/plasma leptin concentration following probiotic/synbiotic supplementation (SMD: -0.38, 95%CI= -0.638, -0.124); P-value= 0.004; I2= 69.4%; P heterogeneity < 0.001). The leptin level decrease from probiotic/synbiotic supplementation was higher in patients with NAFLD than those with overweight/obesity or type 2 diabetes mellitus/ metabolic syndrome/ prediabetes. Probiotic/synbiotic supplementation was associated with a trending increase in adiponectin levels, stronger in patients with type 2 diabetes mellitus, metabolic syndrome, and prediabetes (SMD: 0.25, 95%CI= 0.04, 0.46) µg/mL; P-value= 0.021; I2 = 16.8%; P heterogeneity= 0.30). Additionally, supplementation with probiotic/synbiotic was linked to a slight increase in desire to eat (SMD: 0.34, 95%CI= 0.03, 0.66) P-value = 0.030; I2 = 39.4%; P heterogeneity= 0.16). CONCLUSION Our meta-analysis indicates a favorable impact of probiotic/synbiotic supplementation on regulating leptin and adiponectin secretion.
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Affiliation(s)
- Morvarid Noormohammadi
- Department of Nutrition, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Zeinab Ghorbani
- Department of Clinical Nutrition, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran.
| | - Ulrike Löber
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany; Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site, Berlin, Germany
| | - Marjan Mahdavi-Roshan
- Department of Clinical Nutrition, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Theda U P Bartolomaeus
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany; Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site, Berlin, Germany
| | - Asma Kazemi
- Nutrition Research Center, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Nargeskhatoon Shoaibinobarian
- Department of Nutrition, School of Medical Sciences and Technologies, Islamic Azad University, Science and Research Branch, Tehran, Iran
| | - Sofia K Forslund
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany; Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany; Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site, Berlin, Germany; Structural and Computational Biology Unit, European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany.
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10
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Midha A, Jarquín-Díaz VH, Ebner F, Löber U, Hayani R, Kundik A, Cardilli A, Heitlinger E, Forslund SK, Hartmann S. Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host. Microbiome 2022; 10:229. [PMID: 36527132 PMCID: PMC9756626 DOI: 10.1186/s40168-022-01399-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/18/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Intestinal helminths are extremely prevalent among humans and animals. In particular, intestinal roundworms affect more than 1 billion people around the globe and are a major issue in animal husbandry. These pathogens live in intimate contact with the host gut microbiota and harbor bacteria within their own intestines. Knowledge of the bacterial host microbiome at the site of infection is limited, and data on the parasite microbiome is, to the best of our knowledge, non-existent. RESULTS The intestinal microbiome of the natural parasite and zoonotic macropathogen, Ascaris suum was analyzed in contrast to the diversity and composition of the infected host gut. 16S sequencing of the parasite intestine and host intestinal compartments showed that the parasite gut has a significantly less diverse microbiome than its host, and the host gut exhibits a reduced microbiome diversity at the site of parasite infection in the jejunum. While the host's microbiome composition at the site of infection significantly determines the microbiome composition of its parasite, microbial signatures differentiate the nematodes from their hosts as the Ascaris intestine supports the growth of microbes that are otherwise under-represented in the host gut. CONCLUSION Our data clearly indicate that a nematode infection reduces the microbiome diversity of the host gut, and that the nematode gut represents a selective bacterial niche harboring bacteria that are derived but distinct from the host gut. Video Abstract.
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Affiliation(s)
- Ankur Midha
- Department of Veterinary Medicine, Center for Infection Medicine, Institute of Immunology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
| | - Víctor Hugo Jarquín-Díaz
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité — Universitätsmedizin Berlin, Berlin, Germany
- Charité — Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Lindenberger Weg 80, 13125 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Molecular Parasitology, Institute for Biology, Humboldt-Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
- Research Group Ecology and Evolution of Molecular Parasite-Host Interactions, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Friederike Ebner
- Department of Veterinary Medicine, Center for Infection Medicine, Institute of Immunology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité — Universitätsmedizin Berlin, Berlin, Germany
- Charité — Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Lindenberger Weg 80, 13125 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Rima Hayani
- Department of Veterinary Medicine, Center for Infection Medicine, Institute of Immunology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
| | - Arkadi Kundik
- Department of Veterinary Medicine, Center for Infection Medicine, Institute of Immunology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
| | - Alessio Cardilli
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité — Universitätsmedizin Berlin, Berlin, Germany
- Charité — Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Lindenberger Weg 80, 13125 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Emanuel Heitlinger
- Department of Molecular Parasitology, Institute for Biology, Humboldt-Universität zu Berlin, Philippstraße 13, 10115 Berlin, Germany
- Research Group Ecology and Evolution of Molecular Parasite-Host Interactions, Leibniz-Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Sofia Kirke Forslund
- Experimental and Clinical Research Center, a cooperation between the Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association and the Charité — Universitätsmedizin Berlin, Berlin, Germany
- Charité — Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Lindenberger Weg 80, 13125 Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Susanne Hartmann
- Department of Veterinary Medicine, Center for Infection Medicine, Institute of Immunology, Freie Universität Berlin, Robert-von-Ostertag-Straße 7, 14163 Berlin, Germany
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11
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Holle J, Bartolomaeus H, Löber U, Behrens F, Bartolomaeus TU, Anandakumar H, Wimmer MI, Vu DL, Kuhring M, Brüning U, Maifeld A, Geisberger S, Kempa S, Schumacher F, Kleuser B, Bufler P, Querfeld U, Kitschke S, Engler D, Kuhrt LD, Drechsel O, Eckardt KU, Forslund SK, Thürmer A, McParland V, Kirwan JA, Wilck N, Müller D. Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance. J Am Soc Nephrol 2022; 33:2259-2275. [PMID: 35985814 PMCID: PMC9731629 DOI: 10.1681/asn.2022030378] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/29/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND CKD is characterized by a sustained proinflammatory response of the immune system, promoting hypertension and cardiovascular disease. The underlying mechanisms are incompletely understood but may be linked to gut dysbiosis. Dysbiosis has been described in adults with CKD; however, comorbidities limit CKD-specific conclusions. METHODS We analyzed the fecal microbiome, metabolites, and immune phenotypes in 48 children (with normal kidney function, CKD stage G3-G4, G5 treated by hemodialysis [HD], or kidney transplantation) with a mean±SD age of 10.6±3.8 years. RESULTS Serum TNF-α and sCD14 were stage-dependently elevated, indicating inflammation, gut barrier dysfunction, and endotoxemia. We observed compositional and functional alterations of the microbiome, including diminished production of short-chain fatty acids. Plasma metabolite analysis revealed a stage-dependent increase of tryptophan metabolites of bacterial origin. Serum from patients on HD activated the aryl hydrocarbon receptor and stimulated TNF-α production in monocytes, corresponding to a proinflammatory shift from classic to nonclassic and intermediate monocytes. Unsupervised analysis of T cells revealed a loss of mucosa-associated invariant T (MAIT) cells and regulatory T cell subtypes in patients on HD. CONCLUSIONS Gut barrier dysfunction and microbial metabolite imbalance apparently mediate the proinflammatory immune phenotype, thereby driving the susceptibility to cardiovascular disease. The data highlight the importance of the microbiota-immune axis in CKD, irrespective of confounding comorbidities.
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Affiliation(s)
- Johannes Holle
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité–Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center, a cooperation of Charité–Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Hendrik Bartolomaeus
- Experimental and Clinical Research Center, a cooperation of Charité–Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center, a cooperation of Charité–Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Felix Behrens
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité–Universitätsmedizin Berlin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
- Institute of Physiology, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Theda U.P. Bartolomaeus
- Experimental and Clinical Research Center, a cooperation of Charité–Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Harithaa Anandakumar
- Experimental and Clinical Research Center, a cooperation of Charité–Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Moritz I. Wimmer
- Experimental and Clinical Research Center, a cooperation of Charité–Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Berlin, Germany
- Division of Endocrinology, Diabetology and Nephrology, Department of Internal Medicine IV, University Hospital of Tübingen, Tübingen, Germany
| | - Dai Long Vu
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Core Unit Metabolomics, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Mathias Kuhring
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
- Core Unit Bioinformatics, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Ulrike Brüning
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Core Unit Metabolomics, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Andras Maifeld
- Experimental and Clinical Research Center, a cooperation of Charité–Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Sabrina Geisberger
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- The Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Stefan Kempa
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- The Berlin Institute for Medical Systems Biology, Berlin, Germany
| | | | - Burkhard Kleuser
- Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Philip Bufler
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Uwe Querfeld
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Stefanie Kitschke
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Denise Engler
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Leonard D. Kuhrt
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité–Universitätsmedizin Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | | | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Sofia K. Forslund
- Experimental and Clinical Research Center, a cooperation of Charité–Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andrea Thürmer
- MF2 Genome Sequencing, Robert Koch Institute, Berlin, Germany
| | - Victoria McParland
- Experimental and Clinical Research Center, a cooperation of Charité–Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Jennifer A. Kirwan
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Core Unit Metabolomics, Berlin Institute of Health at Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Nicola Wilck
- Experimental and Clinical Research Center, a cooperation of Charité–Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- Department of Nephrology and Medical Intensive Care, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Dominik Müller
- Department of Pediatric Gastroenterology, Nephrology and Metabolic Diseases, Charité–Universitätsmedizin Berlin, Berlin, Germany
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12
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Worm M, Alexiou A, Höfer V, Birkner T, Jeanrenaud ACSN, Fauchère F, Pazur K, Steinert C, Arnau‐Soler A, Banerjee P, Diefenbach A, Dobbertin‐Welsch J, Dölle‐Bierke S, Francuzik W, Ghauri A, Heller S, Kalb B, Löber U, Marenholz I, Markó L, Scheffel J, Potapenko O, Roll S, Lau S, Lee Y, Braun J, Thiel A, Babina M, Altrichter S, Forslund SK, Beyer K. An interdisciplinary approach to characterize peanut-allergic patients-First data from the FOOD@ consortium. Clin Transl Allergy 2022; 12:e12197. [PMID: 36225266 PMCID: PMC9533219 DOI: 10.1002/clt2.12197] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/29/2022] [Accepted: 09/05/2022] [Indexed: 12/01/2022] Open
Abstract
Background Peanut allergy is a frequent cause of food allergy and potentially life‐threatening. Within this interdisciplinary research approach, we aim to unravel the complex mechanisms of peanut allergy. As a first step were applied in an exploratory manner the analysis of peanut allergic versus non‐allergic controls. Methods Biosamples were studied regarding DNA methylation signatures, gut microbiome, adaptive and innate immune cell populations, soluble signaling molecules and allergen‐reactive antibody specificities. We applied a scalable systems medicine computational workflow to the assembled data. Results We identified combined cellular and soluble biomarker signatures that stratify donors into peanut‐allergic and non‐allergic with high specificity. DNA methylation profiling revealed various genes of interest and stool microbiota differences in bacteria abundances. Conclusion By extending our findings to a larger set of patients (e.g., children vs. adults), we will establish predictors for food allergy and tolerance and translate these as for example, indicators for interventional studies.
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Affiliation(s)
- Margitta Worm
- Division of Allergy and ImmunologyDepartment of Dermatology, Venerology and AllergyCharité – Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Aikaterina Alexiou
- Division of Allergy and ImmunologyDepartment of Dermatology, Venerology and AllergyCharité – Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Veronika Höfer
- Division of Allergy and ImmunologyDepartment of Dermatology, Venerology and AllergyCharité – Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Till Birkner
- Experimental and Clinical Research CenterA Cooperation of Charité‐Universitätsmedizin BerlinMax Delbrück Center for Molecular MedicineBerlinGermany,Charité‐Universitätsmedizin BerlinFreie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of HealthBerlinGermany,Max Delbrück Center for Molecular MedicineHelmholtz AssociationBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Alexander C. S. N. Jeanrenaud
- Max Delbrück Center for Molecular MedicineHelmholtz AssociationBerlinGermany,Clinic for Pediatric Allergy, Experimental and Clinical Research CenterCharité – Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Florent Fauchère
- Si‐M/“Der Simulierte Mensch” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin BerlinBerlinGermany,Regenerative Immunology and AgingBIH Center for Regenerative TherapiesCharité ‐ Universitätsmedizin BerlinCorporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Kristijan Pazur
- Division of Allergy and ImmunologyDepartment of Dermatology, Venerology and AllergyCharité – Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Carolin Steinert
- Institute of Allergology IFACharité‐Universitätsmedizin BerlinFreie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of HealthBerlinGermany,Fraunhofer Institute for Translational Medicine and Pharmacology ITMPAllergology and Immunology AIBerlinGermany,Department of Biology, Chemistry and PharmacyFreie Universität BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Aleix Arnau‐Soler
- Max Delbrück Center for Molecular MedicineHelmholtz AssociationBerlinGermany,Clinic for Pediatric Allergy, Experimental and Clinical Research CenterCharité – Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Priyanka Banerjee
- Institute of PhysiologyCharité – Universitätsmedizin BerlinFreie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of HealthBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Andreas Diefenbach
- Mucosal and Developmental ImmunologyGerman Rheuma Research Center Berlin (DRFZ)BerlinGermany,Department of Microbiology, Infectious Diseases, and ImmunologyLaboratory of Innate ImmunityCharité – Universitätsmedizin BerlinCampus Benjamin FranklinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Josefine Dobbertin‐Welsch
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care MedicineCharité – Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Sabine Dölle‐Bierke
- Division of Allergy and ImmunologyDepartment of Dermatology, Venerology and AllergyCharité – Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Wojciech Francuzik
- Division of Allergy and ImmunologyDepartment of Dermatology, Venerology and AllergyCharité – Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Ahla Ghauri
- Max Delbrück Center for Molecular MedicineHelmholtz AssociationBerlinGermany,Clinic for Pediatric Allergy, Experimental and Clinical Research CenterCharité – Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Stephanie Heller
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care MedicineCharité – Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Birgit Kalb
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care MedicineCharité – Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Ulrike Löber
- Experimental and Clinical Research CenterA Cooperation of Charité‐Universitätsmedizin BerlinMax Delbrück Center for Molecular MedicineBerlinGermany,Charité‐Universitätsmedizin BerlinFreie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of HealthBerlinGermany,Max Delbrück Center for Molecular MedicineHelmholtz AssociationBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Ingo Marenholz
- Max Delbrück Center for Molecular MedicineHelmholtz AssociationBerlinGermany,Clinic for Pediatric Allergy, Experimental and Clinical Research CenterCharité – Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Lajos Markó
- Experimental and Clinical Research CenterA Cooperation of Charité‐Universitätsmedizin BerlinMax Delbrück Center for Molecular MedicineBerlinGermany,Charité‐Universitätsmedizin BerlinFreie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of HealthBerlinGermany,Max Delbrück Center for Molecular MedicineHelmholtz AssociationBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Jörg Scheffel
- Institute of Allergology IFACharité‐Universitätsmedizin BerlinFreie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of HealthBerlinGermany,Fraunhofer Institute for Translational Medicine and Pharmacology ITMPAllergology and Immunology AIBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Olena Potapenko
- Experimental and Clinical Research CenterA Cooperation of Charité‐Universitätsmedizin BerlinMax Delbrück Center for Molecular MedicineBerlinGermany,Charité‐Universitätsmedizin BerlinFreie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of HealthBerlinGermany,Max Delbrück Center for Molecular MedicineHelmholtz AssociationBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Stephanie Roll
- Institute of Social Medicine, Epidemiology and Health EconomicsCharité—Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Susanne Lau
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care MedicineCharité – Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Young‐Ae Lee
- Max Delbrück Center for Molecular MedicineHelmholtz AssociationBerlinGermany,Clinic for Pediatric Allergy, Experimental and Clinical Research CenterCharité – Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Julian Braun
- Si‐M/“Der Simulierte Mensch” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin BerlinBerlinGermany,Regenerative Immunology and AgingBIH Center for Regenerative TherapiesCharité ‐ Universitätsmedizin BerlinCorporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Andreas Thiel
- Si‐M/“Der Simulierte Mensch” a Science Framework of Technische Universität Berlin and Charité – Universitätsmedizin BerlinBerlinGermany,Regenerative Immunology and AgingBIH Center for Regenerative TherapiesCharité ‐ Universitätsmedizin BerlinCorporate Member of Freie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Magda Babina
- Institute of Allergology IFACharité‐Universitätsmedizin BerlinFreie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of HealthBerlinGermany,Fraunhofer Institute for Translational Medicine and Pharmacology ITMPAllergology and Immunology AIBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Sabine Altrichter
- Institute of Allergology IFACharité‐Universitätsmedizin BerlinFreie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of HealthBerlinGermany,Fraunhofer Institute for Translational Medicine and Pharmacology ITMPAllergology and Immunology AIBerlinGermany,Department of Dermatology and VenerologyKepler University HospitalLinzAustria,KFO339, FOOD@BerlinGermany
| | - Sofia Kirke Forslund
- Experimental and Clinical Research CenterA Cooperation of Charité‐Universitätsmedizin BerlinMax Delbrück Center for Molecular MedicineBerlinGermany,Charité‐Universitätsmedizin BerlinFreie Universität BerlinHumboldt‐Universität zu BerlinBerlin Institute of HealthBerlinGermany,Max Delbrück Center for Molecular MedicineHelmholtz AssociationBerlinGermany,KFO339, FOOD@BerlinGermany
| | - Kirsten Beyer
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care MedicineCharité – Universitätsmedizin BerlinFreie Universität Berlin and Humboldt‐Universität zu BerlinBerlinGermany,KFO339, FOOD@BerlinGermany
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13
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Ghorbani Z, Kazemi A, Bartolomaeus TUP, Martami F, Noormohammadi M, Salari A, Löber U, Balou HA, Forslund SK, Mahdavi-Roshan M. The effect of probiotic and synbiotic supplementation on lipid parameters among patients with cardiometabolic risk factors: a systematic review and meta-analysis of clinical trials. Cardiovasc Res 2022; 119:933-956. [PMID: 35934838 DOI: 10.1093/cvr/cvac128] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/28/2022] [Accepted: 07/08/2022] [Indexed: 11/12/2022] Open
Abstract
Although the available evidence emphasizes the beneficial effects of probiotics in normalizing various cardiometabolic markers, there is still substantial uncertainty in this regard. Thus, we set out to determine the effect sizes of probiotics on blood lipid parameters more coherently. A systematic literature search of the Medline (PubMed) and Scopus databases was conducted from inception to February 12, 2021, applying both MeSH terms and free text terms to find the relevant randomized controlled trials (RCTs). The meta-analysis was conducted based on a random-effect model to calculate the mean effect sizes demonstrated as weighted mean differences (WMD) and the 95% confidence intervals (95%CI). To explore the heterogeneity, the Cochrane Chi-squared test, and analysis of Galbraith plots were performed. Meta-analysis of data from 40 RCTs (n = 2795) indicated a significant decrease in serum/plasma triglyceride (WMD (95%CI) -12.26 (-17.11- -7.41) mg/dL; P-value <0.001; I2 (%)= 29.9; P heterogeneity = 0.034)), total cholesterol (with high heterogeneity) (WMD (95%CI) -8.43 (-11.90- -4.95) mg/dL; P-value <0.001; I2 (%) =56.8; P heterogeneity < 0.001), LDL-C (WMD (95%CI) -5.08 (-7.61, -2.56) mg/dL; P-value <0.001; I2 (%) =42.7; P heterogeneity =0.002), and HDL-C (with high heterogeneity) (WMD (95%CI) 1.14 (0.23, 2.05) mg/dL; P-value =0.014; I2 (%) = 59.8; P heterogeneity < 0.001) following receiving probiotic/synbiotic supplements. Collectively, the current preliminary evidence supports the effectiveness of probiotics/synbiotics in improving dyslipidemia and various lipid parameters more prominently among subjects with hyperlipidemia, diabetes, and metabolic syndrome. However, large and well conducted RCTs are required to provide further convincing support for these results.
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Affiliation(s)
- Zeinab Ghorbani
- Cardiovascular Diseases Research Center, Department of Cardiology, Heshmat Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran.,Department of Clinical Nutrition, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Asma Kazemi
- Nutrition Research Center, School of Nutrition and Food Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Theda U P Bartolomaeus
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site, Berlin, Berlin, Germany
| | - Fahimeh Martami
- School of Nutritional Sciences and Dietetics, Tehran University of Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Morvarid Noormohammadi
- Department of Nutrition, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Arsalan Salari
- Cardiovascular Diseases Research Center, Department of Cardiology, Heshmat Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Ulrike Löber
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site, Berlin, Berlin, Germany
| | - Heydar Ali Balou
- Razi Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Sofia K Forslund
- Experimental and Clinical Research Center, A Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site, Berlin, Berlin, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Marjan Mahdavi-Roshan
- Cardiovascular Diseases Research Center, Department of Cardiology, Heshmat Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran.,Department of Clinical Nutrition, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
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14
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Avery EG, Bartolomaeus H, Rauch A, Chen CY, N'Diaye G, Löber U, Bartolomaeus TUP, Fritsche-Guenther R, Rodrigues AF, Yarritu A, Zhong C, Fei L, Tsvetkov D, Todiras M, Park JK, Markó L, Maifeld A, Patzak A, Bader M, Kempa S, Kirwan JA, Forslund SK, Müller DN, Wilck N. Quantifying the impact of gut microbiota on inflammation and hypertensive organ damage. Cardiovasc Res 2022:6651675. [PMID: 35904261 DOI: 10.1093/cvr/cvac121] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [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: 09/23/2021] [Revised: 07/04/2022] [Accepted: 07/08/2022] [Indexed: 11/12/2022] Open
Abstract
AIMS Hypertension (HTN) can lead to heart and kidney damage. The gut microbiota has been linked to HTN, although it is difficult to estimate its significance due to the variety of other features known to influence HTN. In the present study, we used germ-free (GF) and colonized (COL) littermate mice to quantify the impact of microbial colonization on organ damage in HTN. METHODS AND RESULTS Four-week-old male GF C57BL/6J littermates were randomized to remain GF or receive microbial colonization. HTN was induced by subcutaneous infusion with angiotensin (Ang) II (1.44 mg/kg/d) and 1% NaCl in the drinking water; sham-treated mice served as control. Renal damage was exacerbated in GF mice, whereas cardiac damage was more comparable between COL and GF, suggesting that the kidney is more sensitive to microbial influence. Multivariate analysis revealed a larger effect of HTN in GF mice. Serum metabolomics demonstrated that the colonization status influences circulating metabolites relevant to HTN. Importantly, GF mice were deficient in anti-inflammatory fecal short-chain fatty acids (SCFA). Flow cytometry showed that the microbiome has an impact on the induction of anti-hypertensive myeloid-derived suppressor cells and pro-inflammatory Th17 cells in HTN. In vitro inducibility of Th17 cells was significantly higher for cells isolated from GF than conventionally raised mice. CONCLUSIONS Microbial colonization status of mice had potent effects on their phenotypic response to a hypertensive stimulus, and the kidney is a highly microbiota-susceptible target organ in HTN. The magnitude of the pathogenic response in GF mice underscores the role of the microbiome in mediating inflammation in HTN. TRANSLATION PERSPECTIVE To assess the potential of microbiota-targeted interventions to prevent organ damage in hypertension, an accurate quantification of microbial influence is necessary. We provide evidence that the development of hypertensive organ damage is dependent on colonization status and suggest that a healthy microbiota provides anti-hypertensive immune and metabolic signals to the host. In the absence of normal symbiotic host-microbiome interactions, hypertensive damage to the kidney in particular is exacerbated. We suggest that hypertensive patients experiencing perturbations to the microbiota, which are common in CVD, may be at a greater risk for target-organ damage than those with a healthy microbiome.
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Affiliation(s)
- Ellen G Avery
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.,Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Hendrik Bartolomaeus
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Nephrology and Internal Intensive Care Medicine, Berlin, Germany
| | - Ariana Rauch
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Nephrology and Internal Intensive Care Medicine, Berlin, Germany
| | - Chia-Yu Chen
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gabriele N'Diaye
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
| | - Theda U P Bartolomaeus
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Raphaela Fritsche-Guenther
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Metabolomics Platform, Berlin, Germany
| | - André F Rodrigues
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.,Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Alex Yarritu
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Nephrology and Internal Intensive Care Medicine, Berlin, Germany
| | - Cheng Zhong
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Lingyan Fei
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Dmitry Tsvetkov
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Department of Geriatrics, University of Greifswald, University District Hospital Wolgast, Greifswald, Germany
| | - Mihail Todiras
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Nicolae Testemianu State University of Medicine and Pharmacy, Chisinau, Moldova
| | | | - Lajos Markó
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - András Maifeld
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andreas Patzak
- Institute of Translational Physiology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Michael Bader
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stefan Kempa
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Integrative Proteomics and Metabolomics Platform, Berlin Institute for Medical Systems Biology BIMSB, Berlin, Germany
| | - Jennifer A Kirwan
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Metabolomics Platform, Berlin, Germany
| | - Sofia K Forslund
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dominik N Müller
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nicola Wilck
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.,Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Nephrology and Internal Intensive Care Medicine, Berlin, Germany
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Rios Rodriguez V, Essex M, Rademacher J, Torgutalp M, Proft F, Löber U, Marko L, Poddubnyy D, Forslund SK. AB0114 IMPROVEMENT OF GUT MICROBIOTA DYSBIOSIS IN PATIENTS WITH AXIAL SPONDYLOARTHRITIS AFTER ONE YEAR OF BIOLOGICAL TREATMENT. Ann Rheum Dis 2022. [DOI: 10.1136/annrheumdis-2022-eular.4886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BackgroundEmerging evidence suggests that dysbiosis of the gut microbiota is involved in the initiation and perpetuation of spondyloarthritis (SpA). Biological disease-modifying antirheumatic drugs (bDMARDs) are a successful treatment to improve symptoms and reduce structural damage occurring in SpA; however, non-responders are frequent and few predictive factors for clinical response have been identified. Whether or not a patient responds to treatment could be related to gut microbiota composition.ObjectivesTo investigate the gut microbiota changes in patients with radiographic axial SpA (r-axSpA) after receiving one year of treatment with bDMARDs and identify potential microbial biomarkers predictive of treatment response.MethodsPatients with r-axSpA were recruited between 2015 and 2019 in an extension of the prospective GErman SPondyloarthritis Inception Cohort (GESPIC) before beginning bDMARD therapy. All patients had high disease activity (BASDAI >=4 and/or ASDAS >=2.1) despite previous treatment with nonsteroidal anti-inflammatory drugs, and had not received treatment with bDMARDs for at least three months before enrollment in the study. The choice of bDMARD was left to the discretion of the clinical rheumatologists in accordance with standard practice. Disease activity measures (BASDAI, CRP and ASDAS) and fecal samples were assessed at baseline prior to treatment and after one year of treatment. Patients with back pain negative for inflammatory disease served as a control group. Microbiota composition was determined by 16S rRNA gene sequencing, followed by taxonomic profiling with the SILVA138 database. Response to bDMARD therapy was defined as a clinically important improvement of ASDAS (>=1.1).ResultsA total of 99 patients with r-axSpA and 63 control individuals were included based on the availability of clinical and microbiome samples. Average age (mean±SD) was 36.4±10.4 years and 64 patients were males. The prevalence of HLA-B27 was 89.9% among r-axSpA patients compared to 7.9% among control individuals. Simpson indices showed an increase in alpha diversity between baseline and year 1 in r-axSpA patients which was statistically insignificant (paired Wilcoxon p=0.154) but brought the r-axSpA cohort nearer to controls. Likewise, Bray-Curtis dissimilarities to measure beta diversity showed a qualitative normalization to healthy individuals after treatment when visualized in principal coordinate space.At the genus level, patients were mainly depleted in Lachnospiraceae taxa such as Blautia, Roseburia, and Fusicatenibacter, and enriched in Collinsella compared to the control group at baseline. After one year of treatment, most SpA patients exhibited increased abundances of these taxa, most notably Blautia. Patients also exhibited depletions in Bacteroides and Faecalibacterium, which was strongly enriched in HLA-B27+ individuals at baseline (adjusted Wilcoxon p<0.001). Collinsella showed a very slight median increase after one year of treatment, with no significant difference between responders and non-responders (adjusted Wilcoxon p=0.33). Shifts in highly abundant Prevotella and Bacteroides were strongly correlated with the change in ASDAS after one year when controlling for intra-individual variance and overall changes in alpha diversity.ConclusionThe gut microbiota composition of r-axSpA patients who underwent treatment with bDMARDs for one year more closely resembled the controls. The unique enrichment of Collinsella in r-axSpA patients remained stable across time and treatment, suggesting it may be a disease biomarker.Figure 1.a) Flowchart of axSpA patients summarizing the main clinical and disease activity parameters of the cohort. b) Taxa with the most pronounced shifts in median relative abundance in patients with axSpA after receiving biological treatment for one year. c-d) Alpha and beta diversity analyses, respectively, of axSpA patients before and after treatment compared to control individuals. Labeled points in d represent group means.Disclosure of InterestsNone declared
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16
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König RS, Albrich WC, Kahlert CR, Bahr LS, Löber U, Vernazza P, Scheibenbogen C, Forslund SK. The Gut Microbiome in Myalgic Encephalomyelitis (ME)/Chronic Fatigue Syndrome (CFS). Front Immunol 2022; 12:628741. [PMID: 35046929 PMCID: PMC8761622 DOI: 10.3389/fimmu.2021.628741] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/09/2021] [Indexed: 12/16/2022] Open
Abstract
Myalgic encephalomyelitis (ME) or Chronic Fatigue Syndrome (CFS) is a neglected, debilitating multi-systemic disease without diagnostic marker or therapy. Despite evidence for neurological, immunological, infectious, muscular and endocrine pathophysiological abnormalities, the etiology and a clear pathophysiology remains unclear. The gut microbiome gained much attention in the last decade with manifold implications in health and disease. Here we review the current state of knowledge on the interplay between ME/CFS and the microbiome, to identify potential diagnostic or interventional approaches, and propose areas where further research is needed. We iteratively selected and elaborated on key theories about a correlation between microbiome state and ME/CFS pathology, developing further hypotheses. Based on the literature we hypothesize that antibiotic use throughout life favours an intestinal microbiota composition which might be a risk factor for ME/CFS. Main proposed pathomechanisms include gut dysbiosis, altered gut-brain axis activity, increased gut permeability with concomitant bacterial translocation and reduced levels of short-chain-fatty acids, D-lactic acidosis, an abnormal tryptophan metabolism and low activity of the kynurenine pathway. We review options for microbiome manipulation in ME/CFS patients including probiotic and dietary interventions as well as fecal microbiota transplantations. Beyond increasing gut permeability and bacterial translocation, specific dysbiosis may modify fermentation products, affecting peripheral mitochondria. Considering the gut-brain axis we strongly suspect that the microbiome may contribute to neurocognitive impairments of ME/CFS patients. Further larger studies are needed, above all to clarify whether D-lactic acidosis and early-life antibiotic use may be part of ME/CFS etiology and what role changes in the tryptophan metabolism might play. An association between the gut microbiome and the disease ME/CFS is plausible. As causality remains unclear, we recommend longitudinal studies. Activity levels, bedridden hours and disease progression should be compared to antibiotic exposure, drug intakes and alterations in the composition of the microbiota. The therapeutic potential of fecal microbiota transfer and of targeted dietary interventions should be systematically evaluated.
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Affiliation(s)
- Rahel S König
- Faculty of Medicine, University of Basel, Basel, Switzerland
| | - Werner C Albrich
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Christian R Kahlert
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland.,Division of Infectious Diseases and Hospital Epidemiology, Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland
| | - Lina Samira Bahr
- Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Experimental and Clinical Research Center, A Joint Cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ulrike Löber
- Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Experimental and Clinical Research Center, A Joint Cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.,Host-Microbiome Factors in Cardiovascular Disease, Max Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Pietro Vernazza
- Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | - Carmen Scheibenbogen
- Institute for Medical Immunology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sofia K Forslund
- Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.,Experimental and Clinical Research Center, A Joint Cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.,Host-Microbiome Factors in Cardiovascular Disease, Max Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
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Maier L, Goemans CV, Wirbel J, Kuhn M, Eberl C, Pruteanu M, Müller P, Garcia-Santamarina S, Cacace E, Zhang B, Gekeler C, Banerjee T, Anderson EE, Milanese A, Löber U, Forslund SK, Patil KR, Zimmermann M, Stecher B, Zeller G, Bork P, Typas A. Unravelling the collateral damage of antibiotics on gut bacteria. Nature 2021; 599:120-124. [PMID: 34646011 PMCID: PMC7612847 DOI: 10.1038/s41586-021-03986-2] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 09/01/2021] [Indexed: 12/15/2022]
Abstract
Antibiotics are used to fight pathogens but also target commensal bacteria, disturbing the composition of gut microbiota and causing dysbiosis and disease1. Despite this well-known collateral damage, the activity spectrum of different antibiotic classes on gut bacteria remains poorly characterized. Here we characterize further 144 antibiotics from a previous screen of more than 1,000 drugs on 38 representative human gut microbiome species2. Antibiotic classes exhibited distinct inhibition spectra, including generation dependence for quinolones and phylogeny independence for β-lactams. Macrolides and tetracyclines, both prototypic bacteriostatic protein synthesis inhibitors, inhibited nearly all commensals tested but also killed several species. Killed bacteria were more readily eliminated from in vitro communities than those inhibited. This species-specific killing activity challenges the long-standing distinction between bactericidal and bacteriostatic antibiotic classes and provides a possible explanation for the strong effect of macrolides on animal3-5 and human6,7 gut microbiomes. To mitigate this collateral damage of macrolides and tetracyclines, we screened for drugs that specifically antagonized the antibiotic activity against abundant Bacteroides species but not against relevant pathogens. Such antidotes selectively protected Bacteroides species from erythromycin treatment in human-stool-derived communities and gnotobiotic mice. These findings illluminate the activity spectra of antibiotics in commensal bacteria and suggest strategies to circumvent their adverse effects on the gut microbiota.
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Affiliation(s)
- Lisa Maier
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany.
| | - Camille V Goemans
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jakob Wirbel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Kuhn
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Claudia Eberl
- Max-von-Pettenkofer Institute, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany
| | - Mihaela Pruteanu
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Biology, Humboldt University Berlin, Berlin, Germany
| | - Patrick Müller
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | | | - Elisabetta Cacace
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Boyao Zhang
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Cordula Gekeler
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence 'Controlling Microbes to Fight Infections', University of Tübingen, Tübingen, Germany
| | - Tisya Banerjee
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Chemistry, TU Munich, Munich, Germany
| | - Exene Erin Anderson
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- NYU School of Medicine, New York, NY, USA
| | - Alessio Milanese
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center, a cooperation of Charité - Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Sofia K Forslund
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Experimental and Clinical Research Center, a cooperation of Charité - Universitätsmedizin Berlin and Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Kiran Raosaheb Patil
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- The Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Michael Zimmermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Bärbel Stecher
- Max-von-Pettenkofer Institute, LMU Munich, Munich, Germany
- German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Athanasios Typas
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
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Rios Rodriguez V, Essex M, Rademacher J, Proft F, Löber U, Marko L, Pleyer U, Siegmund B, Poddubnyy D, Forslund S. OP0031 SHARED AND DISTINCT GUT MICROBIOME SIGNATURES IN PATIENTS WITH AXIAL SPONDYLOARTHRITIS AND ITS RELATED IMMUNE-MEDIATED DISEASES. Ann Rheum Dis 2021. [DOI: 10.1136/annrheumdis-2021-eular.1965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background:Immune-mediated diseases such as spondyloarthritis (SpA) consistently coincide with dysbiosis of the gut microbiota and frequently present with additional inflammatory pathologies such as Crohn’s disease (CD) and acute anterior uveitis (AAU). Deep profiling of gut microbiota may reveal new pathways of how SpA and its related diseases are initiated and perpetuated.Objectives:To identify the presence of shared and specific gut microbiota signatures for SpA and its related diseases as a whole, as well as for the individual diseases, relative to healthy controls.Methods:Patients were recruited with a definite diagnosis of axial SpA, AAU or CD and were compared to controls (patients with back pain and previously ruled out SpA/CD/AAU diagnosis). All patients were naïve to or did not receive treatment with biological disease-modifying antirheumatic drugs for at least 3 months before enrollment of the study. Fecal samples were collected and microbiota composition was determined by 16S rRNA gene sequencing, followed by computational analysis referencing the SILVA138 database. Nonparametric Wilcoxon tests were used to calculate differential abundances between binary groups, and the Spearman correlation was used with continuous covariates. Nested linear models and likelihood ratio tests were used to assess confounding with respect to patient characteristics, HLA-B27 expression, inflammatory markers, and the presence of other immune-mediated diseases.Results:A total of 300 patients were recruited for the study: 111 axial SpA, 110 AAU, and 79 CD patients and were compared to 63 control individuals. Fifty-three of patients were males with an age (mean±SD) of 39.1±12.3 years. The prevalence of HLA-B27 was 63.0% by patients compared to 7.9% by control individuals. A multivariate PERMANOVA test between the groups was significant (p<0.001), revealing a difference in overall composition between the groups.At the phylum level, patients with axial SpA, AAU and CD contained higher abundances of Proteobacteria, Bacteroidetes and Fusobacteria, and lower abundances of Firmicutes and Actinobacteria compared to the control group. At the genus level, patients (with axial SpA, AAU and CD) displayed a shared gut microbiome signature differing from that of control individuals. Patients samples were strongly depleted in Blautia compared to the control group. Many of the differentially abundant taxa also correlated with increased inflammation as measured by C-reactive protein (CRP), including a depletion of Fusicatenibacter, Lachnospiraceae FCS020 and Roseburia, as well as an enrichment of Lactobacillus and Veillonella. By looking at each separate disease phenotype, CD patients differed significantly from the control individuals with respect to many genera. These primarily consisted of depletions in Clostridiales (Roseburia, Coprococcus, Ruminococcaceae), and enrichments of pathogen-harboring genera such as Escherichia-Shigella and Fusobacterium. Axial SpA patients were uniquely enriched in Collinsella and Holdemanella and depleted in Cupriavidus; the enrichment of Lactobacillus and depletion of Blautia observed in all patient groups was also associated to the presence of axial SpA, though confounded by CRP. There were strong taxa associations to the presence of HLA-B27, including enrichment of Asteroleplasma, Coprococcus, Faecalibacterium, Rominococcaceae, Lachnospiraceae NK4A136 and Rikenellaceae.Conclusion:There is a robust shared taxonomic signature among related immune-mediated diseases, in addition to individual disease phenotype signatures. Patients frequently exhibited a strong depletion in Blautia and an enrichment in Lactobacillus as well as pathogen-harboring genera such as Escherichia-Shigella and Fusobacterium.Figure 1.Taxa associations within and between the groups resulting from comparing each with the control group and accounting for disease concomitance and patient characteristics (FDR ≤ 0.05). AAU, anterior acute uveitis; CD, Crohn’s disease; SpA, spondyloarthritis.Disclosure of Interests:None declared
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Kaczmarczyk M, Löber U, Adamek K, Węgrzyn D, Skonieczna-Żydecka K, Malinowski D, Łoniewski I, Markó L, Ulas T, Forslund SK, Łoniewska B. The gut microbiota is associated with the small intestinal paracellular permeability and the development of the immune system in healthy children during the first two years of life. J Transl Med 2021; 19:177. [PMID: 33910577 PMCID: PMC8082808 DOI: 10.1186/s12967-021-02839-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [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: 01/23/2021] [Accepted: 04/16/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The intestinal barrier plays an important role in the defense against infections, and nutritional, endocrine, and immune functions. The gut microbiota playing an important role in development of the gastrointestinal tract can impact intestinal permeability and immunity during early life, but data concerning this problem are scarce. METHODS We analyzed the microbiota in fecal samples (101 samples in total) collected longitudinally over 24 months from 21 newborns to investigate whether the markers of small intestinal paracellular permeability (zonulin) and immune system development (calprotectin) are linked to the gut microbiota. The results were validated using data from an independent cohort that included the calprotectin and gut microbiota in children during the first year of life. RESULTS Zonulin levels tended to increase for up to 6 months after childbirth and stabilize thereafter remaining at a high level while calprotectin concentration was high after childbirth and began to decline from 6 months of life. The gut microbiota composition and the related metabolic potentials changed during the first 2 years of life and were correlated with zonulin and calprotectin levels. Faecal calprotectin correlated inversely with alpha diversity (Shannon index, r = - 0.30, FDR P (Q) = 0.039). It also correlated with seven taxa; i.a. negatively with Ruminococcaceae (r = - 0.34, Q = 0.046), and Clostridiales (r = - 0.34, Q = 0.048) and positively with Staphylococcus (r = 0.38, Q = 0.023) and Staphylococcaceae (r = 0.35, Q = 0.04), whereas zonulin correlated with 19 taxa; i.a. with Bacillales (r = - 0.52, Q = 0.0004), Clostridiales (r = 0.48, Q = 0.001) and the Ruminococcus (torques group) (r = 0.40, Q = 0.026). When time intervals were considered only changes in abundance of the Ruminococcus (torques group) were associated with changes in calprotectin (β = 2.94, SE = 0.8, Q = 0.015). The dynamics of stool calprotectin was negatively associated with changes in two MetaCyc pathways: pyruvate fermentation to butanoate (β = - 4.54, SE = 1.08, Q = 0.028) and Clostridium acetobutylicum fermentation (β = - 4.48, SE = 1.16, Q = 0.026). CONCLUSIONS The small intestinal paracellular permeability, immune system-related markers and gut microbiota change dynamically during the first 2 years of life. The Ruminococcus (torques group) seems to be especially involved in controlling paracellular permeability. Staphylococcus, Staphylococcaceae, Ruminococcaceae, and Clostridiales, may be potential biomarkers of the immune system. Despite observed correlations their clear causation and health consequences were not proven. Mechanistic studies are required.
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Affiliation(s)
- Mariusz Kaczmarczyk
- Department of Clinical Biochemistry, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
| | - Ulrike Löber
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Karolina Adamek
- Department of Neonatal Diseases, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
| | - Dagmara Węgrzyn
- Department of Neonatal Diseases, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
| | | | - Damian Malinowski
- Department of Pharmacology, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
| | - Igor Łoniewski
- Department of Biochemical Sciences, Pomeranian Medical University in Szczecin, 71-460, Szczecin, Poland.
- Department of Human Nutrition and Metabolomics, Broniewskiego 24, 71-460, Szczecin, Poland.
| | - Lajos Markó
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
| | - Thomas Ulas
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
- PRECISE Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, 53127, Bonn, Germany
| | - Sofia K Forslund
- Experimental and Clinical Research Center, A Cooperation of Charité - Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, 14195, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), 10178, Berlin, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), 53127, Bonn, Germany
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117, Heidelberg, Germany
| | - Beata Łoniewska
- Department of Neonatal Diseases, Pomeranian Medical University in Szczecin, 70-111, Szczecin, Poland
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20
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Kushugulova A, Löber U, Akpanova S, Rysbekov K, Kozhakhmetov S, Khassenbekova Z, Essex M, Nurgozhina A, Nurgaziyev M, Babenko D, Markó L, Forslund SK. Dynamic Changes in Microbiome Composition Following Mare's Milk Intake for Prevention of Collateral Antibiotic Effect. Front Cell Infect Microbiol 2021; 11:622735. [PMID: 33968795 PMCID: PMC8097163 DOI: 10.3389/fcimb.2021.622735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 04/01/2021] [Indexed: 01/22/2023] Open
Abstract
Introduction Probiotics and prebiotics are widely used for recovery of the human gut microbiome after antibiotic treatment. High antibiotic usage is especially common in children with developing microbiome. We hypothesized that dry Mare’s milk, which is rich in biologically active substances without containing live bacteria, could be used as a prebiotic in promoting microbial diversity following antibiotic treatment in children. The present pilot study aims to determine the impacts of dry Mare’s milk on the diversity of gut bacterial communities when administered during antibiotic treatment and throughout the subsequent recovery phase. Methods Six children aged 4 to 5 years and diagnosed with bilateral bronchopneumonia were prescribed cephalosporin antibiotics. During the 60 days of the study, three children consumed dry Mare’s milk whereas the other three did not. Fecal samples were collected daily during antibiotic therapy and every 5 days after antibiotic therapy. Total DNA was isolated and taxonomic composition of gut microbiota was analyzed by 16S rRNA amplicon sequencing. To assess the immune status of the gut, stool samples were analyzed by bead-based multiplex assays. Results Mare’s milk treatment seems to prevent the bloom of Mollicutes, while preventing the loss of Coriobacteriales. Immunological analysis of the stool reveals an effect of Mare’s milk on local immune parameters under the present conditions.
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Affiliation(s)
- Almagul Kushugulova
- Laboratory of Human Microbiome and Longevity, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.,Kazakhstan Society of Human Microbiome Researchers, Nur-Sultan, Kazakhstan.,SaumalBioTech, Nur-Sultan, Kazakhstan
| | - Ulrike Löber
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Saniya Akpanova
- Department of Pediatric Diseases with Courses in Cardio-Rheumatology and Gastroenterology, Nur-sultan (Astana) Medical University, Nur-Sultan, Kazakhstan
| | - Kairat Rysbekov
- Department of Pediatric Diseases with Courses in Cardio-Rheumatology and Gastroenterology, Nur-sultan (Astana) Medical University, Nur-Sultan, Kazakhstan
| | - Samat Kozhakhmetov
- Laboratory of Human Microbiome and Longevity, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.,Kazakhstan Society of Human Microbiome Researchers, Nur-Sultan, Kazakhstan.,SaumalBioTech, Nur-Sultan, Kazakhstan
| | | | - Morgan Essex
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Laboratory of Innate Immunity, Department of Microbiology, Infectious Diseases and Immunology, Charité-Universitätsmedizin, Berlin, Germany
| | - Ayaulym Nurgozhina
- Laboratory of Human Microbiome and Longevity, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.,Kazakhstan Society of Human Microbiome Researchers, Nur-Sultan, Kazakhstan
| | - Madiyar Nurgaziyev
- Laboratory of Human Microbiome and Longevity, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan.,Kazakhstan Society of Human Microbiome Researchers, Nur-Sultan, Kazakhstan
| | - Dmitriy Babenko
- Research Center Karaganda Medical University, Karagandy, Kazakhstan
| | - Lajos Markó
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Sofia K Forslund
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany.,Structural and Computational Biology Unit, The European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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21
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Willers M, Ulas T, Völlger L, Vogl T, Heinemann AS, Pirr S, Pagel J, Fehlhaber B, Halle O, Schöning J, Schreek S, Löber U, Essex M, Hombach P, Graspeuntner S, Basic M, Bleich A, Cloppenborg-Schmidt K, Künzel S, Jonigk D, Rupp J, Hansen G, Förster R, Baines JF, Härtel C, Schultze JL, Forslund SK, Roth J, Viemann D. S100A8 and S100A9 Are Important for Postnatal Development of Gut Microbiota and Immune System in Mice and Infants. Gastroenterology 2020; 159:2130-2145.e5. [PMID: 32805279 DOI: 10.1053/j.gastro.2020.08.019] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 07/14/2020] [Accepted: 08/09/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS After birth, the immune system matures via interactions with microbes in the gut. The S100 calcium binding proteins S100A8 and S100A9, and their extracellular complex form, S100A8-A9, are found in high amounts in human breast milk. We studied levels of S100A8-A9 in fecal samples (also called fecal calprotectin) from newborns and during infancy, and their effects on development of the intestinal microbiota and mucosal immune system. METHODS We collected stool samples (n = 517) from full-term (n = 72) and preterm infants (n = 49) at different timepoints over the first year of life (days 1, 3, 10, 30, 90, 180, and 360). We measured levels of S100A8-A9 by enzyme-linked immunosorbent assay and analyzed fecal microbiomes by 16S sRNA gene sequencing. We also obtained small and large intestine biopsies from 8 adults and 10 newborn infants without inflammatory bowel diseases (controls) and 8 infants with necrotizing enterocolitis and measured levels of S100A8 by immunofluorescence microscopy. Children were followed for 2.5 years and anthropometric data and medical information on infections were collected. We performed studies with newborn C57BL/6J wild-type and S100a9-/- mice (which also lack S100A8). Some mice were fed or given intraperitoneal injections of S100A8 or subcutaneous injections of Staphylococcus aureus. Blood and intestine, mesenterial and celiac lymph nodes were collected; cells and cytokines were measured by flow cytometry and studied in cell culture assays. Colon contents from mice were analyzed by culture-based microbiology assays. RESULTS Loss of S100A8 and S100A9 in mice altered the phenotypes of colonic lamina propria macrophages, compared with wild-type mice. Intestinal tissues from neonatal S100-knockout mice had reduced levels of CX3CR1 protein, and Il10 and Tgfb1 mRNAs, compared with wild-type mice, and fewer T-regulatory cells. S100-knockout mice weighed 21% more than wild-type mice at age 8 weeks and a higher proportion developed fatal sepsis during the neonatal period. S100-knockout mice had alterations in their fecal microbiomes, with higher abundance of Enterobacteriaceae. Feeding mice S100 at birth prevented the expansion of Enterobacteriaceae, increased numbers of T-regulatory cells and levels of CX3CR1 protein and Il10 mRNA in intestine tissues, and reduced body weight and death from neonatal sepsis. Fecal samples from term infants, but not preterm infants, had significantly higher levels of S100A8-A9 during the first 3 months of life than fecal samples from adults; levels decreased to adult levels after weaning. Fecal samples from infants born by cesarean delivery had lower levels of S100A8-A9 than from infants born by vaginal delivery. S100 proteins were expressed by lamina propria macrophages in intestinal tissues from infants, at higher levels than in intestinal tissues from adults. High fecal levels of S100 proteins, from 30 days to 1 year of age, were associated with higher abundance of Actinobacteria and Bifidobacteriaceae, and lower abundance of Gammaproteobacteria-particularly opportunistic Enterobacteriaceae. A low level of S100 proteins in infants' fecal samples associated with development of sepsis and obesity by age 2 years. CONCLUSION S100A8 and S100A9 regulate development of the intestinal microbiota and immune system in neonates. Nutritional supplementation with these proteins might aide in development of preterm infants and prevent microbiota-associated disorders in later years.
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Affiliation(s)
- Maike Willers
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Thomas Ulas
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, Bonn, Germany; PRECISE, Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Lena Völlger
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Thomas Vogl
- Institute of Immunology, University of Münster, Münster, Germany
| | - Anna S Heinemann
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Sabine Pirr
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Julia Pagel
- Department of Pediatrics, University of Lübeck, Lübeck, Germany
| | - Beate Fehlhaber
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Olga Halle
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Jennifer Schöning
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Sabine Schreek
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Morgan Essex
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Hombach
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, Bonn, Germany
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Marijana Basic
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Hannover, Germany
| | - Andre Bleich
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Hannover, Germany
| | | | - Sven Künzel
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Danny Jonigk
- Department of Pathology, Hannover Medical School, Hannover, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, Lübeck, Germany
| | - Gesine Hansen
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Reinhold Förster
- Institute of Immunology, Hannover Medical School, Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - John F Baines
- Institute of Experimental Medicine, University of Kiel, Kiel, Germany; Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Christoph Härtel
- PRIMAL Consortium, Hannover Medical School, Hannover, Germany; Department of Pediatrics, University Hospital of Würzburg, Würzburg, Germany
| | - Joachim L Schultze
- Genomics and Immunoregulation, LIMES-Institute, University of Bonn, Bonn, Germany; PRECISE, Platform for Single Cell Genomics and Epigenomics at the German Center for Neurodegenerative Diseases and the University of Bonn, Bonn, Germany
| | - Sofia K Forslund
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany; European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Johannes Roth
- Institute of Immunology, University of Münster, Münster, Germany
| | - Dorothee Viemann
- Department of Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany; PRIMAL Consortium, Hannover Medical School, Hannover, Germany.
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22
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Alquezar‐Planas DE, Löber U, Cui P, Quedenau C, Chen W, Greenwood AD. DNA sonication inverse PCR for genome scale analysis of uncharacterized flanking sequences. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- David E. Alquezar‐Planas
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Australian Museum Research InstituteAustralian Museum Sydney NSW Australia
| | - Ulrike Löber
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- The Berlin Center for Genomics in Biodiversity Research Berlin Germany
- Experimental and Clinical Research Center A Cooperation of Charité – Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine Berlin Germany
| | - Pin Cui
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Claudia Quedenau
- Genomics Max Delbrück Center for Molecular Medicine Berlin Germany
| | - Wei Chen
- Berlin Institute for Medical Systems BiologyMax‐Delbrück Center for Molecular Medicine Berlin Germany
| | - Alex D. Greenwood
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Department of Veterinary Medicine Freie Universität Berlin Berlin Germany
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23
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Bartolomaeus H, Avery EG, Löber U, Bartolomaeus TU, Chen CY, Tsvetkov D, Kraeker K, Geisberger SY, Markó L, Balogh A, Forslund SK, Mueller DN, Wilck N. Abstract P027: Hypertensive Cardiorenal Damage Is Aggravated In Axenic Mice. Hypertension 2020. [DOI: 10.1161/hyp.76.suppl_1.p027] [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] [Indexed: 11/16/2022]
Abstract
Introduction:
The gut microbiota is suspected to play a role in hypertension and hypertensive end organ damage. In the present study, we used germ-free mice to demonstrate that microbial colonization modulates the response to a hypertensive stimulus.
Methods:
Four-week-old male germ-free C57BL6/J littermates were randomized to remain germ-free (GF) or to receive microbiota transfer from SPF donor mice to achieve full colonization status (COL). At 12 weeks, Angiotensin (Ang) II was infused s.c. for 14 days (1.44mg/kg/d, osmotic minipumps) and 1% NaCl added to the drinking water; sham-treated mice served as control. After 14 days of AngII we assessed inflammation and organ damage.
Results:
Fecal bacterial load in COL mice was similar to SPF donor mice (qPCR). Shotgun metagenomic sequencing of fecal samples revealed hypertension-induced alterations in microbiome composition confirming previous reports. Serum metabolome analysis (
Biocrates MxP Quant 500)
confirmed the absence of microbiota-dependent metabolites in GF. Interestingly, microbiota-dependent metabolites relevant for cardiovascular risk (TMAO, indoxyl sulfate) were elevated in hypertensive COL mice compared to sham-treated. Hypertensive kidney damage was aggravated in GF mice. However, marker genes for tubular damage (
Lcn2
), inflammation (
Ccl2
), and fibrosis (
Col1a3
) showed a stronger increase in GF mice (fold changes [fc] COL vs. GF: 7.5 vs 11.0, 1.2 vs 3.3, 1.3 vs 2.2, respectively). Albuminuria (fc 2 vs 25) and histology for kidney fibrosis (fc 1.1 vs 1.4) confirmed the aggravated kidney damage in GF mice. Similarly, we observed an aggravated cardiac damage in GF mice. Flow cytometry of splenic lymphocytes showed that the adaptive immune response to AngII + 1% NaCl, as evidenced by Th17 (fc 1.4 vs 2) and CD8+ central memory cells, was intensified in GF mice.
In vitro
, naïve T cells isolated from GF mice more readily polarized into Th17 (26 ± 5%) compared to T cells from SPF mice (19 ± 1%).
Conclusion:
The bacterial colonization status has potent effects on the phenotypic response to a hypertensive stimulus, evident to varying degrees in hearts and kidneys. The inflammatory response and the end organ damage in GF compared to COL mice demonstrates the importance of the gut microbiota in hypertension.
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Affiliation(s)
| | - Ellen G Avery
- Max Delbruck Cntr for Molecular Medicine, Berlin, Germany
| | - Ulrike Löber
- Max Delbruck Cntr for Molecular Medicine, Berlin, Germany
| | | | - Chia-Yu Chen
- Charite-Universitatsmedizin Berlin, Berlin, Germany
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24
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Bartolomaeus TUP, Birkner T, Bartolomaeus H, Löber U, Avery EG, Mähler A, Weber D, Kochlik B, Balogh A, Wilck N, Boschmann M, Müller DN, Markó L, Forslund SK. Quantifying technical confounders in microbiome studies. Cardiovasc Res 2020; 117:863-875. [PMID: 32374853 DOI: 10.1093/cvr/cvaa128] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 04/08/2020] [Accepted: 04/28/2020] [Indexed: 12/12/2022] Open
Abstract
AIMS Recent technical developments have allowed the study of the human microbiome to accelerate at an unprecedented pace. Methodological differences may have considerable impact on the results obtained. Thus, we investigated how different storage, isolation, and DNA extraction methods can influence the characterization of the intestinal microbiome, compared to the impact of true biological signals such as intraindividual variability, nutrition, health, and demographics. METHODS AND RESULTS An observative cohort study in 27 healthy subjects was performed. Participants were instructed to collect stool samples twice spaced by a week, using six different methods (naive and Zymo DNA/RNA Shield on dry ice, OMNIgene GUT, RNALater, 95% ethanol, Zymo DNA/RNA Shield at room temperature). DNA extraction from all samples was performed comparatively using QIAamp Power Fecal and ZymoBIOMICS DNA Kits. 16S rRNA sequencing of the gut microbiota as well as qPCRs were performed on the isolated DNA. Metrics included alpha diversity as well as multivariate and univariate comparisons of samples, controlling for covariate patterns computationally. Interindividual differences explained 7.4% of overall microbiome variability, whereas the choice of DNA extraction method explained a further 5.7%. At phylum level, the tested kits differed in their recovery of Gram-positive bacteria, which is reflected in a significantly skewed enterotype distribution. CONCLUSION DNA extraction methods had the highest impact on observed microbiome variability, and were comparable to interindividual differences, thus may spuriously mimic the microbiome signatures of various health and nutrition factors. Conversely, collection methods had a relatively small influence on microbiome composition. The present study provides necessary insight into the technical variables which can lead to divergent results from seemingly similar study designs. We anticipate that these results will contribute to future efforts towards standardization of microbiome quantification procedures in clinical research.
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Affiliation(s)
- Theda U P Bartolomaeus
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,DZHK (German Center for Cardiovascular Research), partner site Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany
| | - Till Birkner
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Hendrik Bartolomaeus
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,DZHK (German Center for Cardiovascular Research), partner site Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany.,Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178 Berlin, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,DZHK (German Center for Cardiovascular Research), partner site Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany
| | - Ellen G Avery
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,DZHK (German Center for Cardiovascular Research), partner site Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany.,Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178 Berlin, Germany.,Freie Universität Berlin, Kaiserswerther Str. 16-18, 14195 Berlin, Germany
| | - Anja Mähler
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany.,DZHK (German Center for Cardiovascular Research), partner site Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany.,Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178 Berlin, Germany
| | - Daniela Weber
- Department of Molecular Toxicology, German Institute of Human Nutrition (DIfE), Potsdam Rehbrücke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany.,NurtiAct-Competence Cluster Nutrition Research Berlin-Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Bastian Kochlik
- Department of Molecular Toxicology, German Institute of Human Nutrition (DIfE), Potsdam Rehbrücke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany.,NurtiAct-Competence Cluster Nutrition Research Berlin-Potsdam, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - András Balogh
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,DZHK (German Center for Cardiovascular Research), partner site Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany.,Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178 Berlin, Germany
| | - Nicola Wilck
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,DZHK (German Center for Cardiovascular Research), partner site Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany.,Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178 Berlin, Germany.,Medizinische Klinik mit Schwerpunkt Nephrologie und Internistische Intensivmedizin, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Michael Boschmann
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178 Berlin, Germany
| | - Dominik N Müller
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,DZHK (German Center for Cardiovascular Research), partner site Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany.,Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178 Berlin, Germany
| | - Lajos Markó
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,DZHK (German Center for Cardiovascular Research), partner site Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany.,Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178 Berlin, Germany
| | - Sofia K Forslund
- Experimental and Clinical Research Center, a Cooperation of Charité-Universitätsmedizin Berlin, Max Delbrück Center for Molecular Medicine, Lindenberger Weg 80, 13125 Berlin, Germany.,Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Helmholtz Association, Robert-Rössle-Straße 10, 13125 Berlin, Germany.,DZHK (German Center for Cardiovascular Research), partner site Berlin, Hessische Strasse 3-4, 10115 Berlin, Germany.,Berlin Institute of Health (BIH), Anna-Louisa-Karsch-Straße 2, 10178 Berlin, Germany.,European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
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25
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Seeber PA, McEwen GK, Löber U, Förster DW, East ML, Melzheimer J, Greenwood AD. Terrestrial mammal surveillance using hybridization capture of environmental DNA from African waterholes. Mol Ecol Resour 2019; 19:1486-1496. [PMID: 31349392 DOI: 10.1111/1755-0998.13069] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 03/11/2019] [Revised: 07/15/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022]
Abstract
Determining species distributions can be extremely challenging but is crucial to ecological and conservation research. Environmental DNA (eDNA) approaches have shown particular promise in aquatic systems for several vertebrate and invertebrate species. For terrestrial animals, however, eDNA-based surveys are considerably more difficult due to the lack of or difficulty in obtaining appropriate sampling substrate. In water-limited ecosystem where terrestrial mammals are often forced to congregate at waterholes, water and sediment from shared water sources may be a suitable substrate for noninvasive eDNA approaches. We characterized mitochondrial DNA sequences from a broad range of terrestrial mammal species in two different African ecosystems (in Namibia and Tanzania) using eDNA isolated from native water, sediment and water filtered through glass fibre filters. A hybridization capture enrichment with RNA probes targeting the mitochondrial genomes of 38 mammal species representing the genera/families expected at the respective ecosystems was employed, and 16 species were identified, with a maximum mitogenome coverage of 99.8%. Conventional genus-specific PCRs were tested on environmental samples for two genera producing fewer positive results than hybridization capture enrichment. An experiment with mock samples using DNA from non-African mammals showed that baits covering 30% of nontarget mitogenomes produced 91% mitogenome coverage after capture. In the mock samples, over-representation of DNA of one species still allowed for the detection of DNA of other species that was at a 100-fold lower concentration. Hybridization capture enrichment of eDNA is therefore an effective method for monitoring terrestrial mammal species from shared water sources.
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Affiliation(s)
- Peter Andreas Seeber
- Department of Wildlife Diseases, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Gayle K McEwen
- Department of Wildlife Diseases, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Ulrike Löber
- Department of Wildlife Diseases, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany.,Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
| | - Daniel W Förster
- Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Marion Linda East
- Department of Ecological Dynamics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Jörg Melzheimer
- Department of Evolutionary Ecology, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany.,Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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26
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Avery EG, Balogh A, Bartolomaeus H, Löber U, Steckhan N, Markó L, Wilck N, Hamad I, Šušnjar U, Mähler A, Hohmann C, Lesker TR, Strowig T, Dechend R, Bzdok D, Kleinewietfeld M, Michalsen A, Müller DN, Forslund SK. Abstract P2072: Integrative Network Analysis Of Microbiome-Immune Axis In Metabolic Syndrome Patients During A Fasting Intervention. Hypertension 2019. [DOI: 10.1161/hyp.74.suppl_1.p2072] [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] [Indexed: 11/16/2022]
Abstract
Fasting can prolong survival and reduce disease burden in rodent models, and possibly in humans. The relationship between diet, gut microbiota, immune system and host (patho)physiology has only recently been explored, and information is lacking on how periodic fasting affects the gut microbiome in patients with metabolic syndrome (MetS). We show a 5-day fast (FAST) in humans, followed by a modified DASH diet is more effective than DASH alone (DASH) at reducing systolic blood pressure (SBP change measured by ABPM, 95% CI; FAST: [-7.053,-1.142], DASH: [-5.880,1.477]), need for antihypertensive medication (FAST: n=15 of n=35, DASH: n=6 of n=36 patients), and body-mass index at three months post intervention. Fasting altered the gut microbiome, impacting bacterial taxa and functional gene modules associated with the production of short-chain fatty acids (e.g.
Faecalibacterium prausnitzii
,
Eubacterium rectale, Coprococcus comes
), previously linked to vascular health and immunity. Immunophenotyping and cross-system analyses revealed that SBP changes correlated with circulating Il-2
+
TNFα
+
mucosa-associated invariant T (MAIT) cells (FDR-corr P(q) =0.044, Spearman’s rho=0.44), Il-17
-
IFNγ
+
MAITs (FDR-corr P(q) =0.022, Spearman’s rho=0.49), and effector CD4
+
T cells (FDR-corr P(q)=0.047, Spearman’s rho=0.43). By stratifying the fasting group into BP responders and non-responders, we identified a set of 76 microbial and 99 immune responder-specific features. Machine learning algorithms could predict long-term SBP responsiveness from baseline immunome data, identifying changes in effector CD8
+
T cells, Th17 cells and Tregs as discriminators (Single-subject prediction: 71%). This is the first high-resolution multi-omics characterization of fasting in MetS. Fasting induced long-term reduction in body weight and SBP, accompanied by changes in microbiome and immune homeostasis. Our data implicate fasting as a promising non-pharmacological intervention in MetS.
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Affiliation(s)
- Ellen G Avery
- Experimental and Clinical Rsch Cntr (Max Delbrück Cntr for Molecular Medicine & Charité Universitätsmedizin), Berlin, Germany
| | - András Balogh
- Experimental and Clinical Rsch Cntr (Max Delbrück Cntr for Molecular Medicine & Charité Universitätsmedizin), Berlin, Germany
| | - Hendrik Bartolomaeus
- Experimental and Clinical Rsch Cntr (Max Delbrück Cntr for Molecular Medicine & Charité Universitätsmedizin), Berlin, Germany
| | - Ulrike Löber
- Experimental and Clinical Rsch Cntr (Max Delbrück Cntr for Molecular Medicine & Charité Universitätsmedizin), Berlin, Germany
| | - Nico Steckhan
- Charité Universitätsmedizin & Immanuel Krankenhaus, Berlin, Germany
| | - Lajos Markó
- Experimental and Clinical Rsch Cntr (Max Delbrück Cntr for Molecular Medicine & Charité Universitätsmedizin), Berlin, Germany
| | - Nicola Wilck
- Experimental and Clinical Rsch Cntr (Max Delbrück Cntr for Molecular Medicine & Charité Universitätsmedizin), Berlin, Germany
| | - Ibrahim Hamad
- VIB Cntr for Inflammation Rsch (IRC), UHasselt, Hasselt, Belgium
| | - Urša Šušnjar
- Experimental and Clinical Rsch Cntr (Max Delbrück Cntr for Molecular Medicine & Charité Universitätsmedizin), Berlin, Germany
| | - Anja Mähler
- Experimental and Clinical Rsch Cntr (Max Delbrück Cntr for Molecular Medicine & Charité Universitätsmedizin), Berlin, Germany
| | | | - Till R Lesker
- Helmholtz Cntr for Infection Rsch, Braunschweig, Germany
| | - Till Strowig
- Helmholtz Cntr for Infection Rsch, Braunschweig, Germany
| | - Ralf Dechend
- Experimental and Clinical Rsch Cntr (Max Delbrück Cntr for Molecular Medicine & Charité Universitätsmedizin), Berlin, Germany
| | - Danilo Bzdok
- Dept of Psychiatry, Psychotherapy, and Psychosomatics, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen Univ, Aachen, Germany
| | | | | | - Dominik N Müller
- Experimental and Clinical Rsch Cntr (Max Delbrück Cntr for Molecular Medicine & Charité Universitätsmedizin), Berlin, Germany
| | - Sofia K Forslund
- Experimental and Clinical Rsch Cntr (Max Delbrück Cntr for Molecular Medicine & Charité Universitätsmedizin), Berlin, Germany
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27
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Zepeda Mendoza ML, Xiong Z, Escalera-Zamudio M, Runge AK, Thézé J, Streicker D, Frank HK, Loza-Rubio E, Liu S, Ryder OA, Samaniego Castruita JA, Katzourakis A, Pacheco G, Taboada B, Löber U, Pybus OG, Li Y, Rojas-Anaya E, Bohmann K, Carmona Baez A, Arias CF, Liu S, Greenwood AD, Bertelsen MF, White NE, Bunce M, Zhang G, Sicheritz-Pontén T, Gilbert MPT. Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat. Nat Ecol Evol 2018; 2:659-668. [PMID: 29459707 PMCID: PMC5868727 DOI: 10.1038/s41559-018-0476-8] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [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: 08/23/2016] [Accepted: 01/11/2018] [Indexed: 11/21/2022]
Abstract
Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat (Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary adaptation. Specifically, we assembled its high-quality reference genome (scaffold N50 = 26.9 Mb, contig N50 = 36.6 kb) and gut metagenome, and compared them against those of insectivorous, frugivorous and carnivorous bats. Our analyses showed a particular common vampire bat genomic landscape regarding integrated viral elements, a dietary and phylogenetic influence on gut microbiome taxonomic and functional profiles, and that both genetic elements harbour key traits related to the nutritional (for example, vitamin and lipid shortage) and non-nutritional (for example, nitrogen waste and osmotic homeostasis) challenges of sanguivory. These findings highlight the value of a holistic study of both the host and its microbiota when attempting to decipher adaptations underlying radical dietary lifestyles.
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Affiliation(s)
- M Lisandra Zepeda Mendoza
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
| | - Zijun Xiong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Marina Escalera-Zamudio
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | - Anne Kathrine Runge
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Julien Thézé
- Department of Zoology, University of Oxford, Oxford, UK
| | - Daniel Streicker
- Institute of Biodiversity, Animal Health and Comparative Medicine & MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Hannah K Frank
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Elizabeth Loza-Rubio
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal-INIFAP, Ciudad de México, Mexico
| | - Shengmao Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | | | | | - George Pacheco
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Ulrike Löber
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
| | | | - Yang Li
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Edith Rojas-Anaya
- Centro Nacional de Investigación Disciplinaria en Microbiología Animal-INIFAP, Ciudad de México, Mexico
| | - Kristine Bohmann
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Aldo Carmona Baez
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Undergraduate Program for Genomic Sciences, Center for Genomic Sciences, National Autonomous University of Mexico, Cuernavaca, Mexico
| | - Carlos F Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Shiping Liu
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Berlin, Germany
- Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Mads F Bertelsen
- Center for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark
| | - Nicole E White
- Australian Wildlife Forensic Services, Department of Environment and Agriculture, Curtin University, Perth, Australia
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Australia
| | - Michael Bunce
- Australian Wildlife Forensic Services, Department of Environment and Agriculture, Curtin University, Perth, Australia
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Australia
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Sicheritz-Pontén
- Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - M P Thomas Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
- Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Australia.
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway.
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28
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Escalera-Zamudio M, Taboada B, Rojas-Anaya E, Löber U, Loza-Rubio E, Arias CF, Greenwood AD. Viral Communities Among Sympatric Vampire Bats and Cattle. Ecohealth 2018; 15:132-142. [PMID: 29164470 DOI: 10.1007/s10393-017-1297-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 10/30/2017] [Accepted: 11/03/2017] [Indexed: 06/07/2023]
Abstract
Vampire bats are the only mammals known to feed exclusively on blood from other animals, often from domestic cattle. We tested the hypothesis that the adaptation of vampire bats to hematophagy would have resulted in shared viral communities among vampire bats and cattle, as a direct result of historic spillover events occurring due to hematophagy. We analyzed the presence of different viruses in sample populations of sympatric bat and prey populations and searched for shared viruses between taxa. A limited number of DNA viral groups were detected within each species. However, there was no evidence for a shared viral community among the vampire bat and cattle populations tested.
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Affiliation(s)
- Marina Escalera-Zamudio
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.
- Peter Medawar Building for Pathogen Research, Department of Zoology, University of Oxford, Parks Rd, Oxford, OX1 3SY, UK.
| | - Blanca Taboada
- Departamento de Genetica del Desarrollo y Fisiología Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, Mexico
| | - Edith Rojas-Anaya
- Centro Nacional de Investigacion Disciplinaria en Microbiologia Animal CENID-INIFAP, Mexico City, Mexico
| | - Ulrike Löber
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - Elizabeth Loza-Rubio
- Centro Nacional de Investigacion Disciplinaria en Microbiologia Animal CENID-INIFAP, Mexico City, Mexico
| | - Carlos F Arias
- Departamento de Genetica del Desarrollo y Fisiología Molecular, Instituto de Biotecnologia, Universidad Nacional Autonoma de México, Cuernavaca, Morelos, Mexico
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315, Berlin, Germany.
- Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.
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29
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Lah L, Löber U, Hsiang T, Hartmann S. A genomic comparison of putative pathogenicity-related gene families in five members of the Ophiostomatales with different lifestyles. Fungal Biol 2016; 121:234-252. [PMID: 28215351 DOI: 10.1016/j.funbio.2016.12.002] [Citation(s) in RCA: 8] [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] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Revised: 12/10/2016] [Accepted: 12/14/2016] [Indexed: 12/20/2022]
Abstract
Ophiostomatoid fungi are vectored by their bark-beetle associates and colonize different host tree species. To survive and proliferate in the host, they have evolved mechanisms for detoxification and elimination of host defence compounds, efficient nutrient sequestration, and, in pathogenic species, virulence towards plants. Here, we assembled a draft genome of the spruce pathogen Ophiostoma bicolor. For our comparative and phylogenetic analyses, we mined the genomes of closely related species (Ophiostoma piceae, Ophiostoma ulmi, Ophiostoma novo-ulmi, and Grosmannia clavigera). Our aim was to acquire a genomic and evolutionary perspective of gene families important in host colonization. Genome comparisons showed that both the nuclear and mitochondrial genomes in our assembly were largely complete. Our O. bicolor 25.3 Mbp draft genome had 10 018 predicted genes, 6041 proteins with gene ontology (GO) annotation, 269 carbohydrate-active enzymes (CAZymes), 559 peptidases and inhibitors, and 1373 genes likely involved in pathogen-host interactions. Phylogenetic analyses of selected protein families revealed core sets of cytochrome P450 genes, ABC transporters and backbone genes involved in secondary metabolite (SM) biosynthesis (polyketide synthases (PKS) and non-ribosomal synthases), and species-specific gene losses and duplications. Phylogenetic analyses of protein families of interest provided insight into evolutionary adaptations to host biochemistry in ophiostomatoid fungi.
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Affiliation(s)
- Ljerka Lah
- Evolutionary Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476 Potsdam, Germany.
| | - Ulrike Löber
- Evolutionary Biology, University of Potsdam, Karl-Liebknecht Str. 24-25, 14476 Potsdam, Germany; Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany; Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, N1G 2W1 Guelph, ON, Canada
| | - Stefanie Hartmann
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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30
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Cui P, Löber U, Alquezar-Planas DE, Ishida Y, Courtiol A, Timms P, Johnson RN, Lenz D, Helgen KM, Roca AL, Hartman S, Greenwood AD. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome. PeerJ 2016; 4:e1847. [PMID: 27069793 PMCID: PMC4824918 DOI: 10.7717/peerj.1847] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 01/28/2016] [Accepted: 03/04/2016] [Indexed: 11/20/2022] Open
Abstract
Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV) is currently invading the germline of the koala (Phascolarctos cinereus) and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS) and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW) koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.
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Affiliation(s)
- Pin Cui
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Ulrike Löber
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.,Institute of Biochemistry & Biology, University of Potsdam, Potsdam, Germany
| | - David E Alquezar-Planas
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Alexandre Courtiol
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Peter Timms
- University of the Sunshine Coast, Sippy Downs Queensland, Australia
| | - Rebecca N Johnson
- Australian Centre for Wildlife Genomics, Australian Museum, Sydney, Australia
| | - Dorina Lenz
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Kristofer M Helgen
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Alfred L Roca
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Stefanie Hartman
- Institute of Biochemistry & Biology, University of Potsdam, Potsdam, Germany
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
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