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Essex M, Millet Pascual-Leone B, Löber U, Kuhring M, Zhang B, Brüning U, Fritsche-Guenther R, Krzanowski M, Fiocca Vernengo F, Brumhard S, Röwekamp I, Anna Bielecka A, Lesker TR, Wyler E, Landthaler M, Mantei A, Meisel C, Caesar S, Thibeault C, Corman VM, Marko L, Suttorp N, Strowig T, Kurth F, Sander LE, Li Y, Kirwan JA, Forslund SK, Opitz B. Gut microbiota dysbiosis is associated with altered tryptophan metabolism and dysregulated inflammatory response in COVID-19. NPJ Biofilms Microbiomes 2024; 10:66. [PMID: 39085233 PMCID: PMC11291933 DOI: 10.1038/s41522-024-00538-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 07/22/2024] [Indexed: 08/02/2024] Open
Abstract
The clinical course of COVID-19 is variable and often unpredictable. To test the hypothesis that disease progression and inflammatory responses associate with alterations in the microbiome and metabolome, we analyzed metagenome, metabolome, cytokine, and transcriptome profiles of repeated samples from hospitalized COVID-19 patients and uninfected controls, and leveraged clinical information and post-hoc confounder analysis. Severe COVID-19 was associated with a depletion of beneficial intestinal microbes, whereas oropharyngeal microbiota disturbance was mainly linked to antibiotic use. COVID-19 severity was also associated with enhanced plasma concentrations of kynurenine and reduced levels of several other tryptophan metabolites, lysophosphatidylcholines, and secondary bile acids. Moreover, reduced concentrations of various tryptophan metabolites were associated with depletion of Faecalibacterium, and tryptophan decrease and kynurenine increase were linked to enhanced production of inflammatory cytokines. Collectively, our study identifies correlated microbiome and metabolome alterations as a potential contributor to inflammatory dysregulation in severe COVID-19.
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Affiliation(s)
- Morgan Essex
- Experimental and Clinical Research Center (ECRC), a cooperation of the Max Delbrück Center and Charité-Universitätsmedizin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin Berlin, a 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, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ulrike Löber
- Experimental and Clinical Research Center (ECRC), a cooperation of the Max Delbrück Center and Charité-Universitätsmedizin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mathias Kuhring
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, BIH Metabolomics Platform, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, Core Unit Bioinformatics, Berlin, Germany
| | - Bowen Zhang
- Department of Computational Biology for Individualized Infection Medicine, Center for Individualized Infection Medicine (CiiM), a joint venture between the Helmholtz-Center for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, joint ventures between the Helmholtz Center for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ulrike Brüning
- Berlin Institute of Health (BIH) at Charité, BIH Metabolomics Platform, Berlin, Germany
| | | | - Marta Krzanowski
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a 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, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sophia Brumhard
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a 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, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Agata Anna Bielecka
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Till Robin Lesker
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany
| | - Emanuel Wyler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Christian Meisel
- Labor Berlin-Charité Vivantes GmbH, Berlin, Germany
- Institute of Medical Immunology, Charité-Universitätsmedizin Berlin, a 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, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Charlotte Thibeault
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Victor M Corman
- Labor Berlin-Charité Vivantes GmbH, Berlin, Germany
- Institute of Virology, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Infection Research (DZIF), Berlin, Germany
| | - Lajos Marko
- Experimental and Clinical Research Center (ECRC), a cooperation of the Max Delbrück Center and Charité-Universitätsmedizin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany
| | - Norbert Suttorp
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Berlin, Germany
| | - Till Strowig
- Department of Computational Biology for Individualized Infection Medicine, Center for Individualized Infection Medicine (CiiM), a joint venture between the Helmholtz-Center for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research (HZI), Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Florian Kurth
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Leif E Sander
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Berlin, Germany
| | - Yang Li
- Department of Computational Biology for Individualized Infection Medicine, Center for Individualized Infection Medicine (CiiM), a joint venture between the Helmholtz-Center for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
- TWINCORE, joint ventures between the Helmholtz Center for Infection Research (HZI) and the Hannover Medical School (MHH), Hannover, Germany
| | - Jennifer A Kirwan
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, BIH Metabolomics Platform, Berlin, Germany
- University of Nottingham School of Veterinary Medicine and Science, Loughborough, UK
| | - Sofia K Forslund
- Experimental and Clinical Research Center (ECRC), a cooperation of the Max Delbrück Center and Charité-Universitätsmedizin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Center for Cardiovascular Research (DZHK), partner site Berlin, Berlin, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Bastian Opitz
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité-Universitätsmedizin Berlin, a corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- Labor Berlin-Charité Vivantes GmbH, Berlin, Germany.
- German Center for Lung Research (DZL), Berlin, Germany.
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Tejeda-Garibay S, Zhao L, Hum NR, Pimentel M, Diep AL, Amiri B, Sindi SS, Weilhammer DR, Loots GG, Hoyer KK. Host tracheal and intestinal microbiomes inhibit Coccidioides growth in vitro. Microbiol Spectr 2024; 12:e0297823. [PMID: 38832766 PMCID: PMC11218535 DOI: 10.1128/spectrum.02978-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/19/2024] [Indexed: 06/05/2024] Open
Abstract
Coccidioidomycosis, also known as Valley fever, is a disease caused by the fungal pathogen Coccidioides. Unfortunately, patients are often misdiagnosed with bacterial pneumonia, leading to inappropriate antibiotic treatment. The soil Bacillus subtilis-like species exhibits antagonistic properties against Coccidioides in vitro; however, the antagonistic capabilities of host microbiota against Coccidioides are unexplored. We sought to examine the potential of the tracheal and intestinal microbiomes to inhibit the growth of Coccidioides in vitro. We hypothesized that an uninterrupted lawn of microbiota obtained from antibiotic-free mice would inhibit the growth of Coccidioides, while partial in vitro depletion through antibiotic disk diffusion assays would allow a niche for fungal growth. We observed that the microbiota grown on 2×GYE (GYE) and Columbia colistin and nalidixic acid with 5% sheep's blood agar inhibited the growth of Coccidioides, but microbiota grown on chocolate agar did not. Partial depletion of the microbiota through antibiotic disk diffusion revealed diminished inhibition and comparable growth of Coccidioides to controls. To characterize the bacteria grown and identify potential candidates contributing to the inhibition of Coccidioides, 16S rRNA sequencing was performed on tracheal and intestinal agar cultures and murine lung extracts. We found that the host bacteria likely responsible for this inhibition primarily included Lactobacillus and Staphylococcus. The results of this study demonstrate the potential of the host microbiota to inhibit the growth of Coccidioides in vitro and suggest that an altered microbiome through antibiotic treatment could negatively impact effective fungal clearance and allow a niche for fungal growth in vivo. IMPORTANCE Coccidioidomycosis is caused by a fungal pathogen that invades the host lungs, causing respiratory distress. In 2019, 20,003 cases of Valley fever were reported to the CDC. However, this number likely vastly underrepresents the true number of Valley fever cases, as many go undetected due to poor testing strategies and a lack of diagnostic models. Valley fever is also often misdiagnosed as bacterial pneumonia, resulting in 60%-80% of patients being treated with antibiotics prior to an accurate diagnosis. Misdiagnosis contributes to a growing problem of antibiotic resistance and antibiotic-induced microbiome dysbiosis; the implications for disease outcomes are currently unknown. About 5%-10% of symptomatic Valley fever patients develop chronic pulmonary disease. Valley fever causes a significant financial burden and a reduced quality of life. Little is known regarding what factors contribute to the development of chronic infections and treatments for the disease are limited.
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Affiliation(s)
- Susana Tejeda-Garibay
- Quantitative and Systems Biology, Graduate Program, University of California, Merced, Merced, California, USA
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
| | - Lihong Zhao
- Department of Applied Mathematics, University of California, Merced, Merced, California, USA
- Health Sciences Research Institute, University of California, Merced, Merced, California, USA
| | - Nicholas R. Hum
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
| | - Maria Pimentel
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, Merced, California, USA
| | - Anh L. Diep
- Quantitative and Systems Biology, Graduate Program, University of California, Merced, Merced, California, USA
| | - Beheshta Amiri
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
| | - Suzanne S. Sindi
- Department of Applied Mathematics, University of California, Merced, Merced, California, USA
- Health Sciences Research Institute, University of California, Merced, Merced, California, USA
| | - Dina R. Weilhammer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
| | - Gabriela G. Loots
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
- />Department of Orthopaedic Surgery, Lawrence J. Ellison Musculoskeletal Research Center, University of California Davis Health, Sacramento, California, USA
| | - Katrina K. Hoyer
- Quantitative and Systems Biology, Graduate Program, University of California, Merced, Merced, California, USA
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore, California, USA
- Health Sciences Research Institute, University of California, Merced, Merced, California, USA
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, Merced, California, USA
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3
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Tsuruga T, Fujimoto H, Yasuma T, D'Alessandro-Gabazza CN, Toda M, Ito T, Tomaru A, Saiki H, Okano T, Alhawsawi MAB, Takeshita A, Nishihama K, Takei R, Kondoh Y, Cann I, Gabazza EC, Kobayashi T. Role of microbiota-derived corisin in coagulation activation during SARS-CoV-2 infection. J Thromb Haemost 2024; 22:1919-1935. [PMID: 38453025 DOI: 10.1016/j.jtha.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/23/2024] [Accepted: 02/13/2024] [Indexed: 03/09/2024]
Abstract
BACKGROUND Coagulopathy is a major cause of morbidity and mortality in COVID-19 patients. Hypercoagulability in COVID-19 results in deep vein thrombosis, thromboembolic complications, and diffuse intravascular coagulation. Microbiome dysbiosis influences the clinical course of COVID-19. However, the role of dysbiosis in COVID-19-associated coagulopathy is not fully understood. OBJECTIVES The present study tested the hypothesis that the microbiota-derived proapoptotic corisin is involved in the coagulation system activation during SARS-CoV-2 infection. METHODS This cross-sectional study included 47 consecutive patients who consulted for symptoms of COVID-19. A mouse acute lung injury model was used to recapitulate the clinical findings. A549 alveolar epithelial, THP-1, and human umbilical vein endothelial cells were used to evaluate procoagulant and anticoagulant activity of corisin. RESULTS COVID-19 patients showed significantly high circulating levels of corisin, thrombin-antithrombin complex, D-dimer, tumor necrosis factor-α, and monocyte-chemoattractant protein-1 with reduced levels of free protein S compared with healthy subjects. The levels of thrombin-antithrombin complex, D-dimer, and corisin were significantly correlated. A monoclonal anticorisin-neutralizing antibody significantly inhibited the inflammatory response and coagulation system activation in a SARS-CoV-2 spike protein-associated acute lung injury mouse model, and the levels of corisin and thrombin-antithrombin complex were significantly correlated. In an in vitro experiment, corisin increased the tissue factor activity and decreased the anticoagulant activity of thrombomodulin in epithelial, endothelial, and monocytic cells. CONCLUSION The microbiota-derived corisin is significantly increased and correlated with activation of the coagulation system during SARS-CoV-2 infection, and corisin may directly increase the procoagulant activity in epithelial, endothelial, and monocytic cells.
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Affiliation(s)
- Tatsuki Tsuruga
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Hajime Fujimoto
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Taro Yasuma
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan; Department of Immunology, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan; Microbiome Research Center, Mie University, Tsu, Mie, Japan; Department of Diabetes, Endocrinology and Metabolism, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Corina N D'Alessandro-Gabazza
- Department of Immunology, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan; Microbiome Research Center, Mie University, Tsu, Mie, Japan; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Masaaki Toda
- Department of Immunology, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Toshiyuki Ito
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Atsushi Tomaru
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Haruko Saiki
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Tomohito Okano
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Manal A B Alhawsawi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Atsuro Takeshita
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan; Department of Diabetes, Endocrinology and Metabolism, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Kota Nishihama
- Department of Diabetes, Endocrinology and Metabolism, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan
| | - Reoto Takei
- Department of Respiratory Medicine and Allergy, Tosei General Hospital, Seto, Aichi, Japan
| | - Yasuhiro Kondoh
- Department of Respiratory Medicine and Allergy, Tosei General Hospital, Seto, Aichi, Japan
| | - Isaac Cann
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA; Division of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Department of Animal Science, University of Illinois Urbana-Champaign, Urbana, Illinois, USA; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Esteban C Gabazza
- Department of Immunology, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan; Microbiome Research Center, Mie University, Tsu, Mie, Japan; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
| | - Tetsu Kobayashi
- Department of Pulmonary and Critical Care Medicine, Faculty and Graduate School of Medicine, Mie University, Tsu, Mie, Japan; Microbiome Research Center, Mie University, Tsu, Mie, Japan
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4
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Phan HV, Tsitsiklis A, Maguire CP, Haddad EK, Becker PM, Kim-Schulze S, Lee B, Chen J, Hoch A, Pickering H, van Zalm P, Altman MC, Augustine AD, Calfee CS, Bosinger S, Cairns CB, Eckalbar W, Guan L, Jayavelu ND, Kleinstein SH, Krammer F, Maecker HT, Ozonoff A, Peters B, Rouphael N, Montgomery RR, Reed E, Schaenman J, Steen H, Levy O, Diray-Arce J, Langelier CR. Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology. Sci Transl Med 2024; 16:eadj5154. [PMID: 38630846 DOI: 10.1126/scitranslmed.adj5154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 03/15/2024] [Indexed: 04/19/2024]
Abstract
Age is a major risk factor for severe coronavirus disease 2019 (COVID-19), yet the mechanisms behind this relationship have remained incompletely understood. To address this, we evaluated the impact of aging on host immune response in the blood and the upper airway, as well as the nasal microbiome in a prospective, multicenter cohort of 1031 vaccine-naïve patients hospitalized for COVID-19 between 18 and 96 years old. We performed mass cytometry, serum protein profiling, anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody assays, and blood and nasal transcriptomics. We found that older age correlated with increased SARS-CoV-2 viral abundance upon hospital admission, delayed viral clearance, and increased type I interferon gene expression in both the blood and upper airway. We also observed age-dependent up-regulation of innate immune signaling pathways and down-regulation of adaptive immune signaling pathways. Older adults had lower naïve T and B cell populations and higher monocyte populations. Over time, older adults demonstrated a sustained induction of pro-inflammatory genes and serum chemokines compared with younger individuals, suggesting an age-dependent impairment in inflammation resolution. Transcriptional and protein biomarkers of disease severity differed with age, with the oldest adults exhibiting greater expression of pro-inflammatory genes and proteins in severe disease. Together, our study finds that aging is associated with impaired viral clearance, dysregulated immune signaling, and persistent and potentially pathologic activation of pro-inflammatory genes and proteins.
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Affiliation(s)
- Hoang Van Phan
- University of California San Francisco, San Francisco, CA 94115, USA
| | | | | | - Elias K Haddad
- Drexel University, Tower Health Hospital, Philadelphia, PA 19104, USA
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | | | - Brian Lee
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jing Chen
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Research Computing, Department of Information Technology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Annmarie Hoch
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Harry Pickering
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Patrick van Zalm
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew C Altman
- Benaroya Research Institute, University of Washington, Seattle, WA 98101, USA
| | - Alison D Augustine
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20814, USA
| | - Carolyn S Calfee
- University of California San Francisco, San Francisco, CA 94115, USA
| | | | - Charles B Cairns
- Drexel University, Tower Health Hospital, Philadelphia, PA 19104, USA
| | - Walter Eckalbar
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Leying Guan
- Yale School of Public Health, New Haven, CT 06510, USA
| | | | | | - Florian Krammer
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Holden T Maecker
- Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Al Ozonoff
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Research Computing, Department of Information Technology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | | | | | - Elaine Reed
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Joanna Schaenman
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Hanno Steen
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Ofer Levy
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Joann Diray-Arce
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Charles R Langelier
- University of California San Francisco, San Francisco, CA 94115, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA 94158, USA
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5
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Siasios P, Giosi E, Ouranos K, Christoforidi M, Dimopoulou I, Leshi E, Exindari M, Anastassopoulou C, Gioula G. Oropharyngeal Microbiome Analysis in Patients with Varying SARS-CoV-2 Infection Severity: A Prospective Cohort Study. J Pers Med 2024; 14:369. [PMID: 38672996 PMCID: PMC11051038 DOI: 10.3390/jpm14040369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/16/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Patients with COVID-19 infection have distinct oropharyngeal microbiota composition and diversity metrics according to disease severity. However, these findings are not consistent across the literature. We conducted a multicenter, prospective study in patients with COVID-19 requiring outpatient versus inpatient management to explore the microbial abundance of taxa at the phylum, family, genus, and species level, and we utilized alpha and beta diversity indices to further describe our findings. We collected oropharyngeal washing specimens at the time of study entry, which coincided with the COVID-19 diagnosis, to conduct all analyses. We included 43 patients in the study, of whom 16 were managed as outpatients and 27 required hospitalization. Proteobacteria, Actinobacteria, Bacteroidetes, Saccharibacteria TM7, Fusobacteria, and Spirochaetes were the most abundant phyla among patients, while 61 different families were detected, of which the Streptococcaceae and Staphylococcaceae families were the most predominant. A total of 132 microbial genera were detected, with Streptococcus being the predominant genus in outpatients, in contrast to hospitalized patients, in whom the Staphylococcus genus was predominant. LeFSe analysis identified 57 microbial species in the oropharyngeal washings of study participants that could discriminate the severity of symptoms of COVID-19 infections. Alpha diversity analysis did not reveal a difference in the abundance of bacterial species between the groups, but beta diversity analysis established distinct microbial communities between inpatients and outpatients. Our study provides information on the complex association between the oropharyngeal microbiota and SARS-CoV-2 infection. Although our study cannot establish causation, knowledge of specific taxonomic changes with increasing SARS-CoV-2 infection severity can provide us with novel clues for the prognostic classification of COVID-19 patients.
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Affiliation(s)
- Panagiotis Siasios
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Evangelia Giosi
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Konstantinos Ouranos
- Department of Medicine, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Maria Christoforidi
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Ifigenia Dimopoulou
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Enada Leshi
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Maria Exindari
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
| | - Cleo Anastassopoulou
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Georgia Gioula
- Microbiology Department, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (P.S.); (E.G.); (M.C.); (I.D.); (E.L.); (M.E.); (G.G.)
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6
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Xie L, Luo G, Yang Z, Wu WC, Chen J, Ren Y, Zeng Z, Ye G, Pan Y, Zhao WJ, Chen YQ, Hou W, Sun Y, Guo D, Yang Z, Li J, Holmes EC, Li Y, Chen L, Shi M. The clinical outcome of COVID-19 is strongly associated with microbiome dynamics in the upper respiratory tract. J Infect 2024; 88:106118. [PMID: 38342382 DOI: 10.1016/j.jinf.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/13/2024]
Abstract
OBJECTIVES The respiratory tract is the portal of entry for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Although a variety of respiratory pathogens other than SARS-CoV-2 have been associated with severe cases of COVID-19 disease, the dynamics of the upper respiratory microbiota during disease the course of disease, and how they impact disease manifestation, remain uncertain. METHODS We collected 349 longitudinal upper respiratory samples from a cohort of 65 COVID-19 patients (cohort 1), 28 samples from 28 recovered COVID-19 patients (cohort 2), and 59 samples from 59 healthy controls (cohort 3). All COVID-19 patients originated from the earliest stage of the epidemic in Wuhan. Based on a modified clinical scale, the disease course was divided into five clinical disease phases (pseudotimes): "Healthy" (pseudotime 0), "Incremental" (pseudotime 1), "Critical" (pseudotime 2), "Complicated" (pseudotime 3), "Convalescent" (pseudotime 4), and "Long-term follow-up" (pseudotime 5). Using meta-transcriptomics, we investigated the features and dynamics of transcriptionally active microbes in the upper respiratory tract (URT) over the course of COVID-19 disease, as well as its association with disease progression and clinical outcomes. RESULTS Our results revealed that the URT microbiome exhibits substantial heterogeneity during disease course. Two clusters of microbial communities characterized by low alpha diversity and enrichment for multiple pathogens or potential pathobionts (including Acinetobacter and Candida) were associated with disease progression and a worse clinical outcome. We also identified a series of microbial indicators that classified disease progression into more severe stages. Longitudinal analysis revealed that although the microbiome exhibited complex and changing patterns during COVID-19, a restoration of URT microbiomes from early dysbiosis toward more diverse status in later disease stages was observed in most patients. In addition, a group of potential pathobionts were strongly associated with the concentration of inflammatory indicators and mortality. CONCLUSION This study revealed strong links between URT microbiome dynamics and disease progression and clinical outcomes in COVID-19, implying that the treatment of severe disease should consider the full spectrum of microbial pathogens present.
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Affiliation(s)
- Linlin Xie
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Gengyan Luo
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Zhongzhou Yang
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Wei-Chen Wu
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Jintao Chen
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yuting Ren
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Zhikun Zeng
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Guangming Ye
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yunbao Pan
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wen-Jing Zhao
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yao-Qing Chen
- School of Public Health (Shenzhen), Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Wei Hou
- State Key Laboratory of Virology/Department of Laboratory Medicine/Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences/Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Yanni Sun
- Department of Electrical Engineering, City University of Hong Kong, Hong Kong, China
| | - Deying Guo
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun Li
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Yirong Li
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Liangjun Chen
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences/Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment/Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Mang Shi
- State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China.
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7
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Li R, Li J, Zhou X. Lung microbiome: new insights into the pathogenesis of respiratory diseases. Signal Transduct Target Ther 2024; 9:19. [PMID: 38228603 DOI: 10.1038/s41392-023-01722-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/25/2023] [Accepted: 11/22/2023] [Indexed: 01/18/2024] Open
Abstract
The lungs were long thought to be sterile until technical advances uncovered the presence of the lung microbial community. The microbiome of healthy lungs is mainly derived from the upper respiratory tract (URT) microbiome but also has its own characteristic flora. The selection mechanisms in the lung, including clearance by coughing, pulmonary macrophages, the oscillation of respiratory cilia, and bacterial inhibition by alveolar surfactant, keep the microbiome transient and mobile, which is different from the microbiome in other organs. The pulmonary bacteriome has been intensively studied recently, but relatively little research has focused on the mycobiome and virome. This up-to-date review retrospectively summarizes the lung microbiome's history, composition, and function. We focus on the interaction of the lung microbiome with the oropharynx and gut microbiome and emphasize the role it plays in the innate and adaptive immune responses. More importantly, we focus on multiple respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), fibrosis, bronchiectasis, and pneumonia. The impact of the lung microbiome on coronavirus disease 2019 (COVID-19) and lung cancer has also been comprehensively studied. Furthermore, by summarizing the therapeutic potential of the lung microbiome in lung diseases and examining the shortcomings of the field, we propose an outlook of the direction of lung microbiome research.
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Affiliation(s)
- Ruomeng Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Xikun Zhou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
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8
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Feghoul L, Caillault A, Peyrony O, Salmona M, Nere ML, Delaugerre C, Azoulay E, Chevret S, LeGoff J. Respiratory torque teno virus load at emergency department visit predicts intensive care unit admission of SARS-CoV-2 infected patients. J Med Virol 2023; 95:e29319. [PMID: 38102899 DOI: 10.1002/jmv.29319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/30/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
Accurate prediction of COVID-19 severity remains a challenge. Torque teno virus (TTV), recognized as a surrogate marker of functional immunity in solid organ transplant recipients, holds the potential for assessing infection outcomes. We investigated whether quantifying TTV in nasopharyngeal samples upon emergency department (ED) admission could serve as an early predictor of COVID-19 severity. Retrospective single-center study in the ED of Saint-Louis Hospital in Paris, France. TTV DNA was quantified in nasopharyngeal swab samples collected for SARS-CoV-2 testing. Among 295 SARS-CoV-2 infected patients, 92 returned home, 160 were admitted to medical wards, and 43 to the intensive care unit (ICU). Elevated TTV loads were observed in ICU patients (median: 3.02 log copies/mL, interquartile range [IQR]: 2.215-3.825), exceeding those in discharged (2.215, [0; 2.962]) or hospitalized patients (2.24, [0; 3.29]) (p = 0.006). Multivariate analysis identified diabetes, obesity, hepatitis, fever, dyspnea, oxygen requirement, and TTV load as predictors of ICU admission. A 2.91 log10 copies/mL TTV threshold independently predicted ICU admission. Nasopharyngeal TTV quantification in SARS-CoV-2 infected patients is linked to the likelihood of ICU admission and might reflect respiratory immunosuppression.
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Affiliation(s)
- Linda Feghoul
- Virology Department, AP-HP, Hôpital Saint-Louis, Paris, France
| | | | - Olivier Peyrony
- Emergency Department, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Maud Salmona
- Virology Department, AP-HP, Hôpital Saint-Louis, Paris, France
- Inserm U976, INSIGHT Team, Université Paris Cité, Paris, France
| | | | | | - Elie Azoulay
- Medical Intensive Care Unit, Famirea Study Group, Paris, France
| | - Sylvie Chevret
- UMR 1153 CRESS, Biostatistics and Clinical Epidemiology Research Team, Université Paris Cité, Paris, France
| | - Jérôme LeGoff
- Virology Department, AP-HP, Hôpital Saint-Louis, Paris, France
- Inserm U976, INSIGHT Team, Université Paris Cité, Paris, France
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9
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Zhou J, Yang X, Yang Y, Wei Y, Lu D, Xie Y, Liang H, Cui P, Ye L, Huang J. Human microbiota dysbiosis after SARS-CoV-2 infection have the potential to predict disease prognosis. BMC Infect Dis 2023; 23:841. [PMID: 38031010 PMCID: PMC10685584 DOI: 10.1186/s12879-023-08784-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 11/02/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND The studies on SARS-CoV-2 and human microbiota have yielded inconsistent results regarding microbiota α-diversity and key microbiota. To address these issues and explore the predictive ability of human microbiota for the prognosis of SARS-CoV-2 infection, we conducted a reanalysis of existing studies. METHODS We reviewed the existing studies on SARS-CoV-2 and human microbiota in the Pubmed and Bioproject databases (from inception through October 29, 2021) and extracted the available raw 16S rRNA sequencing data of human microbiota. Firstly, we used meta-analysis and bioinformatics methods to reanalyze the raw data and evaluate the impact of SARS-CoV-2 on human microbial α-diversity. Secondly, machine learning (ML) was employed to assess the ability of microbiota to predict the prognosis of SARS-CoV-2 infection. Finally, we aimed to identify the key microbiota associated with SARS-CoV-2 infection. RESULTS A total of 20 studies related to SARS-CoV-2 and human microbiota were included, involving gut (n = 9), respiratory (n = 11), oral (n = 3), and skin (n = 1) microbiota. Meta-analysis showed that in gut studies, when limiting factors were studies ruled out the effect of antibiotics, cross-sectional and case-control studies, Chinese studies, American studies, and Illumina MiSeq sequencing studies, SARS-CoV-2 infection was associated with down-regulation of microbiota α-diversity (P < 0.05). In respiratory studies, SARS-CoV-2 infection was associated with down-regulation of α-diversity when the limiting factor was V4 sequencing region (P < 0.05). Additionally, the α-diversity of skin microbiota was down-regulated at multiple time points following SARS-CoV-2 infection (P < 0.05). However, no significant difference in oral microbiota α-diversity was observed after SARS-CoV-2 infection. ML models based on baseline respiratory (oropharynx) microbiota profiles exhibited the ability to predict outcomes (survival and death, Random Forest, AUC = 0.847, Sensitivity = 0.833, Specificity = 0.750) after SARS-CoV-2 infection. The shared differential Prevotella and Streptococcus in the gut, respiratory tract, and oral cavity was associated with the severity and recovery of SARS-CoV-2 infection. CONCLUSIONS SARS-CoV-2 infection was related to the down-regulation of α-diversity in the human gut and respiratory microbiota. The respiratory microbiota had the potential to predict the prognosis of individuals infected with SARS-CoV-2. Prevotella and Streptococcus might be key microbiota in SARS-CoV-2 infection.
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Affiliation(s)
- Jie Zhou
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, Guangxi, China
| | - Xiping Yang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, Guangxi, China
| | - Yuecong Yang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, Guangxi, China
| | - Yiru Wei
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, Guangxi, China
| | - Dongjia Lu
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, Guangxi, China
| | - Yulan Xie
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, Guangxi, China
| | - Hao Liang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, Guangxi, China
- Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-Constructed By the Province and Ministry, Nanning, Guangxi, China
| | - Ping Cui
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University, Nanning, Guangxi, China
- Life Science Institute, Guangxi Medical University, Nanning, Guangxi, China
| | - Li Ye
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University, Nanning, Guangxi, China.
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, Guangxi, China.
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-Constructed By the Province and Ministry, Nanning, Guangxi, China.
| | - Jiegang Huang
- Guangxi Key Laboratory of AIDS Prevention and Treatment & School of Public Health, Guangxi Medical University, Nanning, Guangxi, China.
- Guangxi Universities Key Laboratory of Prevention and Control of Highly Prevalent Disease, Nanning, Guangxi, China.
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10
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Wang H, Xu S, Li S, Su B, Sherrill-Mix S, Liang G. Virome in immunodeficiency: what we know currently. Chin Med J (Engl) 2023; 136:2647-2657. [PMID: 37914672 PMCID: PMC10684123 DOI: 10.1097/cm9.0000000000002899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Indexed: 11/03/2023] Open
Abstract
ABSTRACT Over the past few years, the human virome and its complex interactions with microbial communities and the immune system have gained recognition as a crucial factor in human health. Individuals with compromised immune function encounter distinctive challenges due to their heightened vulnerability to a diverse range of infectious diseases. This review aims to comprehensively explore and analyze the growing evidence regarding the role of the virome in immunocompromised disease status. By surveying the latest literature, we present a detailed overview of virome alterations observed in various immunodeficiency conditions. We then delve into the influence and mechanisms of these virome changes on the pathogenesis of specific diseases in immunocompromised individuals. Furthermore, this review explores the clinical relevance of virome studies in the context of immunodeficiency, highlighting the potential diagnostic and therapeutic gains from a better understanding of virome contributions to disease manifestations.
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Affiliation(s)
- Hu Wang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Siqi Xu
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Shuang Li
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Bin Su
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Scott Sherrill-Mix
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Guanxiang Liang
- Center for Infectious Disease Research, School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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11
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Bourumeau W, Tremblay K, Jourdan G, Girard C, Laprise C. Bacterial Biomarkers of the Oropharyngeal and Oral Cavity during SARS-CoV-2 Infection. Microorganisms 2023; 11:2703. [PMID: 38004715 PMCID: PMC10673573 DOI: 10.3390/microorganisms11112703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
(1) Background: Individuals with COVID-19 display different forms of disease severity and the upper respiratory tract microbiome has been suggested to play a crucial role in the development of its symptoms. (2) Methods: The present study analyzed the microbial profiles of the oral cavity and oropharynx of 182 COVID-19 patients compared to 75 unaffected individuals. The samples were obtained from gargle screening samples. 16S rRNA amplicon sequencing was applied to analyze the samples. (3) Results: The present study shows that SARS-CoV-2 infection induced significant differences in bacterial community assemblages, with Prevotella and Veillonella as biomarkers for positive-tested people and Streptococcus and Actinomyces for negative-tested people. It also suggests a state of dysbiosis on the part of the infected individuals due to significant differences in the bacterial community in favor of a microbiome richer in opportunistic pathogens. (4) Conclusions: SARS-CoV-2 infection induces dysbiosis in the upper respiratory tract. The identification of these opportunistic pathogenic biomarkers could be a new screening and prevention tool for people with prior dysbiosis.
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Affiliation(s)
- William Bourumeau
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada; (W.B.); (C.G.)
- Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada;
| | - Karine Tremblay
- Pharmacology-Physiology Department, Université de Sherbrooke, Saguenay, QC J1K 2R1, Canada;
- Research Centre of Centre Intégré Universitaire de Santé et de Services Sociaux du Saguenay–Lac-Saint-Jean (CIUSSS-SLSJ), Saguenay, QC G7H 7K9, Canada
| | - Guillaume Jourdan
- Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada;
| | - Catherine Girard
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada; (W.B.); (C.G.)
- Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada;
| | - Catherine Laprise
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada; (W.B.); (C.G.)
- Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, QC G7H 2B1, Canada;
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12
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Tejeda-Garibay S, Zhao L, Hum NR, Pimentel M, Diep AL, Amiri B, Sindi SS, Weilhammer DR, Loots GG, Hoyer KK. Host tracheal and intestinal microbiomes inhibit Coccidioides growth in vitro. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563655. [PMID: 37961490 PMCID: PMC10634762 DOI: 10.1101/2023.10.23.563655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Coccidioidomycosis, also known as Valley fever, is a disease caused by the fungal pathogen Coccidioides. Unfortunately, patients are often misdiagnosed with bacterial pneumonia leading to inappropriate antibiotic treatment. Soil bacteria B. subtilis-like species exhibits antagonistic properties against Coccidioides in vitro; however, the antagonistic capabilities of host microbiota against Coccidioides are unexplored. We sought to examine the potential of the tracheal and intestinal microbiomes to inhibit the growth of Coccidioides in vitro. We hypothesized that an uninterrupted lawn of microbiota obtained from antibiotic-free mice would inhibit the growth of Coccidioides while partial in vitro depletion through antibiotic disk diffusion assays would allow a niche for fungal growth. We observed that the microbiota grown on 2xGYE (GYE) and CNA w/ 5% sheep's blood agar (5%SB-CNA) inhibited the growth of Coccidioides, but that grown on chocolate agar does not. Partial depletion of the microbiota through antibiotic disk diffusion revealed that microbiota depletion leads to diminished inhibition and comparable growth of Coccidioides growth to controls. To characterize the bacteria grown and narrow down potential candidates contributing to the inhibition of Coccidioides, 16s rRNA sequencing of tracheal and intestinal agar cultures and murine lung extracts was performed. The identity of host bacteria that may be responsible for this inhibition was revealed. The results of this study demonstrate the potential of the host microbiota to inhibit the growth of Coccidioides in vitro and suggest that an altered microbiome through antibiotic treatment could negatively impact effective fungal clearance and allow a niche for fungal growth in vivo.
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Affiliation(s)
- Susana Tejeda-Garibay
- Quantitative and Systems Biology, Graduate Program, University of California Merced, CA
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
| | - Lihong Zhao
- Department of Applied Mathematics, University of California, Merced, CA
- Health Sciences Research Institute, University of California Merced, Merced, CA
| | - Nicholas R Hum
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
| | - Maria Pimentel
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, CA
| | - Anh L Diep
- Quantitative and Systems Biology, Graduate Program, University of California Merced, CA
| | - Beheshta Amiri
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
| | - Suzanne S Sindi
- Department of Applied Mathematics, University of California, Merced, CA
- Health Sciences Research Institute, University of California Merced, Merced, CA
| | - Dina R Weilhammer
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
| | - Gabriela G Loots
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
- University of California Davis Health, Department of Orthopaedic Surgery, Lawrence J. Ellison Musculo-skeletal Research Center, 2700 Stockton Blvd, Sacramento, CA 95817, CA
| | - Katrina K Hoyer
- Quantitative and Systems Biology, Graduate Program, University of California Merced, CA
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, CA
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratories, Livermore CA
- Health Sciences Research Institute, University of California Merced, Merced, CA
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Moreno-Corona NC, López-Ortega O, Pérez-Martínez CA, Martínez-Castillo M, De Jesús-González LA, León-Reyes G, León-Juárez M. Dynamics of the Microbiota and Its Relationship with Post-COVID-19 Syndrome. Int J Mol Sci 2023; 24:14822. [PMID: 37834270 PMCID: PMC10573029 DOI: 10.3390/ijms241914822] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Coronavirus disease (COVID-19) is an infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which can be asymptomatic or present with multiple organ dysfunction. Many infected individuals have chronic alterations associated with neuropsychiatric, endocrine, gastrointestinal, and musculoskeletal symptoms, even several months after disease onset, developing long-COVID or post-acute COVID-19 syndrome (PACS). Microbiota dysbiosis contributes to the onset and progression of many viral diseases, including COVID-19 and post-COVID-19 manifestations, which could serve as potential diagnostic and prognostic biomarkers. This review aimed to discuss the most recent findings on gut microbiota dysbiosis and its relationship with the sequelae of PACS. Elucidating these mechanisms could help develop personalized and non-invasive clinical strategies to identify individuals at a higher risk of experiencing severe disease progression or complications associated with PACS. Moreover, the review highlights the importance of targeting the gut microbiota composition to avoid dysbiosis and to develop possible prophylactic and therapeutic measures against COVID-19 and PACS in future studies.
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Affiliation(s)
- Nidia Carolina Moreno-Corona
- Laboratory of Human Lymphohematopoiesis, Imagine Institute, INSERM UMR 1163, Université de Paris, 75015 Paris, France;
| | - Orestes López-Ortega
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institute Necker Enfants Malades, 75015 Paris, France;
| | | | - Macario Martínez-Castillo
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico;
| | | | - Guadalupe León-Reyes
- Laboratorio de Nutrigenética y Nutrigenómica, Instituto Nacional de Medicina Genómica (INMEGEN), México City 16610, Mexico;
| | - Moisés León-Juárez
- Laboratorio de Virología Perinatal y Diseño Molecular de Antígenos y Biomarcadores, Departamento de Inmunobioquímica, Instituto Nacional de Perinatología, Mexico City 11000, Mexico
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14
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Szabo D, Ostorhazi E, Stercz B, Makra N, Penzes K, Kristof K, Antal I, Rethelyi JM, Zsigmond RI, Birtalan E, Merkely B, Tamas L. Specific nasopharyngeal Corynebacterium strains serve as gatekeepers against SARS-CoV-2 infection. GeroScience 2023; 45:2927-2938. [PMID: 37338780 PMCID: PMC10643471 DOI: 10.1007/s11357-023-00850-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/01/2023] [Indexed: 06/21/2023] Open
Abstract
The SARS-CoV-2 virus is still causing a worldwide problem. The virus settles primarily on the nasal mucosa, and the infection and its course depend on individual susceptibility. Our aim was to investigate the nasopharynx composition's role in the individual susceptibility. During the first phase of SARS-CoV-2 pandemic, nasopharyngeal microbiome samples of close contact unvaccinated patients were investigated by 16S rRNA analysis and by culturing. The whole genome of cultured Corynebacteria was sequenced. The relative expression of ACE2, TMPRSS2, and cathepsin L on Caco-2 cells and the strength of S1-ACE2 binding were determined in the presence of Corynebacteria. From 55 close contacts exposed to identical SARS-CoV-2 exposure, 26 patients became infected and 29 remained uninfected. The nasopharyngeal microbiome analysis showed significantly higher abundance of Corynebacteria in uninfected group. Corynebacterium accolens could be cultivated only from uninfected individuals and Corynebacterium propinquum from both infected and uninfected. Corynebacteria from uninfected patient significantly reduced the ACE2 and cathepsin L expression. C. accolens significantly reduced the TMPRSS2 expression compared to other Corynebacteria. Furthermore, Corynebacterium spp. weakened the binding of the S1-ACE2. Most C. accolens isolates harbored the TAG lipase LipS1 gene. Based on these results, the presence of Corynebacterium spp. in the nasopharyngeal microbiota, especially C. accolens strains, could reduce the individual susceptibility to SARS-CoV-2 infection by several mechanisms: by downregulation the ACE2, the TMPRSS2 receptors, and cathepsin L in the host; through the inhibition of S1-ACE2 binding; and lipase production. These results suggest the use of C. accolens strains as probiotics in the nasopharynx in the future.
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Affiliation(s)
- Dora Szabo
- Institute of Medical Microbiology, Semmelweis University, Üllői Street 26, 1085, Budapest, Hungary.
- Human Microbiota Study Group, Semmelweis University-Eötvös Lóránd Research Network, Budapest, Hungary.
| | - Eszter Ostorhazi
- Institute of Medical Microbiology, Semmelweis University, Üllői Street 26, 1085, Budapest, Hungary
- Human Microbiota Study Group, Semmelweis University-Eötvös Lóránd Research Network, Budapest, Hungary
| | - Balazs Stercz
- Institute of Medical Microbiology, Semmelweis University, Üllői Street 26, 1085, Budapest, Hungary
- Human Microbiota Study Group, Semmelweis University-Eötvös Lóránd Research Network, Budapest, Hungary
| | - Nora Makra
- Institute of Medical Microbiology, Semmelweis University, Üllői Street 26, 1085, Budapest, Hungary
| | - Kinga Penzes
- Institute of Medical Microbiology, Semmelweis University, Üllői Street 26, 1085, Budapest, Hungary
| | - Katalin Kristof
- Institute of Laboratory Medicine, Clinical Microbiology Laboratory, Semmelweis University, Budapest, Hungary
| | - Istvan Antal
- Department of Pharmaceutics, Semmelweis University, Budapest, Hungary
| | - Janos M Rethelyi
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Reka I Zsigmond
- Department of Psychiatry and Psychotherapy, Semmelweis University, Budapest, Hungary
| | - Ede Birtalan
- Department of Oto-Rhino-Laryngology and Head and Neck Surgery, Semmelweis University, Budapest, Hungary
| | - Bela Merkely
- Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Laszlo Tamas
- Department of Oto-Rhino-Laryngology and Head and Neck Surgery, Semmelweis University, Budapest, Hungary
- Department of Voice, Speech and Swallowing Therapy, Faculty of Health Sciences, Semmelweis University, Budapest, Hungary
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15
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Charlys da Costa A, Mendes-Correa MC, Tozetto-Mendoza TR, Villas-Boas LS, de Paula AV, Paiao HGO, Leal FE, Ferreira NE, Honorato L, Leal E, Grandi G, dos Santos Morais V, Manuli ER, Sabino EC, Witkin SS. Detailed characterization of Redondovirus in saliva of SARS-CoV-2-infected individuals in Sao Paulo, Brazil. PLoS One 2023; 18:e0291027. [PMID: 37651462 PMCID: PMC10470920 DOI: 10.1371/journal.pone.0291027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/20/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND Redondovirus (ReDoV) is a DNA virus present in the respiratory tract of many healthy individuals. Since SARS-CoV-2, the virus responsible for COVID-19, also primarily infects the same site, we evaluated whether ReDoV was present at increased frequency in patients with COVID-19 and influenced infection parameters. METHODS Saliva samples were collected weekly from 59 individuals with COVID-19 and from 132 controls. ReDoV was detected by polymerase chain reaction and the genotypes were identified by metagenomics. Torque Teno Virus (TTV) in these samples were previously reported. RESULTS ReDoV was detected in saliva more frequently from COVID-19 patients (72.9%) than from controls (50.0%) (p = 0.0015). There were no associations between ReDoV detection and either continuous or intermittent SARS-CoV-2 shedding, the duration of SARS-CoV-2 detection in saliva, patients' sex or if infection was by the B1 or Gamma strain. The two ReDoV strains, Brisavirus and Vientovirus, were present in equivalent frequencies in ReDoV-positive COVID-19 patients and controls. Phylogenetic analysis suggested that the two ReDoV strains in Brazil were similar to strains previously detected on other continents. CONCLUSION ReDoV expression in saliva is increased in males and females in Brazil with mild COVID-19 but its presence does not appear to influence properties of the SARS-CoV-2 infection.
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Affiliation(s)
- Antonio Charlys da Costa
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Maria C. Mendes-Correa
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Tania Regina Tozetto-Mendoza
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Paulo, Brazil
| | - Lucy S. Villas-Boas
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Paulo, Brazil
| | - Anderson Vicente de Paula
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Heuder Gustavo Oliveira Paiao
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Fabio E. Leal
- Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Paulo, Brazil
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Noely E. Ferreira
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Layla Honorato
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Elcio Leal
- Laboratório de Diversidade Viral, Instituto de Ciências Biológicas, Universidade Federal do Pará, Pará, Brazil
| | | | - Vanessa dos Santos Morais
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Erika R. Manuli
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Paulo, Brazil
| | - Ester C. Sabino
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Faculdade de Medicina da Universidade Municipal de Sao Caetano do Sul, São Paulo, Brazil
| | - Steven S. Witkin
- Laboratório de Investigação Médica em Virologia, Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, United States of America
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16
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Merenstein C, Fitzgerald AS, Khatib LA, Graham-Wooten J, Bushman FD, Collman RG. Effects of Mask Reuse on the Oropharyngeal, Skin, and Mask Microbiome. J Infect Dis 2023; 228:479-486. [PMID: 37217829 PMCID: PMC10428194 DOI: 10.1093/infdis/jiad167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Face masks have been critical in the coronavirus disease 2019 (COVID-19) pandemic, but supplies were sometimes limited and disposable masks contribute greatly to environmental waste. Studies suggest that filtration capacity is retained with repeated use, and surveys indicate many people reuse surgical masks. However, the impact of mask reuse on the host is understudied. METHODS We applied 16S rRNA gene sequencing to investigate the bacterial microbiome of the facial skin and oropharynx of individuals randomized to wearing fresh surgical masks daily versus masks reused for 1 week. RESULTS Compared to daily fresh masks, reuse was associated with increased richness (number of taxa) of the skin microbiome and trend towards greater diversity, but no difference in the oropharyngeal microbiome. Used masks had either skin-dominant or oropharynx-dominant bacterial sequences, and reused masks had >100-fold higher bacterial content but no change in composition compared to those used for 1 day. CONCLUSIONS One week of mask reuse increased the number of low-abundance taxa on the face but did not impact the upper respiratory microbiome. Thus, face mask reuse has little impact on the host microbiome, although whether minor changes to the skin microbiome might relate to reported skin sequelae of masking (maskne) remains to be determined.
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Affiliation(s)
- Carter Merenstein
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ayannah S Fitzgerald
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Layla A Khatib
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jevon Graham-Wooten
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronald G Collman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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17
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Ablakimova N, Mussina AZ, Smagulova GA, Rachina S, Kurmangazin MS, Balapasheva A, Karimoldayeva D, Zare A, Mahdipour M, Rahmanifar F. Microbial Landscape and Antibiotic-Susceptibility Profiles of Microorganisms in Patients with Bacterial Pneumonia: A Comparative Cross-Sectional Study of COVID-19 and Non-COVID-19 Cases in Aktobe, Kazakhstan. Antibiotics (Basel) 2023; 12:1297. [PMID: 37627717 PMCID: PMC10451206 DOI: 10.3390/antibiotics12081297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/30/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
This cross-sectional study investigated the microbial landscape and antibiotic-resistance patterns in patients with bacterial pneumonia, with a focus on the impact of COVID-19. Sputum samples from individuals with bacterial pneumonia, including coronavirus disease 2019-positive polymerase chain reaction (COVID-19-PCR+), COVID-19-PCR- and non-COVID-19 patients, were analyzed. Surprisingly, the classic etiological factor of bacterial pneumonia, Streptococcus pneumoniae, was rarely isolated from the sputum samples. Furthermore, the frequency of multidrug-resistant pathogens was found to be higher in non-COVID-19 patients, highlighting the potential impact of the pandemic on antimicrobial resistance. Strains obtained from COVID-19-PCR+ patients exhibited significant resistance to commonly used antibiotics, including fluoroquinolones and cephalosporins. Notably, the ESKAPE pathogens, Staphylococcus aureus, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterobacter cloacae, and Enterobacter aerogenes, were identified among the isolated microorganisms. Our findings underscore the urgent need for infection control measures and responsible antibiotic use in healthcare settings, as well as the importance of enhancing pneumonia diagnostics and implementing standardized laboratory protocols.
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Affiliation(s)
- Nurgul Ablakimova
- Department of Pharmacology, West Kazakhstan Marat Ospanov Medical University, Aktobe 030012, Kazakhstan; (A.Z.M.); (G.A.S.); (A.B.)
| | - Aigul Z. Mussina
- Department of Pharmacology, West Kazakhstan Marat Ospanov Medical University, Aktobe 030012, Kazakhstan; (A.Z.M.); (G.A.S.); (A.B.)
| | - Gaziza A. Smagulova
- Department of Pharmacology, West Kazakhstan Marat Ospanov Medical University, Aktobe 030012, Kazakhstan; (A.Z.M.); (G.A.S.); (A.B.)
| | - Svetlana Rachina
- Hospital Therapy Department No. 2, I.M. Sechenov First Moscow State Medical University, Moscow 119435, Russia;
| | - Meirambek S. Kurmangazin
- Department of Infectious Disease, West Kazakhstan Marat Ospanov Medical University, Aktobe 030012, Kazakhstan;
| | - Aigerim Balapasheva
- Department of Pharmacology, West Kazakhstan Marat Ospanov Medical University, Aktobe 030012, Kazakhstan; (A.Z.M.); (G.A.S.); (A.B.)
| | - Dinara Karimoldayeva
- Respiratory Medicine and Allergology Department, Aktobe Medical Center, Aktobe 030017, Kazakhstan;
| | - Afshin Zare
- PerciaVista R & D Co., Shiraz 71676-83745, Iran;
| | - Mahdi Mahdipour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz 51666-53431, Iran;
- Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz 51666-53431, Iran
| | - Farhad Rahmanifar
- Department of Basic Sciences, School of Veterinary Medicine, Shiraz University, Shiraz 71348-14336, Iran;
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18
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Reuben RC, Beugnon R, Jurburg SD. COVID-19 alters human microbiomes: a meta-analysis. Front Cell Infect Microbiol 2023; 13:1211348. [PMID: 37600938 PMCID: PMC10433767 DOI: 10.3389/fcimb.2023.1211348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/23/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected a substantial portion of the world's population, and novel consequences of COVID-19 on the human body are continuously being uncovered. The human microbiome plays an essential role in host health and well-being, and multiple studies targeting specific populations have reported altered microbiomes in patients infected with SARS-CoV-2. Given the global scale and massive incidence of COVID on the global population, determining whether the effects of COVID-19 on the human microbiome are consistent and generalizable across populations is essential. Methods We performed a synthesis of human microbiome responses to COVID-19. We collected 16S rRNA gene amplicon sequence data from 11 studies sampling the oral and nasopharyngeal or gut microbiome of COVID-19-infected and uninfected subjects. Our synthesis included 1,159 respiratory (oral and nasopharyngeal) microbiome samples and 267 gut microbiome samples from patients in 11 cities across four countries. Results Our reanalyses revealed communitywide alterations in the respiratory and gut microbiomes across human populations. We found significant overall reductions in the gut microbial diversity of COVID-19-infected patients, but not in the respiratory microbiome. Furthermore, we found more consistent community shifts in the gut microbiomes of infected patients than in the respiratory microbiomes, although the microbiomes in both sites exhibited higher host-to-host variation in infected patients. In respiratory microbiomes, COVID-19 infection resulted in an increase in the relative abundance of potentially pathogenic bacteria, including Mycoplasma. Discussion Our findings shed light on the impact of COVID-19 on the human-associated microbiome across populations, and highlight the need for further research into the relationship between long-term effects of COVID-19 and altered microbiota.
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Affiliation(s)
- Rine Christopher Reuben
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biology, Leipzig University, Leipzig, Germany
| | - Rémy Beugnon
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Leipzig Institute for Meteorology, Universität Leipzig, Leipzig, Germany
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Stephanie D. Jurburg
- German Centre of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
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19
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Armstrong AJS, Horton DB, Andrews T, Greenberg P, Roy J, Gennaro ML, Carson JL, Panettieri RA, Barrett ES, Blaser MJ. Saliva microbiome in relation to SARS-CoV-2 infection in a prospective cohort of healthy US adults. EBioMedicine 2023; 94:104731. [PMID: 37487417 PMCID: PMC10382861 DOI: 10.1016/j.ebiom.2023.104731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/08/2023] [Accepted: 07/13/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND The clinical outcomes of SARS-CoV-2 infection vary in severity, potentially influenced by the resident human microbiota. There is limited consensus on conserved microbiome changes in response to SARS-CoV-2 infection, with many studies focusing on severely ill individuals. This study aimed to assess the variation in the upper respiratory tract microbiome using saliva specimens in a cohort of individuals with primarily mild to moderate disease. METHODS In early 2020, a cohort of 831 adults without known SARS-CoV-2 infection was followed over a six-month period to assess the occurrence and natural history of SARS-CoV-2 infection. From this cohort, 81 participants with a SARS-CoV-2 infection, along with 57 unexposed counterparts were selected with a total of 748 serial saliva samples were collected for analysis. Total bacterial abundance, composition, population structure, and gene function of the salivary microbiome were measured using 16S rRNA gene and shotgun metagenomic sequencing. FINDINGS The salivary microbiome remained stable in unexposed individuals over the six-month study period, as evidenced by all measured metrics. Similarly, participants with mild to moderate SARS-CoV-2 infection showed microbiome stability throughout and after their infection. However, there were significant reductions in microbiome diversity among SARS-CoV-2-positive participants with severe symptoms early after infection. Over time, the microbiome diversity in these participants showed signs of recovery. INTERPRETATION These findings demonstrate the resilience of the salivary microbiome in relation to SARS-CoV-2 infection. Mild to moderate infections did not significantly disrupt the stability of the salivary microbiome, suggesting its ability to maintain its composition and function. However, severe SARS-CoV-2 infection was associated with temporary reductions in microbiome diversity, indicating the limits of microbiome resilience in the face of severe infection. FUNDING This project was supported in part by Danone North America and grants from the National Institutes of Health, United States.
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Affiliation(s)
- Abigail J S Armstrong
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - Daniel B Horton
- Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA; Rutgers Center for Pharmacoepidemiology and Treatment Science, Institute for Health, Health Care Policy, and Aging Research, New Brunswick, New Jersey, USA; Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey, USA
| | - Tracy Andrews
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey, USA
| | - Patricia Greenberg
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey, USA
| | - Jason Roy
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey, USA
| | - Maria Laura Gennaro
- Department of Medicine, Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Jeffrey L Carson
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Reynold A Panettieri
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Emily S Barrett
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, New Jersey, USA; Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, New Jersey, USA
| | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA.
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20
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Lupu VV, Butnariu LI, Fotea S, Morariu ID, Badescu MC, Starcea IM, Salaru DL, Popp A, Dragan F, Lupu A, Mocanu A, Chisnoiu T, Pantazi AC, Jechel E. The Disease with a Thousand Faces and the Human Microbiome-A Physiopathogenic Intercorrelation in Pediatric Practice. Nutrients 2023; 15:3359. [PMID: 37571295 PMCID: PMC10420997 DOI: 10.3390/nu15153359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/18/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Numerous interrelationships are known in the literature that have the final effect of unmasking or influencing various pathologies. Among these, the present article aims to discuss the connection between systemic lupus erythematosus (SLE) and the human microbiome. The main purpose of this work is to popularize information about the impact of dysbiosis on the pathogenesis and evolutionary course of pediatric patients with SLE. Added to this is the interest in knowledge and awareness of adjunctive therapeutic means that has the ultimate goal of increasing the quality of life. The means by which this can be achieved can be briefly divided into prophylactic or curative, depending on the phase of the condition in which the patient is. We thus reiterate the importance of the clinician acquiring an overview of SLE and the human microbiome, doubled by in-depth knowledge of the physio-pathogenic interactions between the two (in part achieved through the much-studied gut-target organ axes-brain, heart, lung, skin), with the target objective being that of obtaining individualized, multimodal and efficient management for each individual patient.
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Affiliation(s)
- Vasile Valeriu Lupu
- Pediatrics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | | | - Silvia Fotea
- Clinical Medical Department, Faculty of Medicine and Pharmacy, “Dunarea de Jos” University of Galati, 800008 Galati, Romania
| | - Ionela Daniela Morariu
- Faculty of Pharmacy, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Minerva Codruta Badescu
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Iuliana Magdalena Starcea
- Pediatrics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Delia Lidia Salaru
- Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Alina Popp
- Pediatrics Department, Faculty of Medicine, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Felicia Dragan
- Faculty of Medicine and Pharmacy, University of Oradea, 410087 Oradea, Romania
| | - Ancuta Lupu
- Pediatrics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Adriana Mocanu
- Pediatrics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Tatiana Chisnoiu
- Pediatrics Department, Faculty of Medicine, Ovidius University, 900470 Constanta, Romania
| | | | - Elena Jechel
- Pediatrics Department, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
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21
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Xie L, Chen L, Li X, Zhou J, Tian H, Zhao J, Li Z, Li Y. Analysis of Lung Microbiome in COVID-19 Patients during Time of Hospitalization. Pathogens 2023; 12:944. [PMID: 37513791 PMCID: PMC10386632 DOI: 10.3390/pathogens12070944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/11/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the pathogenic agent of the rapidly spreading pneumonia called coronavirus disease 2019 (COVID-19), primarily infects the respiratory and digestive tract. Several studies have indicated the alterations of the bacterial microbiome in the lower respiratory tract during viral infection. However, both bacterial and fungal microbiota in the lung of COVID-19 patients remained to be explored. METHODS In this study, we conducted nanopore sequencing analyses of the lower respiratory tract samples from 38 COVID-19 patients and 26 non-COVID-19 pneumonia controls. Both bacterial and fungal microbiome diversities and microbiota abundances in the lung were compared. RESULTS Our results revealed significant differences in lung microbiome between COVID-19 patients and non-COVID-19 controls, which were strongly associated with SARS-CoV-2 infection and clinical status. COVID-19 patients exhibited a notably higher abundance of opportunistic pathogens, particularly Acinetobacter baumannii and Candida spp. Furthermore, the potential pathogens enriched in COVID-19 patients were positively correlated with inflammation indicators. CONCLUSIONS Our study highlights the differences in lung microbiome diversity and composition between COVID-19 patients and non-COVID-19 patients. This may contribute to predicting co-pathogens and selecting optimal treatments for respiratory infections caused by SARS-CoV-2.
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Affiliation(s)
- Linlin Xie
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Liangjun Chen
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Xinran Li
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Junying Zhou
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Hongpan Tian
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jin Zhao
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Zhiqiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yirong Li
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Wuhan Research Center for Infectious Diseases and Tumors, Chinese Academy of Medical Sciences, Wuhan 430071, China
- Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment, Wuhan 430071, China
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22
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Ling L, Lai CK, Lui G, Yeung ACM, Chan HC, Cheuk CHS, Cheung AN, Chang L, Chiu LCS, Zhang J, Wong WT, Hui DSC, Wong CK, Chan PKS, Chen Z. Characterization of upper airway microbiome across severity of COVID-19 during hospitalization and treatment. Front Cell Infect Microbiol 2023; 13:1205401. [PMID: 37469595 PMCID: PMC10352853 DOI: 10.3389/fcimb.2023.1205401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/13/2023] [Indexed: 07/21/2023] Open
Abstract
Longitudinal studies on upper respiratory tract microbiome in coronavirus disease 2019 (COVID-19) without potential confounders such as antimicrobial therapy are limited. The objective of this study is to assess for longitudinal changes in the upper respiratory microbiome, its association with disease severity, and potential confounders in adult hospitalized patients with COVID-19. Serial nasopharyngeal and throat swabs (NPSTSs) were taken for 16S rRNA gene amplicon sequencing from adults hospitalized for COVID-19. Alpha and beta diversity was assessed between different groups. Principal coordinate analysis was used to assess beta diversity between groups. Linear discriminant analysis was used to identify discriminative bacterial taxa in NPSTS taken early during hospitalization on need for intensive care unit (ICU) admission. A total of 314 NPSTS samples from 197 subjects (asymptomatic = 14, mild/moderate = 106, and severe/critical = 51 patients with COVID-19; non-COVID-19 mechanically ventilated ICU patients = 11; and healthy volunteers = 15) were sequenced. Among all covariates, antibiotic treatment had the largest effect on upper airway microbiota. When samples taken after antibiotics were excluded, alpha diversity (Shannon, Simpson, richness, and evenness) was similar across severity of COVID-19, whereas beta diversity (weighted GUniFrac and Bray-Curtis distance) remained different. Thirteen bacterial genera from NPSTS taken within the first week of hospitalization were associated with a need for ICU admission (area under the receiver operating characteristic curve, 0.96; 95% CI, 0.91-0.99). Longitudinal analysis showed that the upper respiratory microbiota alpha and beta diversity was unchanged during hospitalization in the absence of antimicrobial therapy.
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Affiliation(s)
- Lowell Ling
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Christopher K.C. Lai
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Grace Lui
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Apple Chung Man Yeung
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Hiu Ching Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Chung Hon Shawn Cheuk
- Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Adonia Nicole Cheung
- Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Lok Ching Chang
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Lok Ching Sandra Chiu
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jack Zhenhe Zhang
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Wai-Tat Wong
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - David S. C. Hui
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Chun Kwok Wong
- Department of Chemical Pathology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Paul K. S. Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
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23
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Tejeda-Garibay S, Hoyer KK. Coccidioidomycosis and Host Microbiome Interactions: What We Know and What We Can Infer from Other Respiratory Infections. J Fungi (Basel) 2023; 9:586. [PMID: 37233297 PMCID: PMC10219296 DOI: 10.3390/jof9050586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/25/2023] [Accepted: 05/10/2023] [Indexed: 05/27/2023] Open
Abstract
Between 70 and 80% of Valley fever patients receive one or more rounds of antibiotic treatment prior to accurate diagnosis with coccidioidomycosis. Antibiotic treatment and infection (bacterial, viral, fungal, parasitic) often have negative implications on host microbial dysbiosis, immunological responses, and disease outcome. These perturbations have focused on the impact of gut dysbiosis on pulmonary disease instead of the implications of direct lung dysbiosis. However, recent work highlights a need to establish the direct effects of the lung microbiota on infection outcome. Cystic fibrosis, chronic obstructive pulmonary disease, COVID-19, and M. tuberculosis studies suggest that surveying the lung microbiota composition can serve as a predictive factor of disease severity and could inform treatment options. In addition to traditional treatment options, probiotics can reverse perturbation-induced repercussions on disease outcomes. The purpose of this review is to speculate on the effects perturbations of the host microbiome can have on coccidioidomycosis progression. To do this, parallels are drawn to aa compilation of other host microbiome infection studies.
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Affiliation(s)
- Susana Tejeda-Garibay
- Quantitative and Systems Biology, Graduate Program, University of California Merced, Merced, CA 95343, USA
| | - Katrina K. Hoyer
- Department of Molecular and Cell Biology, University California Merced, Merced, CA 95343, USA
- Health Sciences Research Institute, University of California Merced, Merced, CA 95343, USA
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24
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Cut TG, Mavrea A, Cumpanas AA, Novacescu D, Oancea CI, Bratosin F, Marinescu AR, Laza R, Mocanu A, Pescariu AS, Manolescu D, Dumache R, Enache A, Hogea E, Lazureanu VE. A Retrospective Assessment of Sputum Samples and Antimicrobial Resistance in COVID-19 Patients. Pathogens 2023; 12:pathogens12040620. [PMID: 37111506 PMCID: PMC10143659 DOI: 10.3390/pathogens12040620] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Data on bacterial or fungal pathogens and their impact on the mortality rates of Western Romanian COVID-19 patients are scarce. As a result, the purpose of this research was to determine the prevalence of bacterial and fungal co- and superinfections in Western Romanian adults with COVID-19, hospitalized in in-ward settings during the second half of the pandemic, and its distribution according to sociodemographic and clinical conditions. The unicentric retrospective observational study was conducted on 407 eligible patients. Expectorate sputum was selected as the sampling technique followed by routine microbiological investigations. A total of 31.5% of samples tested positive for Pseudomonas aeruginosa, followed by 26.2% having co-infections with Klebsiella pneumoniae among patients admitted with COVID-19. The third most common Pathogenic bacteria identified in the sputum samples was Escherichia coli, followed by Acinetobacter baumannii in 9.3% of samples. Commensal human pathogens caused respiratory infections in 67 patients, the most prevalent being Streptococcus penumoniae, followed by methicillin-sensitive and methicillin-resistant Staphylococcus aureus. A total of 53.4% of sputum samples tested positive for Candida spp., followed by 41.1% of samples with Aspergillus spp. growth. The three groups with positive microbial growth on sputum cultures had an equally proportional distribution of patients admitted to the ICU, with an average of 30%, compared with only 17.3% among hospitalized COVID-19 patients with negative sputum cultures (p = 0.003). More than 80% of all positive samples showed multidrug resistance. The high prevalence of bacterial and fungal co-infections and superinfections in COVID-19 patients mandates for strict and effective antimicrobial stewardship and infection control policies.
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Affiliation(s)
- Talida Georgiana Cut
- Department XIII, Discipline of Infectious Diseases, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
- Doctoral School, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
- Center for Ethics in Human Genetic Identifications, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
- Academy of Romanian Scientists, Splaiul Independentei, Nr. 54, 50085 Bucharest, Romania
| | - Adelina Mavrea
- Department VII, Internal Medicine II, Discipline of Cardiology, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
| | - Alin Adrian Cumpanas
- Department XV, Discipline of Urology, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
| | - Dorin Novacescu
- Doctoral School, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
- Academy of Romanian Scientists, Splaiul Independentei, Nr. 54, 50085 Bucharest, Romania
| | - Cristian Iulian Oancea
- Department XIII, Discipline of Pneumology, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
- Center for Research and Innovation in Precision Medicine of Respiratory Diseases (CRIPMRD), Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
| | - Felix Bratosin
- Department XIII, Discipline of Infectious Diseases, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
- Doctoral School, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
| | - Adelina Raluca Marinescu
- Department XIII, Discipline of Infectious Diseases, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
| | - Ruxandra Laza
- Department XIII, Discipline of Infectious Diseases, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
| | - Alexandra Mocanu
- Department XIII, Discipline of Infectious Diseases, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
- Doctoral School, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
| | - Alexandru Silvius Pescariu
- Academy of Romanian Scientists, Splaiul Independentei, Nr. 54, 50085 Bucharest, Romania
- Department VII, Internal Medicine II, Discipline of Cardiology, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
| | - Diana Manolescu
- Department XV, Discipline of Radiology, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
| | - Raluca Dumache
- Center for Ethics in Human Genetic Identifications, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
- Department VIII, Discipline of Forensic Medicine, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
| | - Alexandra Enache
- Center for Ethics in Human Genetic Identifications, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
- Department VIII, Discipline of Forensic Medicine, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
| | - Elena Hogea
- Department XIV, Discipline of Microbiology, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
| | - Voichita Elena Lazureanu
- Department XIII, Discipline of Infectious Diseases, Victor Babes University of Medicine and Pharmacy Timisoara, E. Murgu Square, Nr. 2, 300041 Timisoara, Romania
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25
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Wu J, Liu W, Zhu L, Li N, Luo G, Gu M, Peng M, Zeng S, Wu S, Zhang S, Chen Q, Cai M, Cao W, Jiang Y, Luo C, Tian D, Shi M, Shu Y, Chang G, Luo H. Dysbiosis of oropharyngeal microbiome and antibiotic resistance in hospitalized COVID-19 patients. J Med Virol 2023; 95:e28727. [PMID: 37185870 DOI: 10.1002/jmv.28727] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is ongoing and multiple studies have elucidated its pathogenesis, however, the related- microbiome imbalance caused by SARS-CoV-2 is still not clear. In this study, we have comprehensively compared the microbiome composition and associated function alterations in the oropharyngeal swabs of healthy controls and coronavirus disease 2019 (COVID-19) patients with moderate or severe symptoms by metatranscriptomic sequencing. We did observe a reduced microbiome alpha-diversity but significant enrichment of opportunistic microorganisms in patients with COVID-19 compared with healthy controls, and the microbial homeostasis was rebuilt following the recovery of COVID-19 patients. Correspondingly, less functional genes in multiple biological processes and weakened metabolic pathways such as carbohydrate metabolism, energy metabolism were also observed in COVID-19 patients. We only found higher relative abundance of limited genera such as Lachnoanaerobaculum between severe patients and moderate patients while no worthy-noting microbiome diversity and function alteration were observed. Finally, we noticed that the co-occurrence of antibiotic resistance and virulence was closely related to the microbiome alteration caused by SRAS-CoV-2. Overall, our findings demonstrate that microbial dysbiosis may enhance the pathogenesis of SARS-CoV-2 and the antibiotics treatment should be critically considered.
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Affiliation(s)
- Jiani Wu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Department of AIDS and STD Control and Prevention, Shaoxing Center for Disease Control and Prevention, Shaoxing, China
| | - Wei Liu
- Department of Immunology, Center for Disease Prevention and Control of PLA, Beijing, China
| | - Lin Zhu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Nina Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Gengyan Luo
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Ming Gu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Minwu Peng
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Shike Zeng
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Shu Wu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Shengze Zhang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Qiqi Chen
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Meiqi Cai
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Wei Cao
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Ying Jiang
- Environment Health Department, Shenzhen Nanshan Center for Disease Control and Prevention, Shenzhen, China
| | - Chuming Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Dechao Tian
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
| | - Mang Shi
- The Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, China
| | - Yuelong Shu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Guohui Chang
- Department of Immunology, Center for Disease Prevention and Control of PLA, Beijing, China
| | - Huanle Luo
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China
- Key Laboratory of Tropical Disease Control, Ministry of Education, Sun Yat-sen University, Shenzhen, China
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26
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The Association between Previous Antibiotic Consumption and SARS-CoV-2 Infection: A Population-Based Case-Control Study. Antibiotics (Basel) 2023; 12:antibiotics12030587. [PMID: 36978453 PMCID: PMC10044412 DOI: 10.3390/antibiotics12030587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
Background: The susceptibility to SARS-CoV-2 infection is complex and not yet fully elucidated, being related to many variables; these include human microbiome and immune status, which are both affected for a long period by antibiotic use. We therefore aimed to examine the association of previous antibiotic consumption and SARS-CoV-2 infection in a large-scale population-based study with control of known confounders. Methods: A matched case–control study was performed utilizing the electronic medical records of a large Health Maintenance Organization. Cases were subjects with confirmed SARS-CoV-2 infection (n = 31,260), matched individually (1:4 ratio) to controls without a positive SARS-CoV-2 test (n = 125,039). The possible association between previous antibiotic use and SARS-CoV-2 infection was determined by comparing antibiotic consumption in the previous 6 and 12 months between the cases and controls. For each antibiotic consumed we calculated the odds ratio (OR) for documented SARS-CoV-2 infection, 95% confidence interval (CI), and p-value using univariate and multivariate analyses. Results: The association between previous antibiotic consumption and SARS-CoV-2 infection was complex and bi-directional. In the multivariate analysis, phenoxymethylpenicillin was associated with increased rate of SARS-CoV-2 infection (OR 1.110, 95% CI: 1.036–1.191) while decreased rates were associated with previous consumption of trimethoprim-sulfonamides (OR 0.783, 95% CI: 0.632–0.971) and azithromycin (OR 0.882, 95% CI: 0.829–0.938). Fluroquinolones were associated with decreased rates (OR 0.923, 95% CI: 0.861–0.989) only in the univariate analysis. Previous consumption of other antibiotics had no significant association with SARS-CoV-2 infection. Conclusions: Previous consumption of certain antibiotic agents has an independent significant association with increased or decreased rates of SARS-CoV-2 infection. Plausible mechanisms, that should be further elucidated, are mainly antibiotic effects on the human microbiome and immune modulation.
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27
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Ancona G, Alagna L, Alteri C, Palomba E, Tonizzo A, Pastena A, Muscatello A, Gori A, Bandera A. Gut and airway microbiota dysbiosis and their role in COVID-19 and long-COVID. Front Immunol 2023; 14:1080043. [PMID: 36969243 PMCID: PMC10030519 DOI: 10.3389/fimmu.2023.1080043] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
The gut microbiota plays a crucial role in human health and disease. Gut dysbiosis is known to be associated with increased susceptibility to respiratory diseases and modifications in the immune response and homeostasis of the lungs (the so-called gut-lung axis). Furthermore, recent studies have highlighted the possible role of dysbiosis in neurological disturbances, introducing the notion of the "gut-brain axis." During the last 2 years, several studies have described the presence of gut dysbiosis during coronavirus disease 2019 (COVID-19) and its relationship with disease severity, SARS-CoV-2 gastrointestinal replication, and immune inflammation. Moreover, the possible persistence of gut dysbiosis after disease resolution may be linked to long-COVID syndrome and particularly to its neurological manifestations. We reviewed recent evidence on the association between dysbiosis and COVID-19, investigating the possible epidemiologic confounding factors like age, location, sex, sample size, the severity of disease, comorbidities, therapy, and vaccination status on gut and airway microbial dysbiosis in selected studies on both COVID-19 and long-COVID. Moreover, we analyzed the confounding factors strictly related to microbiota, specifically diet investigation and previous use of antibiotics/probiotics, and the methodology used to study the microbiota (α- and β-diversity parameters and relative abundance tools). Of note, only a few studies focused on longitudinal analyses, especially for long-term observation in long-COVID. Lastly, there is a lack of knowledge regarding the role of microbiota transplantation and other therapeutic approaches and their possible impact on disease progression and severity. Preliminary data seem to suggest that gut and airway dysbiosis might play a role in COVID-19 and in long-COVID neurological symptoms. Indeed, the development and interpretation of these data could have important implications for future preventive and therapeutic strategies.
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Affiliation(s)
- Giuseppe Ancona
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Laura Alagna
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Claudia Alteri
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Multimodal Research Area, Bambino Gesù Children Hospital (IRCCS), Rome, Italy
| | - Emanuele Palomba
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Anna Tonizzo
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Andrea Pastena
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Antonio Muscatello
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Andrea Gori
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
| | - Alessandra Bandera
- Infectious Diseases Unit, Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy
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28
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Schmidt J, Cruz M, Tolentino J, Carmo A, Paes M, de Lacerda G, Gjorup A, Schmidt S. COVID-19 Patients with Early Gastrointestinal Symptoms Show Persistent Deficits in Specific Attention Subdomains. J Clin Med 2023; 12:jcm12051931. [PMID: 36902717 PMCID: PMC10003448 DOI: 10.3390/jcm12051931] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/17/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Previous studies have shown that COVID-19 inpatients exhibited significant attentional deficits on the day of discharge. However, the presence of gastrointestinal symptoms (GIS) has not been evaluated. Here, we aimed to verify: (1) whether COVID-19 patients with GIS exhibited specific attention deficits; (2) which attention subdomain deficits discriminated patients with GIS and without gastrointestinal symptoms (NGIS) from healthy controls. On admission, the presence of GIS was recorded. Seventy-four physically functional COVID-19 inpatients at discharge and sixty-eight controls underwent a Go/No-go computerized visual attentional test (CVAT). A Multivariate Analysis of Covariance (MANCOVA) was performed to examine group differences in attentional performance. To discriminate which attention subdomain deficits discriminated GIS and NGIS COVID-19 patients from healthy controls, a discriminant analysis was applied using the CVAT variables. The MANCOVA showed a significant overall effect of COVID-19 with GIS on attention performance. The discriminant analysis indicated that the GIS group could be differentiated from the controls by variability of reaction time and omissions errors. The NGIS group could be differentiated from controls by reaction time. Late attention deficits in COVID-19 patients with GIS may reflect a primary problem in the sustained and focused attention subsystems, whereas in NGIS patients the attention problems are related to the intrinsic-alertness subsystem.
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Affiliation(s)
- Juliana Schmidt
- Postgraduate Neurology Department of Neurology, Federal University of the State of Rio de Janeiro, Rio de Janeiro 202709001, Brazil
| | - Maria Cruz
- Postgraduate Neurology Department of Neurology, Federal University of the State of Rio de Janeiro, Rio de Janeiro 202709001, Brazil
| | - Julio Tolentino
- Postgraduate Neurology Department of Neurology, Federal University of the State of Rio de Janeiro, Rio de Janeiro 202709001, Brazil
| | - Aureo Carmo
- Postgraduate Neurology Department of Neurology, Federal University of the State of Rio de Janeiro, Rio de Janeiro 202709001, Brazil
| | - Maria Paes
- Postgraduate Neurology Department of Neurology, Federal University of the State of Rio de Janeiro, Rio de Janeiro 202709001, Brazil
| | - Glenda de Lacerda
- Postgraduate Neurology Department of Neurology, Federal University of the State of Rio de Janeiro, Rio de Janeiro 202709001, Brazil
| | - Ana Gjorup
- Postgraduate Neurology Department of Neurology, Federal University of the State of Rio de Janeiro, Rio de Janeiro 202709001, Brazil
| | - Sergio Schmidt
- Postgraduate Neurology Department of Neurology, Federal University of the State of Rio de Janeiro, Rio de Janeiro 202709001, Brazil
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Alsayed AR, Abed A, Khader HA, Al-Shdifat LMH, Hasoun L, Al-Rshaidat MMD, Alkhatib M, Zihlif M. Molecular Accounting and Profiling of Human Respiratory Microbial Communities: Toward Precision Medicine by Targeting the Respiratory Microbiome for Disease Diagnosis and Treatment. Int J Mol Sci 2023; 24:4086. [PMID: 36835503 PMCID: PMC9966333 DOI: 10.3390/ijms24044086] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/05/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
The wide diversity of microbiota at the genera and species levels across sites and individuals is related to various causes and the observed differences between individuals. Efforts are underway to further understand and characterize the human-associated microbiota and its microbiome. Using 16S rDNA as a genetic marker for bacterial identification improved the detection and profiling of qualitative and quantitative changes within a bacterial population. In this light, this review provides a comprehensive overview of the basic concepts and clinical applications of the respiratory microbiome, alongside an in-depth explanation of the molecular targets and the potential relationship between the respiratory microbiome and respiratory disease pathogenesis. The paucity of robust evidence supporting the correlation between the respiratory microbiome and disease pathogenesis is currently the main challenge for not considering the microbiome as a novel druggable target for therapeutic intervention. Therefore, further studies are needed, especially prospective studies, to identify other drivers of microbiome diversity and to better understand the changes in the lung microbiome along with the potential association with disease and medications. Thus, finding a therapeutic target and unfolding its clinical significance would be crucial.
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Affiliation(s)
- Ahmad R. Alsayed
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Anas Abed
- Pharmacological and Diagnostic Research Centre, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 11931, Jordan
| | - Heba A. Khader
- Department of Clinical Pharmacy and Pharmacy Practice, Faculty of Pharmaceutical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Laith M. H. Al-Shdifat
- Department of Pharmaceutical Chemistry and Pharmacognosy, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Luai Hasoun
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931, Jordan
| | - Mamoon M. D. Al-Rshaidat
- Laboratory for Molecular and Microbial Ecology (LaMME), Department of Biological Sciences, School of Sciences, The University of Jordan, Amman 11942, Jordan
| | - Mohammad Alkhatib
- Department of Experimental Medicine, University of Rome “Tor Vergata”, 00133 Roma, Italy
| | - Malek Zihlif
- Department of Pharmacology, School of Medicine, The University of Jordan, Amman 11942, Jordan
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Rosas-Salazar C, Kimura KS, Shilts MH, Strickland BA, Freeman MH, Wessinger BC, Gupta V, Brown HM, Boone HH, Rajagopala SV, Turner JH, Das SR. Upper respiratory tract microbiota dynamics following COVID-19 in adults. Microb Genom 2023; 9:mgen000957. [PMID: 36820832 PMCID: PMC9997743 DOI: 10.1099/mgen.0.000957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
To date, little is known about the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic, on the upper respiratory tract (URT) microbiota over time. To fill this knowledge gap, we used 16S ribosomal RNA gene sequencing to characterize the URT microbiota in 48 adults, including (1) 24 participants with mild-to-moderate COVID-19 who had serial mid-turbinate swabs collected up to 21 days after enrolment and (2) 24 asymptomatic, uninfected controls who had mid-turbinate swabs collected at enrolment only. To compare the URT microbiota between groups in a comprehensive manner, different types of statistical analyses that are frequently employed in microbial ecology were used, including ⍺-diversity, β-diversity and differential abundance analyses. Final statistical models included age, sex and the presence of at least one comorbidity as covariates. The median age of all participants was 34.00 (interquartile range=28.75-46.50) years. In comparison to samples from controls, those from participants with COVID-19 had a lower observed species index at day 21 (linear regression coefficient=-13.30; 95 % CI=-21.72 to -4.88; q=0.02). In addition, the Jaccard index was significantly different between samples from participants with COVID-19 and those from controls at all study time points (PERMANOVA q<0.05 for all comparisons). The abundance of three amplicon sequence variants (ASVs) (one Corynebacterium ASV, Frederiksenia canicola, and one Lactobacillus ASV) were decreased in samples from participants with COVID-19 at all seven study time points, whereas the abundance of one ASV (from the family Neisseriaceae) was increased in samples from participants with COVID-19 at five (71.43 %) of the seven study time points. Our results suggest that mild-to-moderate COVID-19 can lead to alterations of the URT microbiota that persist for several weeks after the initial infection.
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Affiliation(s)
- Christian Rosas-Salazar
- Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kyle S Kimura
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Meghan H Shilts
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Britton A Strickland
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Michael H Freeman
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Veerain Gupta
- Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Hunter M Brown
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Helen H Boone
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Seesandra V Rajagopala
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Justin H Turner
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Suman Ranjan Das
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Kim JG, Zhang A, Rauseo AM, Goss CW, Mudd PA, O'Halloran JA, Wang L. The salivary and nasopharyngeal microbiomes are associated with SARS-CoV-2 infection and disease severity. J Med Virol 2023; 95:e28445. [PMID: 36583481 PMCID: PMC9880756 DOI: 10.1002/jmv.28445] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/15/2022] [Accepted: 12/26/2022] [Indexed: 12/31/2022]
Abstract
Emerging evidence suggests the oral and upper respiratory microbiota may play important roles in modulating host immune responses to viral infection. As the host microbiome may be involved in the pathophysiology of coronavirus disease 2019 (COVID-19), we investigated associations between the oral and nasopharyngeal microbiome and COVID-19 severity. We collected saliva (n = 78) and nasopharyngeal swab (n = 66) samples from a COVID-19 cohort and characterized the microbiomes using 16S ribosomal RNA gene sequencing. We also examined associations between the salivary and nasopharyngeal microbiome and age, COVID-19 symptoms, and blood cytokines. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection status, but not COVID-19 severity, was associated with community-level differences in the oral and nasopharyngeal microbiomes. Salivary and nasopharyngeal microbiome alpha diversity negatively correlated with age and were associated with fever and diarrhea. Oral Bifidobacterium, Lactobacillus, and Solobacterium were depleted in patients with severe COVID-19. Nasopharyngeal Paracoccus was depleted while nasopharyngeal Proteus, Cupravidus, and Lactobacillus were increased in patients with severe COVID-19. Further analysis revealed that the abundance of oral Bifidobacterium was negatively associated with plasma concentrations of known COVID-19 biomarkers interleukin 17F and monocyte chemoattractant protein-1. Our results suggest COVID-19 disease severity is associated with the relative abundance of certain bacterial taxa.
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Affiliation(s)
- Josh G. Kim
- Department of Medicine, Division of Allergy and ImmunologyWashington University School of MedicineSt. LouisMissouriUSA
| | - Ai Zhang
- Department of Medicine, Division of Allergy and ImmunologyWashington University School of MedicineSt. LouisMissouriUSA
| | - Adriana M. Rauseo
- Department of Medicine, Division of Infectious DiseasesWashington University School of MedicineSt. LouisMissouriUSA
| | - Charles W. Goss
- Division of BiostatisticsWashington University School of MedicineSt. LouisMissouriUSA
| | - Philip A. Mudd
- Department of Emergency MedicineWashington University School of MedicineSt. LouisMissouriUSA
| | - Jane A. O'Halloran
- Department of Medicine, Division of Infectious DiseasesWashington University School of MedicineSt. LouisMissouriUSA
| | - Leyao Wang
- Department of Medicine, Division of Allergy and ImmunologyWashington University School of MedicineSt. LouisMissouriUSA
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Pathinayake PS, Awatade NT, Wark PAB. Type 2 Immunity and Its Impact on COVID-19 Infection in the Airways. Viruses 2023; 15:402. [PMID: 36851616 PMCID: PMC9967553 DOI: 10.3390/v15020402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/17/2023] [Accepted: 01/28/2023] [Indexed: 02/04/2023] Open
Abstract
Type 2 immune responses are characterized by elevated type 2 cytokines and blood eosinophilia. Emerging evidence suggests that people with chronic type 2 inflammatory lung diseases are not particularly susceptible to SARS-CoV-2 infection. Intriguingly, recent in vitro, ex vivo research demonstrates type 2 cytokines, particularly IL-13, reduce the risk of SARS-CoV-2 infection in the airway epithelium. IL-13 treatment in airway epithelial cells followed by SARS-CoV-2 diminished viral entry, replication, spread, and cell death. IL-13 reduces the expression of the angiotensin-converting enzyme 2 (ACE2) receptor in the airway epithelium and transmembrane serine protease 2 (TMPRSS2), particularly in ciliated cells. It also alters the cellular composition toward a secretory-cell-rich phenotype reducing total ciliated cells and, thus, reducing viral tropism. IL-13 enhances Muc5ac mucin and glycocalyx secretion in the periciliary layer, which acts as a physical barrier to restrict virus attachment. Moreover, type 2 airway immune cells, such as M2 alveolar macrophages, CD4+ tissue-resident memory T cells, and innate lymphoid 2 cells, may also rescue type 2 airways from SARS-CoV-2-induced adverse effects. In this review, we discuss recent findings that demonstrate how type 2 immunity alters immune responses against SARS-CoV-2 and its consequences on COVID-19 pathogenesis.
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Affiliation(s)
- Prabuddha S. Pathinayake
- School of Medicine and Public Health, The University of Newcastle and Immune Health Program Hunter Medical Research Institute, Newcastle, NSW 2308, Australia
| | - Nikhil T. Awatade
- School of Medicine and Public Health, The University of Newcastle and Immune Health Program Hunter Medical Research Institute, Newcastle, NSW 2308, Australia
| | - Peter A. B. Wark
- School of Medicine and Public Health, The University of Newcastle and Immune Health Program Hunter Medical Research Institute, Newcastle, NSW 2308, Australia
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, New Lambton Heights, NSW 2305, Australia
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SeyedAlinaghi S, Afzalian A, Pashaei Z, Varshochi S, Karimi A, Mojdeganlou H, Mojdeganlou P, Razi A, Ghanadinezhad F, Shojaei A, Amiri A, Dashti M, Ghasemzadeh A, Dadras O, Mehraeen E, Afsahi AM. Gut microbiota and COVID-19: A systematic review. Health Sci Rep 2023; 6:e1080. [PMID: 36721396 PMCID: PMC9881458 DOI: 10.1002/hsr2.1080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/24/2022] [Accepted: 01/11/2023] [Indexed: 01/28/2023] Open
Abstract
Background and Aims Alteration in humans' gut microbiota was reported in patients infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The gut and upper respiratory tract (URT) microbiota harbor a dynamic and complex population of microorganisms and have strong interaction with host immune system homeostasis. However, our knowledge about microbiota and its association with SARS-CoV-2 is still limited. We aimed to systematically review the effects of gut microbiota on the SARS-CoV-2 infection and its severity and the impact that SARS-CoV-2 could have on the gut microbiota. Methods We searched the keywords in the online databases of Web of Science, Scopus, PubMed, and Cochrane on December 31, 2021. After duplicate removal, we performed the screening process in two stages; title/abstract and then full-text screening. The data of the eligible studies were extracted into a pre-designed word table. This study adhered to the PRISMA checklist and Newcastle-Ottawa Scale Bias Assessment tool. Results Sixty-three publications were included in this review. Our study shows that among COVID-19 patients, particularly moderate to severe cases, the gut and lung microbiota was different compared to healthy individuals. In addition, the severity, and viral load of COVID-19 disease would probably also be influenced by the gut, and lung microbiota's composition. Conclusion Our study concludes that there was a significant difference in the composition of the URT, and gut microbiota in COVID-19 patients compared to the general healthy individuals, with an increase in opportunistic pathogens. Further, research is needed to investigate the probable bidirectional association of COVID-19 and human microbiome.
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Affiliation(s)
- SeyedAhmad SeyedAlinaghi
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Arian Afzalian
- School of MedicineTehran University of Medical SciencesTehranIran
| | - Zahra Pashaei
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Sanaz Varshochi
- School of MedicineTehran University of Medical SciencesTehranIran
| | - Amirali Karimi
- School of MedicineTehran University of Medical SciencesTehranIran
| | | | | | - Armin Razi
- School of MedicineTehran University of Medical SciencesTehranIran
| | | | - Alireza Shojaei
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Ava Amiri
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Mohsen Dashti
- Department of RadiologyTabriz University of Medical SciencesTabrizIran
| | | | - Omid Dadras
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran,Department of Global Public Health and Primary CareUniversity of BergenBergenNorway
| | - Esmaeil Mehraeen
- Department of Health Information TechnologyKhalkhal University of Medical SciencesKhalkhalIran
| | - Amir Masoud Afsahi
- Department of RadiologyUniversity of California, San Diego (UCSD)CaliforniaUSA
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Lane S, Hilliam Y, Bomberger JM. Microbial and Immune Regulation of the Gut-Lung Axis during Viral-Bacterial Coinfection. J Bacteriol 2023; 205:e0029522. [PMID: 36409130 PMCID: PMC9879096 DOI: 10.1128/jb.00295-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Viral-bacterial coinfections of the respiratory tract have long been associated with worsened disease outcomes. Clinical and basic research studies demonstrate that these infections are driven via complex interactions between the infecting pathogens, microbiome, and host immune response, although how these interactions contribute to disease progression is still not fully understood. Research over the last decade shows that the gut has a significant role in mediating respiratory outcomes, in a phenomenon known as the "gut-lung axis." Emerging literature demonstrates that acute respiratory viruses can modulate the gut-lung axis, suggesting that dysregulation of gut-lung cross talk may be a contributing factor during respiratory coinfection. This review will summarize the current literature regarding modulation of the gut-lung axis during acute respiratory infection, with a focus on the role of the microbiome, secondary infections, and the host immune response.
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Affiliation(s)
- Sidney Lane
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yasmin Hilliam
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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35
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Keeler EL, Merenstein C, Reddy S, Taylor LJ, Cobián-Güemes AG, Zankharia U, Collman RG, Bushman FD. Widespread, human-associated redondoviruses infect the commensal protozoan Entamoeba gingivalis. Cell Host Microbe 2023; 31:58-68.e5. [PMID: 36459997 PMCID: PMC9969835 DOI: 10.1016/j.chom.2022.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/05/2022] [Accepted: 11/04/2022] [Indexed: 12/03/2022]
Abstract
Redondoviruses are circular Rep-encoding single-stranded DNA (CRESS) viruses of high prevalence in healthy humans. Redondovirus abundance is increased in oro-respiratory samples from individuals with periodontitis, acute illness, and severe COVID-19. We investigated potential host cells supporting redondovirus replication in oro-respiratory samples and uncovered the oral amoeba Entamoeba gingivalis as a likely host. Redondoviruses are closely related to viruses of Entamoeba and contain reduced GC nucleotide content, consistent with Entamoeba hosts. Redondovirus and E. gingivalis co-occur in metagenomic data from oral disease and healthy human cohorts. When grown in xenic cultures with feeder bacteria, E. gingivalis was robustly positive for redondovirus RNA and DNA. A DNA proximity-ligation assay (Hi-C) on xenic culture cells showed enriched cross-linking of redondovirus and Entamoeba DNA, supporting E. gingivalis as the redondovirus host. While bacteria are established hosts for bacteriophages within the human virome, this work shows that eukaryotic commensals also contribute an abundant human-associated virus.
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Affiliation(s)
- Emma L Keeler
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Carter Merenstein
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Shantan Reddy
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Louis J Taylor
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ana G Cobián-Güemes
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Urvi Zankharia
- Department of Medicine, Pulmonary, Allergy and Critical Care Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ronald G Collman
- Department of Medicine, Pulmonary, Allergy and Critical Care Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Mancabelli L, Ciociola T, Lugli GA, Tarracchini C, Fontanta F, Viappiani A, Turroni F, Ticinesi A, Meschi T, Conti S, Ventura M, Milani C. Guideline for the analysis of the microbial communities of the human upper airways. J Oral Microbiol 2022; 14:2103282. [PMID: 35923899 PMCID: PMC9341376 DOI: 10.1080/20002297.2022.2103282] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Leonardo Mancabelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Tecla Ciociola
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Chiara Tarracchini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontanta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Francesca Turroni
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Andrea Ticinesi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Geriatric-Rehabilitation Department, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Tiziana Meschi
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Geriatric-Rehabilitation Department, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Stefania Conti
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Marco Ventura
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Christian Milani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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Lai CKC, Cheung MK, Lui GCY, Ling L, Chan JYK, Ng RWY, Chan HC, Yeung ACM, Ho WCS, Boon SS, Chan PKS, Chen Z. Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients. Microbiol Spectr 2022; 10:e0219622. [PMID: 36350127 PMCID: PMC9769582 DOI: 10.1128/spectrum.02196-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 10/13/2022] [Indexed: 11/11/2022] Open
Abstract
Numerous studies have reported dysbiosis in the naso- and/or oro-pharyngeal microbiota of COVID-19 patients compared with healthy individuals; however, only a few small-scale studies have also included a disease control group. In this study, we characterized and compared the bacterial communities of pooled nasopharyngeal and throat swabs from hospitalized COVID-19 patients (n = 76), hospitalized non-COVID-19 patients with respiratory symptoms or related illnesses (n = 69), and local community controls (n = 76) using 16S rRNA gene V3-V4 amplicon sequencing. None of the subjects received antimicrobial therapy within 2 weeks prior to sample collection. Both COVID-19 and non-COVID-19 hospitalized patients differed in the composition, alpha and beta diversity, and metabolic potential of the naso-oropharyngeal microbiota compared with local controls. However, the microbial communities in the two hospitalized patient groups did not differ significantly from each other. Differential abundance analysis revealed the enrichment of nine bacterial genera in the COVID-19 patients compared with local controls; however, six of them were also enriched in the non-COVID-19 patients. Bacterial genera uniquely enriched in the COVID-19 patients included Alloprevotella and Solobacterium. In contrast, Mogibacterium and Lactococcus were dramatically decreased in COVID-19 patients only. Association analysis revealed that Alloprevotella in COVID-19 patients was positively correlated with the level of the inflammation biomarker C-reactive protein. Our findings reveal a limited impact of SARS-CoV-2 on the naso-oropharyngeal microbiota in hospitalized patients and suggest that Alloprevotella and Solobacterium are more specific biomarkers for COVID-19 detection. IMPORTANCE Our results showed that while both COVID-19 and non-COVID-19 hospitalized patients differed in the composition, alpha and beta diversity, and metabolic potential of the naso-oropharyngeal microbiota compared with local controls, the microbial communities in the two hospitalized patient groups did not differ significantly from each other, indicating a limited impact of SARS-CoV-2 on the naso-oropharyngeal microbiota in hospitalized patients. Besides, we identified Alloprevotella and Solobacterium as bacterial genera uniquely enriched in COVID-19 patients, which may serve as more specific biomarkers for COVID-19 detection.
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Affiliation(s)
- Christopher K. C. Lai
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Man Kit Cheung
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Grace C. Y. Lui
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lowell Ling
- Department of Anaesthesia and Intensive Care, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jason Y. K. Chan
- Department of Otorhinolaryngology, Head and Neck Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR China
| | - Rita W. Y. Ng
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hiu Ching Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Apple C. M. Yeung
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wendy C. S. Ho
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Siaw Shi Boon
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Paul K. S. Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
- Stanley Ho Centre for Emerging Infectious Diseases, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
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38
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Li W, Ma ZS. The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2. MICROBIAL ECOLOGY 2022:1-10. [PMID: 36509943 PMCID: PMC9744668 DOI: 10.1007/s00248-022-02148-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/12/2022] [Indexed: 06/17/2023]
Abstract
The microbiome of upper respiratory tract (URT) acts as a gatekeeper to respiratory health of the host. However, little is still known about the impacts of SARS-CoV-2 infection on the microbial species composition and co-occurrence correlations of the URT microbiome, especially the relationships between SARS-CoV-2 and other microbes. Here, we characterized the URT microbiome based on RNA metagenomic-sequencing datasets from 1737 nasopharyngeal samples collected from COVID-19 patients. The URT-microbiome network consisting of bacteria, archaea, and RNA viruses was built and analyzed from aspects of core/periphery species, cluster composition, and balance between positive and negative interactions. It is discovered that the URT microbiome in the COVID-19 patients is enriched with Enterobacteriaceae, a gut associated family containing many pathogens. These pathogens formed a dense cooperative guild that seemed to suppress beneficial microbes collectively. Besides bacteria and archaea, 72 eukaryotic RNA viruses were identified in the URT microbiome of COVID-19 patients. Only five of these viruses were present in more than 10% of all samples, including SARS-CoV-2 and a bat coronavirus (i.e., BatCoV BM48-31) not detected in humans by routine means. SARS-CoV-2 was inhibited by a cooperative alliance of 89 species, but seems to cooperate with BatCoV BM48-31 given their statistically significant, positive correlations. The presence of cooperative bat-coronavirus partner of SARS-CoV-2 (BatCoV BM48-31), which was previously discovered in bat but not in humans to the best of our knowledge, is puzzling and deserves further investigation given their obvious implications. Possible microbial translocation mechanism from gut to URT also deserves future studies.
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Affiliation(s)
- Wendy Li
- Computational Biology and Medical Ecology Lab, State Key Laboratory for Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- College of Biological Sciences and Technology, Taiyuan Normal University, Taiyuan, China
| | - Zhanshan Sam Ma
- Computational Biology and Medical Ecology Lab, State Key Laboratory for Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, China.
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Analysis of bronchoalveolar lavage fluid metatranscriptomes among patients with COVID-19 disease. Sci Rep 2022; 12:21125. [PMID: 36476670 PMCID: PMC9729217 DOI: 10.1038/s41598-022-25463-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
To better understand the potential relationship between COVID-19 disease and hologenome microbial community dynamics and functional profiles, we conducted a multivariate taxonomic and functional microbiome comparison of publicly available human bronchoalveolar lavage fluid (BALF) metatranscriptome samples amongst COVID-19 (n = 32), community acquired pneumonia (CAP) (n = 25), and uninfected samples (n = 29). We then performed a stratified analysis based on mortality amongst the COVID-19 cohort with known outcomes of deceased (n = 10) versus survived (n = 15). Our overarching hypothesis was that there are detectable and functionally significant relationships between BALF microbial metatranscriptomes and the severity of COVID-19 disease onset and progression. We observed 34 functionally discriminant gene ontology (GO) terms in COVID-19 disease compared to the CAP and uninfected cohorts, and 21 GO terms functionally discriminant to COVID-19 mortality (q < 0.05). GO terms enriched in the COVID-19 disease cohort included hydrolase activity, and significant GO terms under the parental terms of biological regulation, viral process, and interspecies interaction between organisms. Notable GO terms associated with COVID-19 mortality included nucleobase-containing compound biosynthetic process, organonitrogen compound catabolic process, pyrimidine-containing compound biosynthetic process, and DNA recombination, RNA binding, magnesium and zinc ion binding, oxidoreductase activity, and endopeptidase activity. A Dirichlet multinomial mixtures clustering analysis resulted in a best model fit using three distinct clusters that were significantly associated with COVID-19 disease and mortality. We additionally observed discriminant taxonomic differences associated with COVID-19 disease and mortality in the genus Sphingomonas, belonging to the Sphingomonadacae family, Variovorax, belonging to the Comamonadaceae family, and in the class Bacteroidia, belonging to the order Bacteroidales. To our knowledge, this is the first study to evaluate significant differences in taxonomic and functional signatures between BALF metatranscriptomes from COVID-19, CAP, and uninfected cohorts, as well as associating these taxa and microbial gene functions with COVID-19 mortality. Collectively, while this data does not speak to causality nor directionality of the association, it does demonstrate a significant relationship between the human microbiome and COVID-19. The results from this study have rendered testable hypotheses that warrant further investigation to better understand the causality and directionality of host-microbiome-pathogen interactions.
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Zhu T, Jin J, Chen M, Chen Y. The impact of infection with COVID-19 on the respiratory microbiome: A narrative review. Virulence 2022; 13:1076-1087. [PMID: 35763685 PMCID: PMC9794016 DOI: 10.1080/21505594.2022.2090071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has affected millions of individuals with various implications. Consistent with the crucial role of the microbiome in determining health and disease in humans, various studies have investigated the gut and respiratory microbiome effect on the COVID-19. Microbiota dysbiosis might support the entry, replication, and establishment of SARS-CoV-2 infection by modulating various mechanisms. One of the main mechanisms that the modulation of respiratory microbiota composition during the COVID-19 infection affects the magnitude of the disease is changes in innate and acquired immune responses, including inflammatory markers and cytokines and B- and T-cells. The diversity of respiratory microbiota in COVID-19 patients is controversial; some studies reported low microbial diversity, while others found high diversity, suggesting the role of respiratory microbiota in this disease. Modulating microbiota diversity and profile by supplementations and nutrients can be applied prophylactic and therapeutic in combating COVID-19. Here, we discussed the lung microbiome dysbiosis during various lung diseases and its interaction with immune cells, focusing on COVID-19.
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Affiliation(s)
- Taiping Zhu
- Internal Medicine Department, Chun’an Maternal and Child Health Hospital, Hangzhou, Zhejiang, China
| | - Jun Jin
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital Hangzhou Medical College), Hangzhou, Zhejiang, China
| | - Minhua Chen
- Emergency and Critical Care Center, Intensive Care Unit, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital Hangzhou Medical College), Hangzhou, Zhejiang, China,CONTACT Minhua Chen
| | - Yingjun Chen
- Department of Infectious Diseases, Tiantai People’s Hospital of Zhejiang Province (Tiantai Branch of Zhejiang People’s Hospital), Taizhou, Zhejiang, China
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Kim JG, Zhang A, Rauseo AM, Goss CW, Mudd PA, O’Halloran JA, Wang L. The nasopharyngeal and salivary microbiomes in COVID-19 patients with and without asthma. Allergy 2022; 77:3676-3679. [PMID: 35837881 PMCID: PMC9350136 DOI: 10.1111/all.15438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 06/19/2022] [Accepted: 07/11/2022] [Indexed: 01/28/2023]
Affiliation(s)
- Josh G. Kim
- Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Ai Zhang
- Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Adriana M. Rauseo
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Charles W. Goss
- Division of Biostatistics, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Philip A. Mudd
- Department of Emergency Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Jane A. O’Halloran
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
| | - Leyao Wang
- Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri
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Detection of Torquetenovirus and Redondovirus DNA in Saliva Samples from SARS-CoV-2-Positive and -Negative Subjects. Viruses 2022; 14:v14112482. [PMID: 36366580 PMCID: PMC9695164 DOI: 10.3390/v14112482] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/04/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
OBJECTIVES Torquetenovirus (TTV) and Redondovirus (ReDoV) are the most prevalent viruses found in the human respiratory virome in viral metagenomics studies. A large-scale epidemiological study was performed to investigate their prevalence and loads in saliva samples according to SARS-CoV-2 status. METHODS Saliva samples from 448 individuals (73% SARS-CoV-2 negative and 27% SARS-CoV-2 positive) aged 23-88 years were tested. SARS-CoV-2 and TTV were determined in saliva by specific qualitative and quantitative real-time PCRs, respectively. A sub-cohort of 377 subjects was additionally tested for the presence and load of ReDoV in saliva, and a different sub-cohort of 120 subjects for which paired saliva and plasma samples were available was tested for TTV and ReDoV viremia at the same timepoints as saliva. RESULTS TTV in saliva was 72% prevalent in the entire cohort, at a mean DNA load of 4.6 log copies/mL, with no difference regardless of SARS-CoV-2 status. ReDoV was found in saliva from 61% of the entire cohort and was more prevalent in the SARS-CoV-2-negative subgroup (65% vs. 52%, respectively). In saliva, the total mean load of ReDoV was very similar to the one of TTV, with a value of 4.4 log copies/mL. The mean viral loads in subjects infected with a single virus, namely, those infected with TTV or ReDoV alone, was lower than in dually infected samples, and Tukey's multiple-comparison test showed that ReDoV single-infected samples resulted in the only true outlier (p = 0.004). Differently from TTV, ReDoV was not detected in any blood samples. CONCLUSIONS This study establishes the prevalence and mean value of TTV and ReDoV in saliva samples and demonstrates the existence of differences between these two components of the human virome.
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Chen J, Liu X, Liu W, Yang C, Jia R, Ke Y, Guo J, Jia L, Wang C, Chen Y. Comparison of the respiratory tract microbiome in hospitalized COVID-19 patients with different disease severity. J Med Virol 2022; 94:5284-5293. [PMID: 35838111 PMCID: PMC9349541 DOI: 10.1002/jmv.28002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 12/15/2022]
Abstract
Little is known about the characteristics of respiratory tract microbiome in Coronavirus disease 2019 (COVID-19) inpatients with different severity. We conducted a study that expected to clarify these characteristics as much as possible. A cross-sectional study was conducted to characterize respiratory tract microbial communities of 69 COVID-19 inpatients from 64 nasopharyngeal swabs and 5 sputum specimens using 16S ribosomal RNA gene V3-V4 region sequencing. The bacterial profiles were analyzed to find potential biomarkers by the two-step method, the combination of random forest model and the linear discriminant analysis effect size, and explore the connections with clinical characteristics by Spearman's rank test. Compared with mild COVID-19 patients, severe patients had significantly decreased bacterial diversity (p-values were less than 0.05 in the alpha and beta diversity) and relative lower abundance of opportunistic pathogens, including Actinomyces, Prevotella, Rothia, Streptococcus, Veillonella. Eight potential biomarkers including Treponema, Leptotrichia, Lachnoanaerobaculum, Parvimonas, Alloprevotella, Porphyromonas, Gemella, and Streptococcus were found to distinguish the mild COVID-19 patients from the severe COVID-19 patients. The genera of Actinomyces and Prevotella were negatively correlated with age in two groups. Intensive care unit admission, neutrophil count, and lymphocyte count were significantly correlated with different genera in the two groups. In addition, there was a positive correlation between Klebsiella and white blood cell count in two groups. The respiratory tract microbiome had significant differences in COVID-19 patients with different severity. The value of the respiratory tract microbiome as predictive biomarkers for COVID-19 severity deserves further exploration.
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Affiliation(s)
- Jiali Chen
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
- School of Public HealthChina Medical UniversityShenyangChina
| | - Xiong Liu
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
| | - Wei Liu
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
| | - Chaojie Yang
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
| | - Ruizhong Jia
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
| | - Yuehua Ke
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
| | - Jinpeng Guo
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
| | - Leili Jia
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
| | - Changjun Wang
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
| | - Yong Chen
- Department of Emergency ResponseChinese PLA Center for Disease Control and PreventionBeijingChina
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44
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Merenstein C, Bushman FD, Collman RG. Alterations in the respiratory tract microbiome in COVID-19: current observations and potential significance. MICROBIOME 2022; 10:165. [PMID: 36195943 PMCID: PMC9532226 DOI: 10.1186/s40168-022-01342-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/02/2022] [Indexed: 06/16/2023]
Abstract
SARS-CoV-2 infection causes COVID-19 disease, which can result in consequences ranging from undetectable to fatal, focusing attention on the modulators of outcomes. The respiratory tract microbiome is thought to modulate the outcomes of infections such as influenza as well as acute lung injury, raising the question to what degree does the airway microbiome influence COVID-19? Here, we review the results of 56 studies examining COVID-19 and the respiratory tract microbiome, summarize the main generalizations, and point to useful avenues for further research. Although the results vary among studies, a few consistent findings stand out. The diversity of bacterial communities in the oropharynx typically declined with increasing disease severity. The relative abundance of Haemophilus and Neisseria also declined with severity. Multiple microbiome measures tracked with measures of systemic immune responses and COVID outcomes. For many of the conclusions drawn in these studies, the direction of causality is unknown-did an alteration in the microbiome result in increased COVID severity, did COVID severity alter the microbiome, or was some third factor the primary driver, such as medication use. Follow-up mechanistic studies can help answer these questions. Video Abstract.
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Affiliation(s)
- Carter Merenstein
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Ronald G. Collman
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104 USA
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Kullberg RFJ, de Brabander J, Boers LS, Biemond JJ, Nossent EJ, Heunks LMA, Vlaar APJ, Bonta PI, van der Poll T, Duitman J, Bos LDJ, Wiersinga WJ. Lung Microbiota of Critically Ill Patients with COVID-19 Are Associated with Nonresolving Acute Respiratory Distress Syndrome. Am J Respir Crit Care Med 2022; 206:846-856. [PMID: 35616585 PMCID: PMC9799265 DOI: 10.1164/rccm.202202-0274oc] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Rationale: Bacterial lung microbiota are correlated with lung inflammation and acute respiratory distress syndrome (ARDS) and altered in severe coronavirus disease (COVID-19). However, the association between lung microbiota (including fungi) and resolution of ARDS in COVID-19 remains unclear. We hypothesized that increased lung bacterial and fungal burdens are related to nonresolving ARDS and mortality in COVID-19. Objectives: To determine the relation between lung microbiota and clinical outcomes of COVID-19-related ARDS. Methods: This observational cohort study enrolled mechanically ventilated patients with COVID-19. All patients had ARDS and underwent bronchoscopy with BAL. Lung microbiota were profiled using 16S rRNA gene sequencing and quantitative PCR targeting the 16S and 18S rRNA genes. Key features of lung microbiota (bacterial and fungal burden, α-diversity, and community composition) served as predictors. Our primary outcome was successful extubation adjudicated 60 days after intubation, analyzed using a competing risk regression model with mortality as competing risk. Measurements and Main Results: BAL samples of 114 unique patients with COVID-19 were analyzed. Patients with increased lung bacterial and fungal burden were less likely to be extubated (subdistribution hazard ratio, 0.64 [95% confidence interval, 0.42-0.97]; P = 0.034 and 0.59 [95% confidence interval, 0.42-0.83]; P = 0.0027 per log10 increase in bacterial and fungal burden, respectively) and had higher mortality (bacterial burden, P = 0.012; fungal burden, P = 0.0498). Lung microbiota composition was associated with successful extubation (P = 0.0045). Proinflammatory cytokines (e.g., tumor necrosis factor-α) were associated with the microbial burdens. Conclusions: Bacterial and fungal lung microbiota are related to nonresolving ARDS in COVID-19 and represent an important contributor to heterogeneity in COVID-19-related ARDS.
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Affiliation(s)
| | | | - Leonoor S. Boers
- Department of Intensive Care Medicine,,Laboratory of Experimental Intensive Care and Anesthesiology
| | | | | | | | - Alexander P. J. Vlaar
- Department of Intensive Care Medicine,,Laboratory of Experimental Intensive Care and Anesthesiology
| | | | - Tom van der Poll
- Center for Experimental and Molecular Medicine,,Division of Infectious Diseases, and
| | - JanWillem Duitman
- Department of Pulmonary Medicine,,Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Lieuwe D. J. Bos
- Department of Intensive Care Medicine,,Laboratory of Experimental Intensive Care and Anesthesiology,,Department of Pulmonary Medicine
| | - W. Joost Wiersinga
- Center for Experimental and Molecular Medicine,,Division of Infectious Diseases, and
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46
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Bencze D, Fekete T, Pázmándi K. Correlation between Type I Interferon Associated Factors and COVID-19 Severity. Int J Mol Sci 2022; 23:ijms231810968. [PMID: 36142877 PMCID: PMC9506204 DOI: 10.3390/ijms231810968] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 11/18/2022] Open
Abstract
Antiviral type I interferons (IFN) produced in the early phase of viral infections effectively inhibit viral replication, prevent virus-mediated tissue damages and promote innate and adaptive immune responses that are all essential to the successful elimination of viruses. As professional type I IFN producing cells, plasmacytoid dendritic cells (pDC) have the ability to rapidly produce waste amounts of type I IFNs. Therefore, their low frequency, dysfunction or decreased capacity to produce type I IFNs might increase the risk of severe viral infections. In accordance with that, declined pDC numbers and delayed or inadequate type I IFN responses could be observed in patients with severe coronavirus disease (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as compared to individuals with mild or no symptoms. Thus, besides chronic diseases, all those conditions, which negatively affect the antiviral IFN responses lengthen the list of risk factors for severe COVID-19. In the current review, we would like to briefly discuss the role and dysregulation of pDC/type I IFN axis in COVID-19, and introduce those type I IFN-dependent factors, which account for an increased risk of COVID-19 severity and thus are responsible for the different magnitude of individual immune responses to SARS-CoV-2.
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Affiliation(s)
- Dóra Bencze
- Department of Immunology, Faculty of Medicine, University of Debrecen, 1 Egyetem Square, H-4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 1 Egyetem Square, H-4032 Debrecen, Hungary
| | - Tünde Fekete
- Department of Immunology, Faculty of Medicine, University of Debrecen, 1 Egyetem Square, H-4032 Debrecen, Hungary
| | - Kitti Pázmándi
- Department of Immunology, Faculty of Medicine, University of Debrecen, 1 Egyetem Square, H-4032 Debrecen, Hungary
- Correspondence: ; Tel./Fax: +36-52-417-159
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Li X, Tu B, Zhang X, Xu W, Chen J, Xu B, Zheng J, Hao P, Cole R, Jalloh MB, Lu Q, Li C, Sevalie S, Liu W, Chen W. Dysregulation of glutamine/glutamate metabolism in COVID-19 patients: A metabolism study in African population and mini meta-analysis. J Med Virol 2022; 95:e28150. [PMID: 36112136 PMCID: PMC9538869 DOI: 10.1002/jmv.28150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/25/2022] [Accepted: 09/13/2022] [Indexed: 01/11/2023]
Abstract
Coronavirus disease 2019 (COVID-19) remains a serious global threat. The metabolic analysis had been successfully applied in the efforts to uncover the pathological mechanisms and biomarkers of disease severity. Here we performed a quasi-targeted metabolomic analysis on 56 COVID-19 patients from Sierra Leone in western Africa, revealing the metabolomic profiles and the association with disease severity, which was confirmed by the targeted metabolomic analysis of 19 pairs of COVID-19 patients. A meta-analysis was performed on published metabolic data of COVID-19 to verify our findings. Of the 596 identified metabolites, 58 showed significant differences between severe and nonsevere groups. The pathway enrichment of these differential metabolites revealed glutamine and glutamate metabolism as the most significant metabolic pathway (Impact = 0.5; -log10P = 1.959). Further targeted metabolic analysis revealed six metabolites with significant intergroup differences, with glutamine/glutamate ratio significantly associated with severe disease, negatively correlated with 10 clinical parameters and positively correlated with SPO2 (rs = 0.442, p = 0.005). Mini meta-analysis indicated elevated glutamate was related to increased risk of COVID-19 infection (pooled odd ratio [OR] = 2.02; 95% confidence interval [CI]: 1.17-3.50) and severe COVID-19 (pooled OR = 2.28; 95% CI: 1.14-4.56). In contrast, elevated glutamine related to decreased risk of infection and severe COVID-19, the pooled OR were 0.30 (95% CI: 0.20-0.44), and 0.44 (95% CI: 0.19-0.98), respectively. Glutamine and glutamate metabolism are associated with COVID-19 severity in multiple populations, which might confer potential therapeutic target of COVID-19, especially for severe patients.
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Affiliation(s)
- Xiao‐kun Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Bo Tu
- Fifth Medical Center of Chinese PLA General HospitalBeijing100039China
| | - Xiao‐Ai Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Wen Xu
- Fifth Medical Center of Chinese PLA General HospitalBeijing100039China
| | - Jia‐hao Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Biao Xu
- Fifth Medical Center of Chinese PLA General HospitalBeijing100039China
| | - Jun‐Jie Zheng
- Fifth Medical Center of Chinese PLA General HospitalBeijing100039China
| | - Peng‐fei Hao
- Department of Laboratorial Science and Technology School of Public HealthPeking University
| | - Reginald Cole
- Joint Medical Unit, Republic of Sierra Leone Armed Forces34 Military Hospital Wilberforce FreetownFreetownSierra Leone
| | - Mohamed Boie Jalloh
- Joint Medical Unit, Republic of Sierra Leone Armed Forces34 Military Hospital Wilberforce FreetownFreetownSierra Leone
| | - Qing‐bin Lu
- Department of Laboratorial Science and Technology School of Public HealthPeking University
| | - Chang Li
- Department of Laboratorial Science and Technology School of Public HealthPeking University
| | - Stephen Sevalie
- Joint Medical Unit, Republic of Sierra Leone Armed Forces34 Military Hospital Wilberforce FreetownFreetownSierra Leone
| | - Wei Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Wei‐wei Chen
- Fifth Medical Center of Chinese PLA General HospitalBeijing100039China
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48
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Costantini C, Nunzi E, Romani L. From the nose to the lungs: the intricate journey of airborne pathogens amidst commensal bacteria. Am J Physiol Cell Physiol 2022; 323:C1036-C1043. [PMID: 36036448 PMCID: PMC9529274 DOI: 10.1152/ajpcell.00287.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The recent COVID-19 pandemic has dramatically brought the pitfalls of airborne pathogens to the attention of the scientific community. Not only viruses but also bacteria and fungi may exploit air transmission to colonize and infect potential hosts and be the cause of significant morbidity and mortality in susceptible populations. The efforts to decipher the mechanisms of pathogenicity of airborne microbes have brought to light the delicate equilibrium that governs the homeostasis of mucosal membranes. The microorganisms already thriving in the permissive environment of the respiratory tract represent a critical component of this equilibrium and a potent barrier to infection by means of direct competition with airborne pathogens or indirectly via modulation of the immune response. Moving down the respiratory tract, physicochemical and biological constraints promote site-specific expansion of microbes that engage in cross talk with the local immune system to maintain homeostasis and promote protection. In this review, we critically assess the site-specific microbial communities that an airborne pathogen encounters in its hypothetical travel along the respiratory tract and discuss the changes in the composition and function of the microbiome in airborne diseases by taking fungal and SARS-CoV-2 infections as examples. Finally, we discuss how technological and bioinformatics advancements may turn microbiome analysis into a valuable tool in the hands of clinicians to predict the risk of disease onset, the clinical course, and the response to treatment of individual patients in the direction of personalized medicine implementation.
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Affiliation(s)
- Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Emilia Nunzi
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Luigina Romani
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
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49
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Gang J, Wang H, Xue X, Zhang S. Microbiota and COVID-19: Long-term and complex influencing factors. Front Microbiol 2022; 13:963488. [PMID: 36033885 PMCID: PMC9417543 DOI: 10.3389/fmicb.2022.963488] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/25/2022] [Indexed: 01/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). According to the World Health Organization statistics, more than 500 million individuals have been infected and more than 6 million deaths have resulted worldwide. Although COVID-19 mainly affects the respiratory system, considerable evidence shows that the digestive, cardiovascular, nervous, and reproductive systems can all be involved. Angiotensin-converting enzyme 2 (AEC2), the target of SARS-CoV-2 invasion of the host is mainly distributed in the respiratory and gastrointestinal tract. Studies found that microbiota contributes to the onset and progression of many diseases, including COVID-19. Here, we firstly conclude the characterization of respiratory, gut, and oral microbial dysbiosis, including bacteria, fungi, and viruses. Then we explore the potential mechanisms of microbial involvement in COVID-19. Microbial dysbiosis could influence COVID-19 by complex interactions with SARS-CoV-2 and host immunity. Moreover, microbiota may have an impact on COVID-19 through their metabolites or modulation of ACE2 expression. Subsequently, we generalize the potential of microbiota as diagnostic markers for COVID-19 patients and its possible association with post-acute COVID-19 syndrome (PACS) and relapse after recovery. Finally, we proposed directed microbiota-targeted treatments from the perspective of gut microecology such as probiotics and prebiotics, fecal transplantation and antibiotics, and other interventions such as traditional Chinese medicine, COVID-19 vaccines, and ACE2-based treatments.
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Affiliation(s)
- Jiaqi Gang
- Department of Emergency, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Oncology, Xiuwu County People’s Hospital, Jiaozuo, China
| | - Haiyu Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangsheng Xue
- Department of Oncology, Xiuwu County People’s Hospital, Jiaozuo, China
- *Correspondence: Xiangsheng Xue,
| | - Shu Zhang
- Department of Emergency, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Shu Zhang,
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50
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Taylo LJ, Keeler EL, Bushman FD, Collman RG. The enigmatic roles of Anelloviridae and Redondoviridae in humans. Curr Opin Virol 2022; 55:101248. [PMID: 35870315 DOI: 10.1016/j.coviro.2022.101248] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/06/2022] [Accepted: 06/09/2022] [Indexed: 12/26/2022]
Abstract
Anelloviridae and Redondoviridae are virus families with small, circular, single-stranded DNA genomes that are common components of the human virome. Despite their small genome size of less than 5000 bases, they are remarkably successful - anelloviruses colonize over 90% of adult humans, while the recently discovered redondoviruses have been found at up to 80% prevalence in some populations. Anelloviruses are present in blood and many organs, while redondoviruses are found mainly in the ororespiratory tract. Despite their high prevalence, little is known about their biology or pathogenic potential. In this review, we discuss anelloviruses and redondoviruses and explore their enigmatic roles in human health and disease.
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Affiliation(s)
- Louis J Taylo
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Emma L Keeler
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ronald G Collman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Medicine, Pulmonary, Allergy and Critical Care Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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