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Cai J, Xu J, Tan Y, Xiang Y, Li Z, Zheng J, Li Y. Gut microbiota alteration and its association with immune function in post-COVID-19 patients. Folia Microbiol (Praha) 2024; 69:857-864. [PMID: 38177971 DOI: 10.1007/s12223-023-01118-z] [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: 07/15/2023] [Accepted: 12/02/2023] [Indexed: 01/06/2024]
Abstract
To reveal the variation of gut microbiota and its association with immune function in cured patients with coronavirus 2019 (COVID-19) disease, gut microbiota of patients discharged from hospital for 20 ~ 23 months and healthy volunteers was analyzed by high throughput 16S rRNA sequencing. The diversity and abundance were compared, and the correlation with immunity factors was investigated, and changes in the content of 6 genera microorganisms with proportion higher than 0.1% were revealed in patients with COVID-19 disease: reduced content of Subdoligranulum, Haemophilus, Coprococcus, Eubacterium vertriosum group, and Lachnospiraceae ND3007 group and increased content of Hungatella. NK cells were negatively correlated to Subdoligranulum, while CD8 cells were positively correlated to Subdoligranulum but negative to Hungatella. IL-8 concentration was negatively correlated to Subdoligranulum, Haemophilus, Coprococcus, Eubacterium vertriosum group, and Lachnospiraceae ND3007 group but positively to Hungatella, while IL-1β concentration was negatively correlated to Haemophilus and Eubacterium ventriosum group but positively to Hungatella. The variation of probiotics and potential pathogenic bacteria implies a higher risk in diseases and inflammation, and the modulation of the gut microbiota may help the healing of COVID-19 patients.
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Affiliation(s)
- Jiaojiao Cai
- College of Public Health, Chongqing Medical University, Chongqing, 400016, China
- Microbiological Laboratory, Chongqing Center for Disease Control and Prevention, Chongqing, 400042, China
| | - Jingru Xu
- Microbiological Laboratory, Chongqing Center for Disease Control and Prevention, Chongqing, 400042, China
| | - Yan Tan
- Microbiological Laboratory, Chongqing Center for Disease Control and Prevention, Chongqing, 400042, China
| | - Yao Xiang
- Microbiological Laboratory, Chongqing Center for Disease Control and Prevention, Chongqing, 400042, China
| | - Zhifeng Li
- Microbiological Laboratory, Chongqing Center for Disease Control and Prevention, Chongqing, 400042, China
| | - Juan Zheng
- Department of Neurology, Chongqing Red Cross Hospital (People's Hospital of Jiangbei District), Chongqing, 400020, China
| | - Yingli Li
- College of Public Health, Chongqing Medical University, Chongqing, 400016, China.
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2
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Wilson JD, Dworsky-Fried M, Ismail N. Neurodevelopmental implications of COVID-19-induced gut microbiome dysbiosis in pregnant women. J Reprod Immunol 2024; 165:104300. [PMID: 39004033 DOI: 10.1016/j.jri.2024.104300] [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: 04/04/2024] [Revised: 06/25/2024] [Accepted: 07/10/2024] [Indexed: 07/16/2024]
Abstract
The global public health emergency of COVID-19 in January 2020 prompted a surge in research focusing on the pathogenesis and clinical manifestations of the virus. While numerous reports have been published on the acute effects of COVID-19 infection, the review explores the multifaceted long-term implications of COVID-19, with a particular focus on severe maternal COVID-19 infection, gut microbiome dysbiosis, and neurodevelopmental disorders in offspring. Severe COVID-19 infection has been associated with heightened immune system activation and gastrointestinal symptoms. Severe COVID-19 may also result in gut microbiome dysbiosis and a compromised intestinal mucosal barrier, often referred to as 'leaky gut'. Increased gut permeability facilitates the passage of inflammatory cytokines, originating from the inflamed intestinal mucosa and gut, into the bloodstream, thereby influencing fetal development during pregnancy and potentially elevating the risk of neurodevelopmental disorders such as autism and schizophrenia. The current review discusses the role of cytokine signaling molecules, microglia, and synaptic pruning, highlighting their potential involvement in the pathogenesis of neurodevelopmental disorders following maternal COVID-19 infection. Additionally, this review addresses the potential of probiotic interventions to mitigate gut dysbiosis and inflammatory responses associated with COVID-19, offering avenues for future research in optimizing maternal and fetal health outcomes.
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Affiliation(s)
- Jacob D Wilson
- NISE Laboratory, School of Psychology, Faculty of Social Science, University of Ottawa, Ottawa, Ontario K1N 9A4, Canada
| | - Michaela Dworsky-Fried
- NISE Laboratory, School of Psychology, Faculty of Social Science, University of Ottawa, Ottawa, Ontario K1N 9A4, Canada
| | - Nafissa Ismail
- NISE Laboratory, School of Psychology, Faculty of Social Science, University of Ottawa, Ottawa, Ontario K1N 9A4, Canada; LIFE Research Institute, Ottawa, Ontario K1N 6N5, Canada; University of Ottawa Brain and Mind Research Institute, Ottawa, Ontario K1H 8M5, Canada.
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3
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Kopera K, Gromowski T, Wydmański W, Skonieczna-Żydecka K, Muszyńska A, Zielińska K, Wierzbicka-Woś A, Kaczmarczyk M, Kadaj-Lipka R, Cembrowska-Lech D, Januszkiewicz K, Kotfis K, Witkiewicz W, Nalewajska M, Feret W, Marlicz W, Łoniewski I, Łabaj PP, Rydzewska G, Kosciolek T. Gut microbiome dynamics and predictive value in hospitalized COVID-19 patients: a comparative analysis of shallow and deep shotgun sequencing. Front Microbiol 2024; 15:1342749. [PMID: 38962119 PMCID: PMC11219902 DOI: 10.3389/fmicb.2024.1342749] [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: 11/22/2023] [Accepted: 05/20/2024] [Indexed: 07/05/2024] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has led to a wide range of clinical presentations, with respiratory symptoms being common. However, emerging evidence suggests that the gastrointestinal (GI) tract is also affected, with angiotensin-converting enzyme 2, a key receptor for SARS-CoV-2, abundantly expressed in the ileum and colon. The virus has been detected in GI tissues and fecal samples, even in cases with negative results of the reverse transcription polymerase chain reaction in the respiratory tract. GI symptoms have been associated with an increased risk of ICU admission and mortality. The gut microbiome, a complex ecosystem of around 40 trillion bacteria, plays a crucial role in immunological and metabolic pathways. Dysbiosis of the gut microbiota, characterized by a loss of beneficial microbes and decreased microbial diversity, has been observed in COVID-19 patients, potentially contributing to disease severity. We conducted a comprehensive gut microbiome study in 204 hospitalized COVID-19 patients using both shallow and deep shotgun sequencing methods. We aimed to track microbiota composition changes induced by hospitalization, link these alterations to clinical procedures (antibiotics administration) and outcomes (ICU referral, survival), and assess the predictive potential of the gut microbiome for COVID-19 prognosis. Shallow shotgun sequencing was evaluated as a cost-effective diagnostic alternative for clinical settings. Our study demonstrated the diverse effects of various combinations of clinical parameters, microbiome profiles, and patient metadata on the precision of outcome prognostication in patients. It indicates that microbiological data possesses greater reliability in forecasting patient outcomes when contrasted with clinical data or metadata. Furthermore, we established that shallow shotgun sequencing presents a viable and cost-effective diagnostic alternative to deep sequencing within clinical environments.
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Affiliation(s)
- Katarzyna Kopera
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Tomasz Gromowski
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Witold Wydmański
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Faculty of Mathematics and Computer Science, Jagiellonian University, Kraków, Poland
| | | | - Agata Muszyńska
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Kinga Zielińska
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | | | - Mariusz Kaczmarczyk
- Sanprobi Sp. z o.o. Sp. k., Szczecin, Poland
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, Szczecin, Poland
| | - Roland Kadaj-Lipka
- Department of Internal Medicine and Gastroenterology, Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
| | - Danuta Cembrowska-Lech
- Department of Biochemical Science, Pomeranian Medical University, Szczecin, Poland
- Sanprobi Sp. z o.o. Sp. k., Szczecin, Poland
| | | | - Katarzyna Kotfis
- Department of Anesthesiology, Intensive Care and Pain Management, Pomeranian Medical University, Szczecin, Poland
| | | | | | - Wiktoria Feret
- Clinical Department of Nephrology, Transplantology and Internal Medicine, Pomeranian Medical University, Szczecin, Poland
| | - Wojciech Marlicz
- Sanprobi Sp. z o.o. Sp. k., Szczecin, Poland
- Department of Gastroenterology, Pomeranian Medical University, Szczecin, Poland
| | - Igor Łoniewski
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Biochemical Science, Pomeranian Medical University, Szczecin, Poland
- Sanprobi Sp. z o.o. Sp. k., Szczecin, Poland
| | - Paweł P. Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Grażyna Rydzewska
- Department of Internal Medicine and Gastroenterology, Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
| | - Tomasz Kosciolek
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
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4
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Raj ST, Bruce AW, Anbalagan M, Srinivasan H, Chinnappan S, Rajagopal M, Khanna K, Chandramoorthy HC, Mani RR. COVID-19 influenced gut dysbiosis, post-acute sequelae, immune regulation, and therapeutic regimens. Front Cell Infect Microbiol 2024; 14:1384939. [PMID: 38863829 PMCID: PMC11165100 DOI: 10.3389/fcimb.2024.1384939] [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: 02/11/2024] [Accepted: 05/13/2024] [Indexed: 06/13/2024] Open
Abstract
The novel coronavirus disease 2019 (COVID-19) pandemic outbreak caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has garnered unprecedented global attention. It caused over 2.47 million deaths through various syndromes such as acute respiratory distress, hypercoagulability, and multiple organ failure. The viral invasion proceeds through the ACE2 receptor, expressed in multiple cell types, and in some patients caused serious damage to tissues, organs, immune cells, and the microbes that colonize the gastrointestinal tract (GIT). Some patients who survived the SARS-CoV-2 infection have developed months of persistent long-COVID-19 symptoms or post-acute sequelae of COVID-19 (PASC). Diagnosis of these patients has revealed multiple biological effects, none of which are mutually exclusive. However, the severity of COVID-19 also depends on numerous comorbidities such as obesity, age, diabetes, and hypertension and care must be taken with respect to other multiple morbidities, such as host immunity. Gut microbiota in relation to SARS-CoV-2 immunopathology is considered to evolve COVID-19 progression via mechanisms of biochemical metabolism, exacerbation of inflammation, intestinal mucosal secretion, cytokine storm, and immunity regulation. Therefore, modulation of gut microbiome equilibrium through food supplements and probiotics remains a hot topic of current research and debate. In this review, we discuss the biological complications of the physio-pathological effects of COVID-19 infection, GIT immune response, and therapeutic pharmacological strategies. We also summarize the therapeutic targets of probiotics, their limitations, and the efficacy of preclinical and clinical drugs to effectively inhibit the spread of SARS-CoV-2.
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Affiliation(s)
- Sterlin T. Raj
- Department of Molecular Biology, Ekka Diagnostics, Chennai, Tamil Nadu, India
| | - Alexander W. Bruce
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Muralidharan Anbalagan
- Department of Structural & Cellular Biology, Tulane University School of Medicine, New Orleans, LA, United States
| | - Hemalatha Srinivasan
- School of Life Sciences, B. S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, India
| | - Sasikala Chinnappan
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, University College of Sedaya International UCSI University, Kuala Lumpur, Malaysia
| | - Mogana Rajagopal
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, University College of Sedaya International UCSI University, Kuala Lumpur, Malaysia
| | - Kushagra Khanna
- Department of Pharmaceutical Technology, Faculty of Pharmaceutical Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Harish C. Chandramoorthy
- Department of Microbiology and Clinical Parasitology, College of Medicine, King Khalid University, Abha, Saudi Arabia
- Center for Stem Cell Research, College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Ravishankar Ram Mani
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, University College of Sedaya International UCSI University, Kuala Lumpur, Malaysia
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5
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Zhong J, Guo L, Wang Y, Jiang X, Wang C, Xiao Y, Wang Y, Zhou F, Wu C, Chen L, Wang X, Wang J, Cao B, Li M, Ren L. Gut Microbiota Improves Prognostic Prediction in Critically Ill COVID-19 Patients Alongside Immunological and Hematological Indicators. RESEARCH (WASHINGTON, D.C.) 2024; 7:0389. [PMID: 38779486 PMCID: PMC11109594 DOI: 10.34133/research.0389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024]
Abstract
The gut microbiota undergoes substantial changes in COVID-19 patients; yet, the utility of these alterations as prognostic biomarkers at the time of hospital admission, and its correlation with immunological and hematological parameters, remains unclear. The objective of this study is to investigate the gut microbiota's dynamic change in critically ill patients with COVID-19 and evaluate its predictive capability for clinical outcomes alongside immunological and hematological parameters. In this study, anal swabs were consecutively collected from 192 COVID-19 patients (583 samples) upon hospital admission for metagenome sequencing. Simultaneously, blood samples were obtained to measure the concentrations of 27 cytokines and chemokines, along with hematological and biochemical indicators. Our findings indicate a significant correlation between the composition and dynamics of gut microbiota with disease severity and mortality in COVID-19 patients. Recovered patients exhibited a higher abundance of Veillonella and denser interactions among gut commensal bacteria compared to deceased patients. Furthermore, the abundance of gut commensal bacteria exhibited a negative correlation with the concentration of proinflammatory cytokines and organ damage markers. The gut microbiota upon admission showed moderate prognostic prediction ability with an AUC of 0.78, which was less effective compared to predictions based on immunological and hematological parameters (AUC 0.80 and 0.88, respectively). Noteworthy, the integration of these three datasets yielded a higher predictive accuracy (AUC 0.93). Our findings suggest the gut microbiota as an informative biomarker for COVID-19 prognosis, augmenting existing immune and hematological indicators.
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Affiliation(s)
- Jiaxin Zhong
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Guo
- National Health Commission Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity and Christophe Mérieux Laboratory, National Institute of Pathogen Biology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yeming Wang
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital,
Capital Medical University, Beijing, China
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, National Clinical Research Center for Respiratory Diseases,
Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xuan Jiang
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chun Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Xiao
- National Health Commission Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity and Christophe Mérieux Laboratory, National Institute of Pathogen Biology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity and Christophe Mérieux Laboratory, National Institute of Pathogen Biology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fei Zhou
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital,
Capital Medical University, Beijing, China
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, National Clinical Research Center for Respiratory Diseases,
Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Chao Wu
- National Health Commission Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity and Christophe Mérieux Laboratory, National Institute of Pathogen Biology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lan Chen
- National Health Commission Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity and Christophe Mérieux Laboratory, National Institute of Pathogen Biology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinming Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity and Christophe Mérieux Laboratory, National Institute of Pathogen Biology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianwei Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity and Christophe Mérieux Laboratory, National Institute of Pathogen Biology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital,
Capital Medical University, Beijing, China
- National Center for Respiratory Medicine, State Key Laboratory of Respiratory Health and Multimorbidity, National Clinical Research Center for Respiratory Diseases,
Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Mingkun Li
- Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - LiLi Ren
- National Health Commission Key Laboratory of Systems Biology of Pathogens, State Key Laboratory of Respiratory Health and Multimorbidity and Christophe Mérieux Laboratory, National Institute of Pathogen Biology,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics,
Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Brilakis L, Theofilogiannakou E, Lykoudis PM. Current remarks and future directions on the interactions between metabolic dysfunction-associated fatty liver disease and COVID-19. World J Gastroenterol 2024; 30:1480-1487. [PMID: 38617460 PMCID: PMC11008415 DOI: 10.3748/wjg.v30.i11.1480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/30/2024] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
During the outbreak of the coronavirus disease 2019 (COVID-19) pandemic, particular interest rose regarding the interaction between metabolic dysfunction-associated fatty liver disease (MAFLD) and the COVID-19 infection. Several studies highlighted the fact that individuals with MAFLD had higher probability of severe acute respiratory syndrome coronavirus 2 infection and more severe adverse clinical outcomes. One of the proposed mechanisms is the inflammatory response pathway, especially the one involving cytokines, such as interleukin 6, which appeared particularly elevated in those patients and was deemed responsible for additional insult to the already damaged liver. This should increase our vigilance in terms of early detection, close follow up and early treatment for individuals with MAFLD and COVID-19 infection. In the direction of early diagnosis, biomarkers such as cytokeratin-18 and scoring systems such as Fibrosis-4 index score are proposed. COVID-19 is a newly described entity, expected to be of concern for the years to come, and MAFLD is a condition with an ever-increasing impact. Delineating the interaction between these two entities should be brought into the focus of research. Reducing morbidity and mortality of patients with COVID-19 and MAFLD should be the ultimate objective, and the optimal way to achieve this is by designing evidence-based prevention and treatment policies.
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Affiliation(s)
- Leonidas Brilakis
- School of Medicine, National & Kapodistrian University of Athens, Athens 11527, Greece
| | | | - Panagis M Lykoudis
- School of Medicine, National & Kapodistrian University of Athens, Athens 11527, Greece
- Division of Surgery & Interventional Science, University College London, London WC1E 6BT, United Kingdom
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7
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Piazzesi A, Pane S, Del Chierico F, Romani L, Campana A, Palma P, Putignani L. The pediatric gut bacteriome and virome in response to SARS-CoV-2 infection. Front Cell Infect Microbiol 2024; 14:1335450. [PMID: 38318164 PMCID: PMC10839054 DOI: 10.3389/fcimb.2024.1335450] [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: 11/08/2023] [Accepted: 01/02/2024] [Indexed: 02/07/2024] Open
Abstract
Introduction Since the beginning of the SARS-CoV-2 pandemic in early 2020, it has been apparent that children were partially protected from both infection and the more severe forms of the disease. Many different mechanisms have been proposed to explain this phenomenon, including children's frequent exposure to other upper respiratory infections and vaccines, and which inflammatory cytokines they are more likely to produce in response to infection. Furthermore, given the presence of SARS-CoV-2 in the intestine and its ability to infect enterocytes, combined with the well described immunomodulatory capabilities of the microbiome, another potential contributing factor may be the presence of certain protective microbial members of the gut microbiota (GM). Methods We performed shotgun metagenomic sequencing and profiled both the bacteriome and virome of the GM of pediatric SARS-CoV-2 patients compared to healthy, age-matched subjects. Results We found that, while pediatric patients do share some pro-inflammatory microbial signatures with adult patients, they also possess a distinct microbial signature of protective bacteria previously found to be negatively correlated with SARS-CoV-2 infectivity and COVID-19 severity. COVID-19 was also associated with higher fecal Cytomegalovirus load, and with shifts in the relative abundances of bacteriophages in the GM. Furthermore, we address how the preventative treatment of COVID-19 patients with antibiotics, a common practice especially in the early days of the pandemic, affected the bacteriome and virome, as well as the abundances of antimicrobial resistance and virulence genes in these patients. Discussion To our knowledge, this is the first study to address the bacteriome, virome, and resistome of pediatric patients in response to COVID-19 and to preventative antibiotics use.
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Affiliation(s)
- Antonia Piazzesi
- Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Stefania Pane
- Unit of Microbiomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | | | - Lorenza Romani
- Infectious Diseases Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Andrea Campana
- Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Paolo Palma
- Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Chair of Pediatrics, Department of Systems Medicine, University of Rome “Tor Vergata”, Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiomics and Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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8
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Mir TUG, Manhas S, Khurshid Wani A, Akhtar N, Shukla S, Prakash A. Alterations in microbiome of COVID-19 patients and its impact on forensic investigations. Sci Justice 2024; 64:81-94. [PMID: 38182316 DOI: 10.1016/j.scijus.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 11/12/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024]
Abstract
The human microbiome is vital for maintaining human health and has garnered substantial attention in recent years, particularly in the context of the coronavirus disease 2019 (COVID-19) outbreak. Studies have underscored significant alterations in the microbiome of COVID-19 patients across various body niches, including the gut, respiratory tract, oral cavity, skin, and vagina. These changes manifest as shifts in microbiota composition, characterized by an increase in opportunistic pathogens and a decrease in beneficial commensal bacteria. Such microbiome transformations may play a pivotal role in influencing the course and severity of COVID-19, potentially contributing to the inflammatory response. This ongoing relationship between COVID-19 and the human microbiome serves as a compelling subject of research, underscoring the necessity for further investigations into the underlying mechanisms and their implications for patient health. Additionally, these alterations in the microbiome may have significant ramifications for forensic investigations, given the microbiome's potential in establishing individual characteristics. Consequently, changes in the microbiome could introduce a level of complexity into forensic determinations. As research progresses, a more profound understanding of the human microbiome within the context of COVID-19 may offer valuable insights into disease prevention, treatment strategies, and its potential applications in forensic science. Consequently, this paper aims to provide an overarching review of microbiome alterations due to COVID-19 and the associated impact on forensic applications, bridging the gap between the altered microbiome of COVID-19 patients and the challenges forensic investigations may encounter when analyzing this microbiome as a forensic biomarker.
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Affiliation(s)
- Tahir Ul Gani Mir
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India; State Forensic Science Laboratory, Srinagar, Jammu and Kashmir 190001, India.
| | - Sakshi Manhas
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Saurabh Shukla
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India.
| | - Ajit Prakash
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
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9
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Fan R, Liu S, Sun N, Yang Y, Deng X, Hu B, Sun C, Wen C, Li H, Cheng D, Huang C, Hou P, Zhang T. Gut microbiota composition is associated with disease severity and host immune responses in COVID-19. Front Cell Infect Microbiol 2023; 13:1274690. [PMID: 38149007 PMCID: PMC10749918 DOI: 10.3389/fcimb.2023.1274690] [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: 08/08/2023] [Accepted: 11/21/2023] [Indexed: 12/28/2023] Open
Abstract
Background Human gut microbiota play a crucial role in the immune response of the host to respiratory viral infection. However, evidence regarding the association between the gut microbiome, host immune responses, and disease severity in coronavirus disease 2019 (COVID-19) remains insufficient. Methods To better comprehend the interactions between the host and gut microbiota in COVID-19, we conducted 16S rRNA sequencing and characterized the gut microbiome compositions in stool samples from 40 COVID-19 patients and 33 non-pneumonia controls. We assessed several hematological parameters to determine the immune status. Results We found that the gut microbial composition was significantly changed in COVID-19 patients, which was characterized by increased opportunistic pathogens and decreased commensal bacteria. The frequency of prevalent opportunistic pathogens Enterococcus and Lactobacillus increased, especially in severe patients; yet the abundance of butyrate-producing bacteria, Faecalibacterium, Roseburia, and Anaerostipes, decreased significantly, and Faecalibacterium prausnitzii might help discriminate severe patients from moderate patients and non-pneumonia people. Furthermore, we then obtained a correlation map between the clinical characteristics of COVID-19 and severity-related gut microbiota. We observed a notable correlation between the abundance of Enterococcus faecium and abnormal neutrophil or lymphocyte percentage in all COVID-19 patients. Faecalibacterium was positively correlated with lymphocyte counts, while negatively correlated with neutrophil percentage. Conclusion These results suggested that the gut microbiome could have a potential function in regulating host immune responses and impacting the severity or consequences of diseases.
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Affiliation(s)
- Ruyue Fan
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Shuai Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Shandong Key Laboratory of Infectious Respiratory Disease, Jinan, Shandong, China
| | - Na Sun
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Ying Yang
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Xia Deng
- School of Public Healthy, Weifang Medical University, Weifang, Shandong, China
| | - Bin Hu
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Changhua Sun
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Chengli Wen
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Hui Li
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Dong Cheng
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Chuanjun Huang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Shandong Key Laboratory of Infectious Respiratory Disease, Jinan, Shandong, China
| | - Peibin Hou
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Tianliang Zhang
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
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Wolszczak-Biedrzycka B, Dorf J, Wojewódzka-Żelezniakowicz M, Żendzian-Piotrowska M, Dymicka-Piekarska VJ, Matowicka-Karna J, Maciejczyk M. Unveiling COVID-19 Secrets: Harnessing Cytokines as Powerful Biomarkers for Diagnosis and Predicting Severity. J Inflamm Res 2023; 16:6055-6070. [PMID: 38107380 PMCID: PMC10723593 DOI: 10.2147/jir.s439217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023] Open
Abstract
Introduction In coronavirus disease (COVID-19), inflammation takes center stage, with a cascade of cytokines released, contributing to both inflammation and lung damage. The objective of this study is to identify biomarkers for diagnosing and predicting the severity of COVID-19. Materials and Methods Cytokine levels were determined in the serum from venous blood samples collected from 100 patients with COVID-19 and 50 healthy controls. COVID-19 patients classified based on the Modified Early Warning (MEWS) score. Cytokine concentrations were determined with a multiplex ELISA kit (Bio-Plex Pro™ Human Cytokine Screening Panel). Results The concentrations of all analyzed cytokines were elevated in the serum of COVID-19 patients relative to the control group, but no significant differences were observed in interleukin-9 (IL-9) and IL-12 p70 levels. In addition, the concentrations of IL-1α, IL-1β, IL-1ra, IL-2Rα, IL-6, IL-12 p40, IL-18, and tumor necrosis factor alpha (TNFα) were significantly higher in symptomatic patients with accompanying pneumonia without respiratory failure (stage 2) than in asymptomatic/mildly symptomatic patients (stage 1). Conclusion The study revealed that IL-1ra, IL-2Rα, IL-6, IL-8, IL-12 p40, IL-16, and IL-18 levels serve as potential diagnostic biomarkers in COVID-19 patients. Furthermore, elevated IL-1α levels proved to be valuable in assessing the severity of COVID-19.
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Affiliation(s)
- Blanka Wolszczak-Biedrzycka
- Department of Psychology and Sociology of Health and Public Health, University of Warmia and Mazury in Olsztyn, Olsztyn, 10-900, Poland
| | - Justyna Dorf
- Department of Clinical Laboratory Diagnostics, Medical University of Bialystok, Bialystok, 15-089, Poland
| | | | | | | | - Joanna Matowicka-Karna
- Department of Clinical Laboratory Diagnostics, Medical University of Bialystok, Bialystok, 15-089, Poland
| | - Mateusz Maciejczyk
- Department of Hygiene, Epidemiology and Ergonomics, Medical University of Bialystok, Bialystok, 15-089, Poland
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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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Krasaewes K, Chaiwarith R, Chattipakorn N, Chattipakorn SC. Profiles of gut microbiota associated with clinical outcomes in patients with different stages of SARS-CoV-2 infection. Life Sci 2023; 332:122136. [PMID: 37783267 DOI: 10.1016/j.lfs.2023.122136] [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: 06/03/2023] [Revised: 08/29/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
The correlation between SARS-CoV-2 infection and gut microbiota has been a subject of growing interest in recent research endeavors. It is postulated that SARS-CoV-2 might lead to gut dysbiosis by affecting the gut-lung axis and reducing the production of antimicrobial peptides in the gastrointestinal tract. Our comprehensive review of both in vivo and clinical studies has revealed a consistent decline in alpha diversity and increased dissimilarity in beta diversity of gut microbiota in comparison to healthy populations, observed during both the acute and post-infection phases of COVID-19. Furthermore, there is a notable reduction in the number of beneficial butyrate-producing bacteria, alongside an upsurge in opportunistic bacteria. Concomitantly, the functional and metabolic characteristics of gut microbiota are significantly altered. Consequently, COVID-19 patients exhibit a heightened inflammatory state, which has been linked to the severity of the disease in the acute phase and the occurrence of post-acute COVID-19 syndrome (PACS) in the post-infection phase. Notably, certain specific gut microbiota species have emerged as potential candidates for aiding in the diagnosis, prediction of disease severity, or treatment of severe cases of COVID-19. This review also underscores the significance of gut microbiota in the context of post-acute COVID-19 syndrome (PACS) and offers valuable insights into possible biomarkers for diagnosis and therapeutic targets for PACS in the future.
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Affiliation(s)
- Kawisara Krasaewes
- Division of Infectious Disease and Tropical Medicine, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Romanee Chaiwarith
- Division of Infectious Disease and Tropical Medicine, Department of Internal Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nipon Chattipakorn
- Neuroelectrophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Siriporn C Chattipakorn
- Neuroelectrophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai 50200, Thailand; Department of Oral Biology and Diagnostic Sciences, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand.
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13
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Liu S, Zhao Y, Feng X, Xu H. SARS-CoV-2 infection threatening intestinal health: A review of potential mechanisms and treatment strategies. Crit Rev Food Sci Nutr 2023; 63:12578-12596. [PMID: 35894645 DOI: 10.1080/10408398.2022.2103090] [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] [Indexed: 01/08/2023]
Abstract
The outbreak of the COVID-19 pandemic has brought great problems to mankind, including economic recession and poor health. COVID-19 patients are frequently reported with gastrointestinal symptoms such as diarrhea and vomiting in clinical diagnosis. Maintaining intestinal health is the key guarantee to maintain the normal function of multiple organs, otherwise it will be a disaster. Therefore, the purpose of this review was deeply understanded the potential mechanism of SARS-CoV-2 infection threatening intestinal health and put forward reasonable treatment strategies. Combined with the existing researches, we summarized the mechanism of SARS-CoV-2 infection threatening intestinal health, including intestinal microbiome disruption, intestinal barrier dysfunction, intestinal oxidative stress and intestinal cytokine storm. These adverse intestinal events may affect other organs through the circulatory system or aggravate the course of the disease. Typically, intestinal disadvantage may promote the progression of SARS-CoV-2 through the gut-lung axis and increase the disease degree of COVID-19 patients. In view of the lack of specific drugs to inhibit SARS-CoV-2 replication, the current review described new strategies of probiotics, prebiotics, postbiotics and nutrients to combat SARS-CoV-2 infection and maintain intestinal health. To provide new insights for the prevention and treatment of gastrointestinal symptoms and pneumonia in patients with COVID-19.
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Affiliation(s)
- Shanji Liu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Yu Zhao
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Xiaoyan Feng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Hengyi Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
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14
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Huang G, Mao Y, Zhang W, Luo Q, Xie R, Huang D, Liang Y. Explore the changes of intestinal flora in patients with coronavirus disease 2019 based on bioinformatics. Front Cell Infect Microbiol 2023; 13:1265028. [PMID: 37900316 PMCID: PMC10611479 DOI: 10.3389/fcimb.2023.1265028] [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: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 10/31/2023] Open
Abstract
Background Studies have revealed that there were significant changes in intestinal flora composition in patients with coronavirus disease 2019 (COVID-19) compared to non-COVID-19 patients, regardless of whether they were treated with medication. Therefore, a comprehensive study of the intestinal flora of COVID-19 patients is needed to further understand the mechanisms of COVID-19 development. Methods In total, 20 healthy samples and 20 COVID-19 samples were collected in this study. Firstly, alpha diversity and beta diversity were analyzed to assess whether there were difference in species richness and diversity as well as species composition between COVID-19 and control groups. The observed features index, Evenness index, PD index, and Shannon index were utilized to measure alpha diversity. The principal coordinates analysis (PCoA) and non-metric multidimensional scaling (NMDS) were performed to analyzed beta diversity. Linear discriminant analysis Effect Size (LEfSe) was utilized to analyze the variability in the abundance of bacterial taxa from different classification levels. The random forest (RF), Least absolute shrinkage and selection operator (LASSO), and univariate logistic regression were utilized to identify key Amplicon Sequence Variant (ASVs). Finally, the relevant networks of bacterial taxa were created in COVID-19 and control groups, separately. Results There were more species in the control group than in COVID-19 group. The observed features index, Shannon index, and Evenness index in the control groups were markedly higher than in the COVID-19 group. Therefore, there were marked variations in bacterial taxa composition between the COVID-19 and control groups. The nine bacterial taxa were significantly more abundant in the COVID-19 group, such as g-Streptococcus, f-Streptococcaceae, o-Lactobacillales, c-Bacilli and so on. In the control group, 26 bacterial taxa were significantly more abundant, such as c-Clostrjdia, o-Oscillospirales, f-Ruminococcaceae, etc. The 5 key ASVs were obtained through taking the intersection of the characteristic ASVs obtained by the three algorithms, namely ASV6, ASV53, ASV92, ASV96, and ASV105, which had diagnostic value for COVID-19. The relevance network in the control group was more complex compared to the COVID-19 group. Conclusion Our findings provide five key ASVs for diagnosis of COVID-19, providing a scientific reference for further studies of COVID-19.
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Affiliation(s)
- Gangding Huang
- Department of Gastroenterology, the Fifth Affiliated Hospital of Guangxi Medical University, Nanning, China
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15
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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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Vernia F, Ashktorab H, Cesaro N, Monaco S, Faenza S, Sgamma E, Viscido A, Latella G. COVID-19 and Gastrointestinal Tract: From Pathophysiology to Clinical Manifestations. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:1709. [PMID: 37893427 PMCID: PMC10608106 DOI: 10.3390/medicina59101709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/10/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023]
Abstract
Background: Since its first report in Wuhan, China, in December 2019, COVID-19 has become a pandemic, affecting millions of people worldwide. Although the virus primarily affects the respiratory tract, gastrointestinal symptoms are also common. The aim of this narrative review is to provide an overview of the pathophysiology and clinical manifestations of gastrointestinal COVID-19. Methods: We conducted a systematic electronic search of English literature up to January 2023 using Medline, Scopus, and the Cochrane Library, focusing on papers that analyzed the role of SARS-CoV-2 in the gastrointestinal tract. Results: Our review highlights that SARS-CoV-2 directly infects the gastrointestinal tract and can cause symptoms such as diarrhea, nausea/vomiting, abdominal pain, anorexia, loss of taste, and increased liver enzymes. These symptoms result from mucosal barrier damage, inflammation, and changes in the microbiota composition. The exact mechanism of how the virus overcomes the acid gastric environment and leads to the intestinal damage is still being studied. Conclusions: Although vaccination has increased the prevalence of less severe symptoms, the long-term interaction with SARS-CoV-2 remains a concern. Understanding the interplay between SARS-CoV-2 and the gastrointestinal tract is essential for future management of the virus.
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Affiliation(s)
- Filippo Vernia
- Gastroenterology Unit, Division of Gastroenterology, Hepatology, and Nutrition, Department of Life, Health and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division, Howard University College of Medicine, Washington, DC 20060, USA
| | - Nicola Cesaro
- Gastroenterology Unit, Division of Gastroenterology, Hepatology, and Nutrition, Department of Life, Health and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Sabrina Monaco
- Gastroenterology Unit, Division of Gastroenterology, Hepatology, and Nutrition, Department of Life, Health and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Susanna Faenza
- Gastroenterology Unit, Division of Gastroenterology, Hepatology, and Nutrition, Department of Life, Health and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Emanuele Sgamma
- Gastroenterology Unit, Division of Gastroenterology, Hepatology, and Nutrition, Department of Life, Health and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Angelo Viscido
- Gastroenterology Unit, Division of Gastroenterology, Hepatology, and Nutrition, Department of Life, Health and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
| | - Giovanni Latella
- Gastroenterology Unit, Division of Gastroenterology, Hepatology, and Nutrition, Department of Life, Health and Environmental Sciences, University of L'Aquila, Piazzale Salvatore Tommasi 1, 67100 L'Aquila, Italy
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Galperine T, Choi Y, Pagani JL, Kritikos A, Papadimitriou-Olivgeris M, Méan M, Scherz V, Opota O, Greub G, Guery B, Bertelli C. Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort. BMC Infect Dis 2023; 23:537. [PMID: 37596518 PMCID: PMC10436399 DOI: 10.1186/s12879-023-08511-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/04/2023] [Indexed: 08/20/2023] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a multifaceted disease potentially responsible for various clinical manifestations including gastro-intestinal symptoms. Several evidences suggest that the intestine is a critical site of immune cell development, gut microbiota could therefore play a key role in lung immune response. We designed a monocentric longitudinal observational study to describe the gut microbiota profile in COVID-19 patients and compare it to a pre-existing cohort of ventilated non-COVID-19 patients. METHODS From March to December 2020, we included patients admitted for COVID-19 in medicine (43 not ventilated) or intensive care unit (ICU) (14 ventilated) with a positive SARS-CoV-2 RT-PCR assay in a respiratory tract sample. 16S metagenomics was performed on rectal swabs from these 57 COVID-19 patients, 35 with one and 22 with multiple stool collections. Nineteen non-COVID-19 ICU controls were also enrolled, among which 14 developed ventilator-associated pneumonia (pneumonia group) and five remained without infection (control group). SARS-CoV-2 viral loads in fecal samples were measured by qPCR. RESULTS Although similar at inclusion, Shannon alpha diversity appeared significantly lower in COVID-19 and pneumonia groups than in the control group at day 7. Furthermore, the microbiota composition became distinct between COVID-19 and non-COVID-19 groups. The fecal microbiota of COVID-19 patients was characterized by increased Bacteroides and the pneumonia group by Prevotella. In a distance-based redundancy analysis, only COVID-19 presented significant effects on the microbiota composition. Moreover, patients in ICU harbored increased Campylobacter and decreased butyrate-producing bacteria, such as Lachnospiraceae, Roseburia and Faecalibacterium as compared to patients in medicine. Both the stay in ICU and patient were significant factors affecting the microbiota composition. SARS-CoV-2 viral loads were higher in ICU than in non-ICU patients. CONCLUSIONS Overall, we identified distinct characteristics of the gut microbiota in COVID-19 patients compared to control groups. COVID-19 patients were primarily characterized by increased Bacteroides and decreased Prevotella. Moreover, disease severity showed a negative correlation with butyrate-producing bacteria. These features could offer valuable insights into potential targets for modulating the host response through the microbiota and contribute to a better understanding of the disease's pathophysiology. TRIAL REGISTRATION CER-VD 2020-00755 (05.05.2020) & 2017-01820 (08.06.2018).
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Affiliation(s)
- Tatiana Galperine
- Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, BH10-553, 1011, Lausanne, Switzerland
| | - Yangji Choi
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jean-Luc Pagani
- Service of Intensive Care, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Antonios Kritikos
- Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, BH10-553, 1011, Lausanne, Switzerland
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Matthaios Papadimitriou-Olivgeris
- Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, BH10-553, 1011, Lausanne, Switzerland
| | - Marie Méan
- Division of Internal Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Valentin Scherz
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Onya Opota
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Benoit Guery
- Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Rue du Bugnon 46, BH10-553, 1011, Lausanne, Switzerland.
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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18
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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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19
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Golla R, Vuyyuru SK, Kante B, Kedia S, Ahuja V. Disorders of gut-brain interaction in post-acute COVID-19 syndrome. Postgrad Med J 2023; 99:834-843. [PMID: 37130814 DOI: 10.1136/pmj-2022-141749] [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: 03/16/2022] [Accepted: 06/18/2022] [Indexed: 11/03/2022]
Abstract
The novel coronavirus SARS-CoV-2 is responsible for the devastating pandemic which has caused more than 5 million deaths across the world until today. Apart from causing acute respiratory illness and multiorgan dysfunction, there can be long-term multiorgan sequalae after recovery, which is termed 'long COVID-19' or 'post-acute COVID-19 syndrome'. Little is known about long-term gastrointestinal (GI) consequences, occurrence of post-infection functional gastrointestinal disorders and impact the virus may have on overall intestinal health. In this review, we put forth the various mechanisms which may lead to this entity and possible ways to diagnose and manage this disorder. Hence, making physicians aware of this spectrum of disease is of utmost importance in the present pandemic and this review will help clinicians understand and suspect the occurrence of functional GI disease post recovery from COVID-19 and manage it accordingly, avoiding unnecessary misconceptions and delay in treatment.
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Affiliation(s)
- Rithvik Golla
- Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, Delhi, India
| | - Sudheer Kumar Vuyyuru
- Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, Delhi, India
| | - Bhaskar Kante
- Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, Delhi, India
| | - Saurabh Kedia
- Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, Delhi, India
| | - Vineet Ahuja
- Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, Delhi, India
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20
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Daddi L, Dorsett Y, Geng T, Bokoliya S, Yuan H, Wang P, Xu W, Zhou Y. Baseline Gut Microbiome Signatures Correlate with Immunogenicity of SARS-CoV-2 mRNA Vaccines. Int J Mol Sci 2023; 24:11703. [PMID: 37511464 PMCID: PMC10380288 DOI: 10.3390/ijms241411703] [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: 05/30/2023] [Revised: 07/01/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
The powerful immune responses elicited by the mRNA vaccines targeting the SARS-CoV-2 Spike protein contribute to their high efficacy. Yet, their efficacy can vary greatly between individuals. For vaccines not based on mRNA, cumulative evidence suggests that differences in the composition of the gut microbiome, which impact vaccine immunogenicity, are some of the factors that contribute to variations in efficacy. However, it is unclear if the microbiome impacts the novel mode of immunogenicity of the SARS-CoV-2 mRNA vaccines. We conducted a prospective longitudinal cohort study of individuals receiving SARS-CoV-2 mRNA vaccines where we measured levels of anti-Spike IgG and characterized microbiome composition, at pre-vaccination (baseline), and one week following the first and second immunizations. While we found that microbial diversity at all timepoints correlated with final IgG levels, only at baseline did microbial composition and predicted function correlate with vaccine immunogenicity. Specifically, the phylum Desulfobacterota and genus Bilophila, producers of immunostimulatory LPS, positively correlated with IgG, while Bacteroides was negatively correlated. KEGG predicted pathways relating to SCFA metabolism and sulfur metabolism, as well as structural components such as flagellin and capsular polysaccharides, also positively correlated with IgG levels. Consistent with these findings, depleting the microbiome with antibiotics reduced the immunogenicity of the BNT162b2 vaccine in mice. These findings suggest that gut microbiome composition impacts the immunogenicity of the SARS-CoV-2 mRNA vaccines.
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Affiliation(s)
- Lauren Daddi
- Department of Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Yair Dorsett
- Department of Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Tingting Geng
- Department of Immunology, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Suresh Bokoliya
- Department of Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Hanshu Yuan
- Department of Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Penghua Wang
- Department of Immunology, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Wanli Xu
- School of Nursing, University of Connecticut, Storrs, CT 06269, USA
| | - Yanjiao Zhou
- Department of Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA
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21
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Jiang Z, Yang L, Qian X, Su K, Huang Y, Qu Y, Zhang Z, Liu W. Tongue coating microbiome composition reflects disease severity in patients with COVID-19 in Nanjing, China. J Oral Microbiol 2023; 15:2236429. [PMID: 37483641 PMCID: PMC10360987 DOI: 10.1080/20002297.2023.2236429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/02/2023] [Accepted: 07/11/2023] [Indexed: 07/25/2023] Open
Abstract
Our purpose is to investigate the relationship between the microbiota of patients' tongue coating microbiota and the severity of COVID-19, and to identify the severity of COVID-19 patients' condition as early as possible. The participants were categorized into three groups: healthy controls (Con group) consisting of 37 individuals, patients with mild to moderate symptoms (M group) comprising 49 individuals, and patients with severe and critical symptoms (S-C group) consisting of 44 individuals. We collected oral swabs from all participants and performed 16S rRNA gene sequencing to analyze the microbiome. The α and β diversity differences were assessed respectively. Additionally, we employed the Linear Discriminant Analysis Effect Size (LEfSe) analysis to evaluate taxonomic differences among the three groups. Our findings revealed a significantly higher richness of tongue coating microbiota in both the S-C group and M group compared to the Con group. When compared with Con group, decreased Prevotella, Neisseria, Fusobacterium and Alloprevotella, and over-expressed Streptococcus and Rothia in M and S-C group were identified. LEfSe analysis indicated a greater abundance of Pseudomonas, Acinetbacter, Lactobacillus, Corynebacterium, Rothia in S-C group. Our study suggests a potential association between tongue coating microbiome and the severity of COVID-19 patients.
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Affiliation(s)
- Zongdan Jiang
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Lu Yang
- Department of Gastroenterology, Nanjing Integrated Traditional Chinese and Western Medical Hospital, Nanjing, China
| | - Xuetian Qian
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Kunhan Su
- Department of Gastroenterology, Nanjing Integrated Traditional Chinese and Western Medical Hospital, Nanjing, China
| | - Yuzhen Huang
- Department of Gastroenterology, Nanjing Integrated Traditional Chinese and Western Medical Hospital, Nanjing, China
| | - Yi Qu
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Zhenyu Zhang
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Wanli Liu
- Department of Gastroenterology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
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22
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Rezzoug I, Visseaux B, Bertine M, Parisey M, Bonnal C, Ruppe E, Descamps D, Timsit JF, Yazdanpanah Y, Armand-Lefevre L, Houze S, Argy N. Faecal Viral Excretion and Gastrointestinal Co-Infection Do Not Explain Digestive Presentation in COVID-19 Patients. Microorganisms 2023; 11:1780. [PMID: 37512952 PMCID: PMC10383301 DOI: 10.3390/microorganisms11071780] [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: 06/01/2023] [Revised: 06/28/2023] [Accepted: 07/02/2023] [Indexed: 07/30/2023] Open
Abstract
The physiopathological mechanisms responsible for digestive symptoms in COVID-19 patients are still unclear. The aim of this study was to determine the influence of faecal viral shedding on digestive symptoms and propose differential diagnoses in order to understand the gastrointestinal clinical spectrum in acute cases of COVID-19. All patients managed between March and May 2020, from whom stool samples were collected for microbiological investigations, were included. Microbiological analysis consisted of syndromic PCR screening and microscopic parasitological examination supplemented with microsporidia and multiplex protozoa PCR. SARS-CoV-2 infection was diagnosed via viral detection in respiratory and frozen stool samples, completed via serological test when necessary. Epidemiological, clinical, radiological, and biological data and clinical courses were compared according to COVID-19 status and faecal SARS-CoV-2 shedding and enteric co-infection status. The sample included 50 COVID+ and 67 COVID- patients. Faecal viral shedding was detected in 50% of stool samples and was associated with a higher viral load in the upper respiratory tract. Detected enteric pathogens were not different between subjects with different COVID-19 statuses or faecal SARS-CoV-2 shedding and had no impact on the clinical course for COVID-19 patients. The connection between SARS-CoV-2 shedding and enteric pathogen co-infection involvement in gastrointestinal presentation and clinical course is still unclear, suggesting other processes are involved in digestive disorders in COVID-19 patients.
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Affiliation(s)
- Inès Rezzoug
- Laboratoire de Parasitologie-Mycologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
| | - Benoit Visseaux
- Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
- IAME Unit, INSERM, Faculté de Médecine, Université de Paris Cité, 75018 Paris, France
| | - Mélanie Bertine
- Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
| | - Marion Parisey
- Service des Maladies Infectieuses et Tropicales, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
| | - Christine Bonnal
- Laboratoire de Parasitologie-Mycologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
| | - Etienne Ruppe
- IAME Unit, INSERM, Faculté de Médecine, Université de Paris Cité, 75018 Paris, France
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
| | - Diane Descamps
- Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
- IAME Unit, INSERM, Faculté de Médecine, Université de Paris Cité, 75018 Paris, France
| | - Jean François Timsit
- IAME Unit, INSERM, Faculté de Médecine, Université de Paris Cité, 75018 Paris, France
- Service de Réanimation Médicale et Infectieuses, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
| | - Yazdan Yazdanpanah
- IAME Unit, INSERM, Faculté de Médecine, Université de Paris Cité, 75018 Paris, France
- Service des Maladies Infectieuses et Tropicales, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
| | - Laurence Armand-Lefevre
- IAME Unit, INSERM, Faculté de Médecine, Université de Paris Cité, 75018 Paris, France
- Laboratoire de Bactériologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
| | - Sandrine Houze
- Laboratoire de Parasitologie-Mycologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
- MERIT UMR 261 Unit, IRD, Faculté de Pharmacie, Université de Paris Cité, 75006 Paris, France
| | - Nicolas Argy
- Laboratoire de Parasitologie-Mycologie, Hôpital Bichat-Claude Bernard, Assistance Publique des Hôpitaux de Paris, 75018 Paris, France
- MERIT UMR 261 Unit, IRD, Faculté de Pharmacie, Université de Paris Cité, 75006 Paris, France
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23
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Grinevich VB, Lazebnik LB, Kravchuk YA, Radchenko VG, Tkachenko EI, Pershko AM, Seliverstov PV, Salikova CP, Zhdanov KV, Kozlov KV, Makienko VV, Potapova IV, Ivanyuk ES, Egorov DV, Sas EI, Korzheva MD, Kozlova NM, Ratnikova AK, Ratnikov VA, Sitkin SI, Bolieva LZ, Turkina CV, Abdulganieva DI, Ermolova TV, Kozhevnikova SA, Tarasova LV, Myazin RG, Khomeriki NM, Pilat TL, Kuzmina LP, Khanferyan RA, Novikova VP, Polunina AV, Khavkin AI. Gastrointestinal disorders in post-COVID syndrome. Clinical guidelines. EXPERIMENTAL AND CLINICAL GASTROENTEROLOGY 2023:4-68. [DOI: 10.31146/1682-8658-ecg-208-12-4-68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Summary Post- COVID syndrome refers to the long-term consequences of a new coronavirus infection COVID-19, which includes a set of symptoms that develop or persist after COVID-19. Symptoms of gastrointestinal disorders in post- COVID syndrome, due to chronic infl ammation, the consequences of organ damage, prolonged hospitalization, social isolation, and other causes, can be persistent and require a multidisciplinary approach. The presented clinical practice guidelines consider the main preventive and therapeutic and diagnostic approaches to the management of patients with gastroenterological manifestations of postCOVID syndrome. The Guidelines were approved by the 17th National Congress of Internal Medicine and the 25th Congress of Gastroenterological Scientifi c Society of Russia.
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Affiliation(s)
| | - L. B. Lazebnik
- A. I. Yevdokimov Moscow State University of Medicine and Dentistry
| | | | | | | | | | | | | | | | - K. V. Kozlov
- Military Medical Academy named after S. M. Kirov
| | | | | | | | - D. V. Egorov
- Military Medical Academy named after S. M. Kirov
| | - E. I. Sas
- Military Medical Academy named after S. M. Kirov
| | | | | | - A. K. Ratnikova
- North-West District Scientifi c and Clinical Center named after L. G. Sokolov Federal Medical and Biological Agency
| | - V. A. Ratnikov
- North-West District Scientifi c and Clinical Center named after L. G. Sokolov Federal Medical and Biological Agency
| | - S. I. Sitkin
- North-Western state medical University named after I. I. Mechnikov;
Almazov National Medical Research Centre
| | | | | | | | - T. V. Ermolova
- North-Western state medical University named after I. I. Mechnikov
| | | | | | | | - N. M. Khomeriki
- Moscow Regional Research Clinical Institute n. a. M. F. Vladimirsky”
| | - T. L. Pilat
- Scientifi c Research Institute of labour medicine named after academician N. F. Izmerov
| | - L. P. Kuzmina
- Scientifi c Research Institute of labour medicine named after academician N. F. Izmerov;
I. M. Sechenov First Moscow State Medical University (Sechenov University)
| | | | | | | | - A. I. Khavkin
- Russian National Research Medical University named after N. I. Pirogov
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24
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Zhang F, Lau RI, Liu Q, Su Q, Chan FKL, Ng SC. Gut microbiota in COVID-19: key microbial changes, potential mechanisms and clinical applications. Nat Rev Gastroenterol Hepatol 2023; 20:323-337. [PMID: 36271144 PMCID: PMC9589856 DOI: 10.1038/s41575-022-00698-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/22/2022] [Indexed: 01/14/2023]
Abstract
The gastrointestinal tract is involved in coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The gut microbiota has important roles in viral entry receptor angiotensin-converting enzyme 2 (ACE2) expression, immune homeostasis, and crosstalk between the gut and lungs, the 'gut-lung axis'. Emerging preclinical and clinical studies indicate that the gut microbiota might contribute to COVID-19 pathogenesis and disease outcomes; SARS-CoV-2 infection was associated with altered intestinal microbiota and correlated with inflammatory and immune responses. Here, we discuss the cutting-edge evidence on the interactions between SARS-CoV-2 infection and the gut microbiota, key microbial changes in relation to COVID-19 severity and host immune dysregulations with the possible underlying mechanisms, and the conceivable consequences of the pandemic on the human microbiome and post-pandemic health. Finally, potential modulatory strategies of the gut microbiota are discussed. These insights could shed light on the development of microbiota-based interventions for COVID-19.
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Affiliation(s)
- Fen Zhang
- Microbiota I-Center (MagIC), Shatin, Hong Kong S.A.R., China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong S.A.R., China
- State Key Laboratory for Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong S.A.R., China
| | - Raphaela I Lau
- Microbiota I-Center (MagIC), Shatin, Hong Kong S.A.R., China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong S.A.R., China
- State Key Laboratory for Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong S.A.R., China
| | - Qin Liu
- Microbiota I-Center (MagIC), Shatin, Hong Kong S.A.R., China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong S.A.R., China
- State Key Laboratory for Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong S.A.R., China
| | - Qi Su
- Microbiota I-Center (MagIC), Shatin, Hong Kong S.A.R., China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong S.A.R., China
- State Key Laboratory for Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong S.A.R., China
| | - Francis K L Chan
- Microbiota I-Center (MagIC), Shatin, Hong Kong S.A.R., China
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong S.A.R., China
- State Key Laboratory for Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong S.A.R., China
| | - Siew C Ng
- Microbiota I-Center (MagIC), Shatin, Hong Kong S.A.R., China.
- Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong S.A.R., China.
- State Key Laboratory for Digestive Disease, Institute of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong S.A.R., China.
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25
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Tsounis EP, Triantos C, Konstantakis C, Marangos M, Assimakopoulos SF. Intestinal barrier dysfunction as a key driver of severe COVID-19. World J Virol 2023; 12:68-90. [PMID: 37033148 PMCID: PMC10075050 DOI: 10.5501/wjv.v12.i2.68] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/08/2022] [Accepted: 01/16/2023] [Indexed: 03/21/2023] Open
Abstract
The intestinal lumen harbors a diverse consortium of microorganisms that participate in reciprocal crosstalk with intestinal immune cells and with epithelial and endothelial cells, forming a multi-layered barrier that enables the efficient absorption of nutrients without an excessive influx of pathogens. Despite being a lung-centered disease, severe coronavirus disease 2019 (COVID-19) affects multiple systems, including the gastrointestinal tract and the pertinent gut barrier function. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can inflict either direct cytopathic injury to intestinal epithelial and endothelial cells or indirect immune-mediated damage. Alternatively, SARS-CoV-2 undermines the structural integrity of the barrier by modifying the expression of tight junction proteins. In addition, SARS-CoV-2 induces profound alterations to the intestinal microflora at phylogenetic and metabolomic levels (dysbiosis) that are accompanied by disruption of local immune responses. The ensuing dysregulation of the gut-lung axis impairs the ability of the respiratory immune system to elicit robust and timely responses to restrict viral infection. The intestinal vasculature is vulnerable to SARS-CoV-2-induced endothelial injury, which simultaneously triggers the activation of the innate immune and coagulation systems, a condition referred to as “immunothrombosis” that drives severe thrombotic complications. Finally, increased intestinal permeability allows an aberrant dissemination of bacteria, fungi, and endotoxin into the systemic circulation and contributes, to a certain degree, to the over-exuberant immune responses and hyper-inflammation that dictate the severe form of COVID-19. In this review, we aim to elucidate SARS-CoV-2-mediated effects on gut barrier homeostasis and their implications on the progression of the disease.
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Affiliation(s)
- Efthymios P Tsounis
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University Hospital of Patras, Patras 26504, Greece
| | - Christos Triantos
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University Hospital of Patras, Patras 26504, Greece
| | - Christos Konstantakis
- Division of Gastroenterology, Department of Internal Medicine, Medical School, University Hospital of Patras, Patras 26504, Greece
| | - Markos Marangos
- Division of Infectious Diseases, Department of Internal Medicine, Medical School, University of Patras, University Hospital of Patras, Patras 26504, Greece
| | - Stelios F Assimakopoulos
- Division of Infectious Diseases, Department of Internal Medicine, Medical School, University of Patras, University Hospital of Patras, Patras 26504, Greece
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26
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Wei L, Zhang L, Zhang Y, Yan L, Liu B, Cao Z, Zhao N, He X, Li L, Lu C. Intestinal Escherichia coli and related dysfunction as potential targets of Traditional Chinese Medicine for respiratory infectious diseases. JOURNAL OF ETHNOPHARMACOLOGY 2023; 313:116381. [PMID: 36940735 DOI: 10.1016/j.jep.2023.116381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/24/2023] [Accepted: 03/08/2023] [Indexed: 05/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Traditional Chinese medicine (TCM) has saved countless lives and maintained human health over its long history, especially in respiratory infectious diseases. The relationship between the intestinal flora and the respiratory system has been a popular research topic in recent years. According to the theory of the "gut-lung axis" in modern medicine and the idea that "the lung stands in an interior-exterior relationship with the large intestine" in TCM, gut microbiota dysbiosis is a contributing factor to respiratory infectious diseases, and there is potential means for manipulation of the gut microbiota in the treatment of lung diseases. Emerging studies have indicated intestinal Escherichia coli (E. coli) overgrowth in multiple respiratory infectious diseases, which could exacerbate respiratory infectious diseases by disrupting immune homeostasis, the gut barrier and metabolic balance. TCM is an effective microecological regulator, that can regulate the intestinal flora including E. coli, and restore the balance of the immune system, gut barrier, and metabolism. AIM OF THE REVIEW This review discusses the changes and effects of intestinal E. coli in respiratory infection, as well as the role of TCM in the intestinal flora, E. coli and related immunity, the gut barrier and the metabolism, thereby suggesting the possibility of TCM therapy regulating intestinal E. coli and related immunity, the gut barrier and the metabolism to alleviate respiratory infectious diseases. We aimed to make a modest contribution to the research and development of new therapies for intestinal flora in respiratory infectious diseases and the full utilization of TCM resources. Relevant information about the therapeutic potential of TCM to regulate intestinal E. coli against diseases was collected from PubMed, China National Knowledge Infrastructure (CNKI), and so on. The Plants of the World Online (https://wcsp.science.kew.org) and the Plant List (www.theplantlist.org) databases were used to provide the scientific names and species of plants. RESULTS Intestinal E. coli is a very important bacterium in respiratory infectious diseases that affects the respiratory system through immunity, the gut barrier and the metabolism. Many TCMs can inhibit the abundance of E. coli and regulate related immunity, the gut barrier and the metabolism to promote lung health. CONCLUSION TCM targeting intestinal E. coli and related immune, gut barrier, and metabolic dysfunction could be a potential therapy to promote the treatment and prognosis of respiratory infectious diseases.
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Affiliation(s)
- Lini Wei
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Lulu Zhang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Yan Zhang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Lan Yan
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Bin Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Zhiwen Cao
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Ning Zhao
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China
| | - Xiaojuan He
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China.
| | - Li Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China.
| | - Cheng Lu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, PR China.
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Eleftheriotis G, Tsounis EP, Aggeletopoulou I, Dousdampanis P, Triantos C, Mouzaki A, Marangos M, Assimakopoulos SF. Alterations in gut immunological barrier in SARS-CoV-2 infection and their prognostic potential. Front Immunol 2023; 14:1129190. [PMID: 37006316 PMCID: PMC10050566 DOI: 10.3389/fimmu.2023.1129190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/06/2023] [Indexed: 03/17/2023] Open
Abstract
Although coronavirus disease 2019 (COVID-19) is primarily associated with mild respiratory symptoms, a subset of patients may develop more complicated disease with systemic complications and multiple organ injury. The gastrointestinal tract may be directly infected by SARS-CoV-2 or secondarily affected by viremia and the release of inflammatory mediators that cause viral entry from the respiratory epithelium. Impaired intestinal barrier function in SARS-CoV-2 infection is a key factor leading to excessive microbial and endotoxin translocation, which triggers a strong systemic immune response and leads to the development of viral sepsis syndrome with severe sequelae. Multiple components of the gut immune system are affected, resulting in a diminished or dysfunctional gut immunological barrier. Antiviral peptides, inflammatory mediators, immune cell chemotaxis, and secretory immunoglobulins are important parameters that are negatively affected in SARS-CoV-2 infection. Mucosal CD4+ and CD8+ T cells, Th17 cells, neutrophils, dendritic cells, and macrophages are activated, and the number of regulatory T cells decreases, promoting an overactivated immune response with increased expression of type I and III interferons and other proinflammatory cytokines. The changes in the immunologic barrier could be promoted in part by a dysbiotic gut microbiota, through commensal-derived signals and metabolites. On the other hand, the proinflammatory intestinal environment could further compromise the integrity of the intestinal epithelium by promoting enterocyte apoptosis and disruption of tight junctions. This review summarizes the changes in the gut immunological barrier during SARS-CoV-2 infection and their prognostic potential.
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Affiliation(s)
- Gerasimos Eleftheriotis
- Division of Infectious Diseases, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Efthymios P. Tsounis
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, Patras, Greece
| | - Ioanna Aggeletopoulou
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, Patras, Greece
- Laboratory of Immunohematology, Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Periklis Dousdampanis
- Department of Renal Diseases, “Agios Andreas” Patras State General Hospital, Patras, Greece
| | - Christos Triantos
- Division of Gastroenterology, Department of Internal Medicine, University Hospital of Patras, Patras, Greece
| | - Athanasia Mouzaki
- Laboratory of Immunohematology, Division of Hematology, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Markos Marangos
- Division of Infectious Diseases, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
| | - Stelios F. Assimakopoulos
- Division of Infectious Diseases, Department of Internal Medicine, Medical School, University of Patras, Patras, Greece
- *Correspondence: Stelios F. Assimakopoulos,
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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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Trøseid M, Holter JC, Holm K, Vestad B, Sazonova T, Granerud BK, Dyrhol-Riise AM, Holten AR, Tonby K, Kildal AB, Heggelund L, Tveita A, Bøe S, Müller KE, Jenum S, Hov JR, Ueland T. Gut microbiota composition during hospitalization is associated with 60-day mortality after severe COVID-19. Crit Care 2023; 27:69. [PMID: 36814280 PMCID: PMC9946863 DOI: 10.1186/s13054-023-04356-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/12/2023] [Indexed: 02/24/2023] Open
Abstract
BACKGROUND Gut microbiota alterations have been reported in hospitalized COVID-19 patients, with reduced alpha diversity and altered microbiota composition related to respiratory failure. However, data regarding gut microbiota and mortality are scarce. METHODS Rectal swabs for gut microbiota analyses were collected within 48 h after hospital admission (baseline; n = 123) and three-month post-admission (n = 50) in a subset of patients included in the Norwegian SARS-CoV2 cohort study. Samples were analysed by sequencing the 16S rRNA gene. Gut microbiota diversity and composition at baseline were assessed in relation to need for intensive care unit (ICU) admission during hospitalization. The primary objective was to investigate whether the ICU-related gut microbiota was associated with 60-day mortality. RESULTS Gut microbiota diversity (Shannon index) at baseline was lower in COVID-19 patients requiring ICU admission during hospitalization than in those managed in general wards. A dysbiosis index representing a balance of enriched and reduced taxa in ICU compared with ward patients, including decreased abundance of butyrate-producing microbes and enrichment of a partly oral bacterial flora, was associated with need of ICU admission independent of antibiotic use, dexamethasone use, chronic pulmonary disease, PO2/FiO2 ratio, C-reactive protein, neutrophil counts or creatinine levels (adjusted p < 0.001). The ICU-related dysbiosis index at baseline correlated with systemic inflammation and was associated with 60-day mortality in univariate analyses (Hazard ratio 3.70 [2.00-8.6], p < 0.001), as well as after separate adjustment for covariates. At the three-month follow-up, the dysbiosis index remained elevated in ICU patients compared with ward patients (adjusted p = 0.007). CONCLUSIONS Although our data should be regarded as exploratory due to low number of clinical end points, they suggest that gut microbiota alterations during hospitalization could be related to poor prognosis after severe COVID-19. Larger studies of gut involvement during COVID-19 in relation to long-term clinical outcome are warranted. Trial registration NCT04381819 . Retrospectively registered May 11, 2020.
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Affiliation(s)
- Marius Trøseid
- Research Institute of Internal Medicine, Oslo University Hospital, 0424, Oslo, Norway. .,Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, 0424, Oslo, Norway. .,Institute of Clinical Medicine, University of Oslo, 0315, Oslo, Norway.
| | - Jan Cato Holter
- grid.5510.10000 0004 1936 8921Institute of Clinical Medicine, University of Oslo, 0315 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Kristian Holm
- grid.55325.340000 0004 0389 8485Research Institute of Internal Medicine, Oslo University Hospital, 0424 Oslo, Norway ,grid.5510.10000 0004 1936 8921Institute of Clinical Medicine, University of Oslo, 0315 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Transplantation Medicine, Norwegian PSC Research Center, Oslo University Hospital, Oslo, Norway
| | - Beate Vestad
- grid.55325.340000 0004 0389 8485Research Institute of Internal Medicine, Oslo University Hospital, 0424 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Transplantation Medicine, Norwegian PSC Research Center, Oslo University Hospital, Oslo, Norway
| | - Taisiia Sazonova
- grid.55325.340000 0004 0389 8485Research Institute of Internal Medicine, Oslo University Hospital, 0424 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Transplantation Medicine, Norwegian PSC Research Center, Oslo University Hospital, Oslo, Norway
| | - Beathe K. Granerud
- grid.5510.10000 0004 1936 8921Institute of Clinical Medicine, University of Oslo, 0315 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Anne Ma Dyrhol-Riise
- grid.5510.10000 0004 1936 8921Institute of Clinical Medicine, University of Oslo, 0315 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Infectious Diseases, Oslo University Hospital, 0424 Oslo, Norway
| | - Aleksander R. Holten
- grid.5510.10000 0004 1936 8921Institute of Clinical Medicine, University of Oslo, 0315 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Acute Medicine, Oslo University Hospital, Oslo, Norway
| | - Kristian Tonby
- grid.5510.10000 0004 1936 8921Institute of Clinical Medicine, University of Oslo, 0315 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Infectious Diseases, Oslo University Hospital, 0424 Oslo, Norway
| | - Anders Benjamin Kildal
- grid.412244.50000 0004 4689 5540Department of Anesthesiology and Intensive Care, University Hospital of North Norway, 9019 Tromsö, Norway ,grid.10919.300000000122595234Department of Clinical Medicine, Faculty of Health Sciences, UIT – The Arctic University of Norway, 9019 Tromsö, Norway
| | - Lars Heggelund
- grid.470118.b0000 0004 0627 3835Department of Internal Medicine, Drammen Hospital, Vestre Viken Hospital Trust, 3004 Drammen, Norway ,grid.7914.b0000 0004 1936 7443Department of Clinical Science, Faculty of Medicine, University of Bergen, 5009 Bergen, Norway
| | - Anders Tveita
- grid.55325.340000 0004 0389 8485Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, 0424 Oslo, Norway ,grid.414168.e0000 0004 0627 3595Department of Internal Medicine, Bærum Hospital, Vestre Viken Hospital Trust, 1346 Gjettum, Norway
| | - Simen Bøe
- Department of Anesthesiology and Intensive Care, Hammerfest County Hospital, Hammerfest, Norway
| | - Karl Erik Müller
- grid.470118.b0000 0004 0627 3835Department of Internal Medicine, Drammen Hospital, Vestre Viken Hospital Trust, 3004 Drammen, Norway
| | - Synne Jenum
- grid.55325.340000 0004 0389 8485Department of Infectious Diseases, Oslo University Hospital, 0424 Oslo, Norway
| | - Johannes R. Hov
- grid.55325.340000 0004 0389 8485Research Institute of Internal Medicine, Oslo University Hospital, 0424 Oslo, Norway ,grid.5510.10000 0004 1936 8921Institute of Clinical Medicine, University of Oslo, 0315 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Transplantation Medicine, Norwegian PSC Research Center, Oslo University Hospital, Oslo, Norway ,grid.55325.340000 0004 0389 8485Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Thor Ueland
- grid.55325.340000 0004 0389 8485Research Institute of Internal Medicine, Oslo University Hospital, 0424 Oslo, Norway ,grid.5510.10000 0004 1936 8921Institute of Clinical Medicine, University of Oslo, 0315 Oslo, Norway ,grid.10919.300000000122595234K.G. Jebsen-Thrombosis Research and Expertise Center (TREC), UIT – The Arctic University of Norway, Tromsö, Norway
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30
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Association between Gut Microbiota and SARS-CoV-2 Infection and Vaccine Immunogenicity. Microorganisms 2023; 11:microorganisms11020452. [PMID: 36838417 PMCID: PMC9961186 DOI: 10.3390/microorganisms11020452] [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: 01/08/2023] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Gut microbiota is increasingly recognized to play a pivotal role in various human physiological functions and diseases. Amidst the COVID-19 pandemic, research has suggested that dysbiosis of the gut microbiota is also involved in the development and severity of COVID-19 symptoms by regulating SARS-CoV-2 entry and modulating inflammation. Previous studies have also suggested that gut microbiota and their metabolites could have immunomodulatory effects on vaccine immunogenicity, including influenza vaccines and oral rotavirus vaccines. In light of these observations, it is possible that gut microbiota plays a role in influencing the immune responses to COVID-19 vaccinations via similar mechanisms including effects of lipopolysaccharides, flagellin, peptidoglycan, and short-chain fatty acids. In this review, we give an overview of the current understanding on the role of the gut microbiota in COVID-19 manifestations and vaccine immunogenicity. We then discuss the limitations of currently published studies on the associations between gut microbiota and COVID-19 vaccine outcomes. Future research directions shall be focused on the development of microbiota-based interventions on improving immune response to SARS-CoV-2 infection and vaccinations.
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31
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Zhang L, Zhang Y, Wang R, Liu X, Zhao J, Tsuda M, Li Y. SARS-CoV-2 infection of intestinal epithelia cells sensed by RIG-I and DHX-15 evokes innate immune response and immune cross-talk. Front Cell Infect Microbiol 2023; 12:1035711. [PMID: 36825215 PMCID: PMC9941539 DOI: 10.3389/fcimb.2022.1035711] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 12/13/2022] [Indexed: 02/10/2023] Open
Abstract
SARS-CoV-2 causes a spectrum of clinical symptoms from respiratory damage to gastrointestinal disorders. Intestinal infection of SARS-CoV-2 triggers immune response. However, the cellular mechanism that how SARS-CoV-2 initiates and induces intestinal immunity is not understood. Here, we exploited SARS-CoV-2-GFP/ΔN trVLP pseudo-virus system and demonstrated that RIG-I and DHX15 are required for sensing SARS-CoV-2 and inducing cellular immune response through MAVS signaling in intestinal epithelial cells (IECs) upon SARS-CoV-2 infection. NLRP6 also engages in the regulation of SARS-CoV-2 immunity by producing IL-18. Furthermore, primary cellular immune response provoked by SARS-CoV-2 in IECs further cascades activation of MAIT cells and produces cytotoxic cytokines including IFN-γ, granzyme B via an IL-18 dependent mechanism. These findings taken together unveil molecular basis of immune recognition in IECs in response to SARS-CoV-2, and provide insights that intestinal immune cross-talk with other immune cells triggers amplified immunity and probably contributes to immunopathogenesis of COVID-19.
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Affiliation(s)
- Lijuan Zhang
- School of Medicine, Huanghe Science and Technology College, Zhengzhou, China
| | - Yize Zhang
- Precision Medicine Center, Gene Hospital of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ruiqin Wang
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Xiaoning Liu
- School of Medicine, Huanghe Science and Technology College, Zhengzhou, China
| | - Jinmeng Zhao
- School of Life Science, Zhengzhou University, Zhengzhou, China
| | - Masato Tsuda
- School of Medicine, Niigata University, Niigata, Japan
| | - You Li
- School of Medicine, Huanghe Science and Technology College, Zhengzhou, China,School of Life Science and Technology, Tongji University, Shanghai, China,*Correspondence: You Li,
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32
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Muske J, Knoop K. Contributions of the microbiota to the systemic inflammatory response. MICROBIOTA AND HOST 2023; 1:e230018. [PMID: 38872988 PMCID: PMC11170979 DOI: 10.1530/mah-23-0018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
The health of the intestinal microbiota impacts tolerance at homeostasis and the strength of the inflammation response during acute bloodstream infections. A complete understanding of the feedback loop between systemic inflammation and dysregulation of the gut microbiota is necessary for inflammation management. Here we will review the many ways in which the microbiota can influence the systemic pro-inflammatory response. Short-chain fatty acids, produced through the microbial metabolism of dietary fibers, can suppress inflammation systemically; in the absence of a balanced diet or disruption of the microbiota through antibiotics, there is disrupted metabolite production, leading to systemic inflammation. Dysbiosis or inflammation in the intestines can lead to a breakdown of the sturdy intestinal-epithelial barrier. When this barrier is perturbed, immunogenic lipopolysaccharides or extracellular vesicles enter the bloodstream and induce excessive inflammation. Necessary clinical treatments, such as antifungals or antibacterials, induce microbiota dysregulation and thus increased risk of endotoxemia; though probiotics may aid in improving the microbiota health and have been shown to deflate inflammation during sepsis. Within this complicated relationship: What is in control, the dysbiotic microbiota or the systemic inflammation?
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Affiliation(s)
- Josey Muske
- Mayo Graduate School of Biomedical Sciences
- Department of Immunology, Mayo Clinic Rochester, MN USA
| | - Kathryn Knoop
- Department of Immunology, Mayo Clinic Rochester, MN USA
- Department of Pediatrics, Mayo Clinic Rochester, MN USA
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Mauro CSI, Hassani MK, Barone M, Esposito MT, Calle Y, Behrends V, Garcia S, Brigidi P, Turroni S, Costabile A. Cerrado and Pantanal fruit flours affect gut microbiota composition in healthy and post-COVID-19 individuals: an in vitro pilot fermentation study. Int J Food Sci Technol 2023; 58:IJFS16274. [PMID: 36721386 PMCID: PMC9880733 DOI: 10.1111/ijfs.16274] [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: 11/02/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
Cerrado and Pantanal plants can provide fruits with high nutritional value and antioxidants. This study aims to evaluate four fruit flours (from jatobá pulp, cumbaru almond, bocaiuva pulp and bocaiuva almond) and their effects on the gut microbiota in healthy (HD) and post-COVID-19 individuals (PC). An in vitro batch system was carried out, the microbiota was analysed by 16S rRNA amplicon sequencing and the short-chain fatty acids ratio was determined. Furthermore, the effect of jatobá pulp flour oil (JAO) on cell viability, oxidative stress and DNA damage was investigated in a myelo-monocytic cell line. Beyond confirming a microbiota imbalance in PC, we identified flour-specific effects: (i) reduction of Veillonellaceae with jatobá extract in PC samples; (ii) decrease in Akkermansia with jatoba and cumbaru flours; (iii) decreasing trend of Faecalibacterium and Ruminococcus with all flours tested, with the exception of the bocaiuva almond in HD samples for Ruminococcus and (iv) increase in Lactobacillus and Bifidobacterium in PC samples with bocaiuva almond flour. JAO displayed antioxidant properties protecting cells from daunorubicin-induced cytotoxicity, oxidative stress and DNA damage. The promising microbiota-modulating abilities of some flours and the chemopreventive effects of JAO deserve to be further explored in human intervention studies.
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Affiliation(s)
| | | | - Monica Barone
- Microbiomics Unit, Department of Medical and Surgical SciencesUniversity of BolognaBologna40138Italy
| | | | - Yolanda Calle
- School of Life and Health SciencesUniversity of RoehamptonLondonSW15 4JDUK
| | - Volker Behrends
- School of Life and Health SciencesUniversity of RoehamptonLondonSW15 4JDUK
| | - Sandra Garcia
- Department of Food Science and TechnologyState University of LondrinaLondrina86057‐970Brazil
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical SciencesUniversity of BolognaBologna40138Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and BiotechnologyUniversity of BolognaBologna40126Italy
| | - Adele Costabile
- School of Life and Health SciencesUniversity of RoehamptonLondonSW15 4JDUK
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Gradisteanu Pircalabioru G, Grigore GA, Czobor Barbu I, Chifiriuc MC, Savu O. Impact of COVID-19 on the Microbiome and Inflammatory Status of Type 2 Diabetes Patients. Biomedicines 2023; 11:biomedicines11010179. [PMID: 36672688 PMCID: PMC9856008 DOI: 10.3390/biomedicines11010179] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/12/2023] Open
Abstract
The severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) pandemic has advanced our understanding of the host-microbiome-virus interplay. Several studies in various geographical regions report that SARS-CoV-2 infection disrupts the intestinal microbiota, allowing pathogenic bacteria such as Enterobacteriaceae to thrive, and triggering more severe disease outcomes. Here, we profile the microbiota of 30 individuals, 15 healthy controls and 15 type 2 diabetes (T2D) patients, before and after coronavirus disease 2019 (COVID-19). Despite similar viral loads in both patients and controls, SARS-CoV-2 infection led to exacerbated microbiome changes in T2D patients, characterized by higher levels of Enterobacteriaceae, loss of butyrate producers and an enrichment in fungi such as Candida spp. and Aspergillus spp. Several members of the microbiota were associated with more severe clinical and inflammatory (IL-8 and IL-17) parameters. Future studies to delineate the connection between cytokine release and microbiota disturbances will enhance our understanding of whether these microbial shifts directly impact the cytokine storm in COVID-19 patients or whether they are consecutive to the critical disease.
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Affiliation(s)
- Gratiela Gradisteanu Pircalabioru
- Research Institute of University of Bucharest (ICUB), 050095 Bucharest, Romania
- Academy of Romanian Scientists, 050045 Bucharest, Romania
- Correspondence:
| | - Georgiana Alexandra Grigore
- Academy of Romanian Scientists, 050045 Bucharest, Romania
- Faculty of Biology, University of Bucharest, 050095 Bucharesti, Romania
| | - Ilda Czobor Barbu
- Academy of Romanian Scientists, 050045 Bucharest, Romania
- Faculty of Biology, University of Bucharest, 050095 Bucharesti, Romania
| | - Mariana-Carmen Chifiriuc
- Research Institute of University of Bucharest (ICUB), 050095 Bucharest, Romania
- Academy of Romanian Scientists, 050045 Bucharest, Romania
- Faculty of Biology, University of Bucharest, 050095 Bucharesti, Romania
- Romanian Academy, 010071 Bucharest, Romania
| | - Octavian Savu
- “N.C. Paulescu” National Institute of Diabetes, Nutrition and Metabolic Diseases, 020042 Bucharest, Romania
- Department of Doctoral School, “Carol Davila” University of Medicine and Pharmacy, 5th District, 050474 Bucharest, Romania
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Khreefa Z, Barbier MT, Koksal AR, Love G, Del Valle L. Pathogenesis and Mechanisms of SARS-CoV-2 Infection in the Intestine, Liver, and Pancreas. Cells 2023; 12:cells12020262. [PMID: 36672197 PMCID: PMC9856332 DOI: 10.3390/cells12020262] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/30/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
The novel coronavirus, SARS-CoV-2, rapidly spread worldwide, causing an ongoing global pandemic. While the respiratory system is the most common site of infection, a significant number of reported cases indicate gastrointestinal (GI) involvement. GI symptoms include anorexia, abdominal pain, nausea, vomiting, and diarrhea. Although the mechanisms of GI pathogenesis are still being examined, viral components isolated from stool samples of infected patients suggest a potential fecal-oral transmission route. In addition, viral RNA has been detected in blood samples of infected patients, making hematologic dissemination of the virus a proposed route for GI involvement. Angiotensin-converting enzyme 2 (ACE2) receptors serve as the cellular entry mechanism for the virus, and these receptors are particularly abundant throughout the GI tract, making the intestine, liver, and pancreas potential extrapulmonary sites for infection and reservoirs sites for developing mutations and new variants that contribute to the uncontrolled spread of the disease and resistance to treatments. This transmission mechanism and the dysregulation of the immune system play a significant role in the profound inflammatory and coagulative cascades that contribute to the increased severity and risk of death in several COVID-19 patients. This article reviews various potential mechanisms of gastrointestinal, liver, and pancreatic injury.
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Affiliation(s)
- Zaid Khreefa
- Department of Pathology, School of Medicine, Louisiana State University Health School of Medicine, New Orleans, LA 70112, USA
| | - Mallory T. Barbier
- Louisiana Cancer Research Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Ali Riza Koksal
- Department of Pathology and Laboratory Medicine, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Gordon Love
- Department of Pathology, School of Medicine, Louisiana State University Health School of Medicine, New Orleans, LA 70112, USA
| | - Luis Del Valle
- Department of Pathology, School of Medicine, Louisiana State University Health School of Medicine, New Orleans, LA 70112, USA
- Louisiana Cancer Research Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
- Correspondence:
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36
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Malan-Müller S, Valles-Colomer M, Palomo T, Leza JC. The gut-microbiota-brain axis in a Spanish population in the aftermath of the COVID-19 pandemic: microbiota composition linked to anxiety, trauma, and depression profiles. Gut Microbes 2023; 15:2162306. [PMID: 36651663 PMCID: PMC9851210 DOI: 10.1080/19490976.2022.2162306] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
The prevalence of anxiety and depression soared following the COVID-19 pandemic. To effectively treat these conditions, a comprehensive understanding of all etiological factors is needed. This study investigated fecal microbial features associated with mental health outcomes (symptoms of anxiety, depression, or posttraumatic stress disorder (PTSD)) in a Spanish cohort in the aftermath of the COVID-19 pandemic. Microbial communities from stool samples were profiled in 198 individuals who completed validated, self-report questionnaires. 16S ribosomal RNA gene V3-4 amplicon sequencing was performed. Microbial diversity and community structure were analyzed, together with relative taxonomic abundance. In our cohort of N=198, 17.17% reported depressive symptoms, 37.37% state anxiety symptoms, 40.90% trait anxiety symptoms, and 8.08% PTSD symptoms, with high levels of comorbidity. Individuals with trait anxiety had lower Simpson's diversity. Fusicatenibacter saccharivorans was reduced in individuals with comorbid PTSD + depression + state and trait anxiety symptoms, whilst an expansion of Proteobacteria and depletion of Synergistetes phyla were noted in individuals with depressive symptoms. The relative abundance of Anaerostipes was positively correlated with childhood trauma, and higher levels of Turicibacter sanguinis and lower levels of Lentisphaerae were found in individuals who experienced life-threatening traumas. COVID-19 infection and vaccination influenced the overall microbial composition and were associated with distinct relative taxonomic abundance profiles. These findings will help lay the foundation for future studies to identify microbial role players in symptoms of anxiety, depression, and PTSD and provide future therapeutic targets to improve mental health outcomes.
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Affiliation(s)
- Stefanie Malan-Müller
- Department of Pharmacology and Toxicology, Faculty of Medicine, University Complutense Madrid (UCM), Madrid, Spain
- Biomedical Network Research Center of Mental Health (CIBERSAM), Institute of Health Carlos III, Madrid, Spain
- Neurochemistry Research Institute UCM, Hospital 12 de Octubre Research Institute (Imas12), Madrid, Spain
| | - Mireia Valles-Colomer
- Department of Cellular Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Tomás Palomo
- Biomedical Network Research Center of Mental Health (CIBERSAM), Institute of Health Carlos III, Madrid, Spain
- Neurochemistry Research Institute UCM, Hospital 12 de Octubre Research Institute (Imas12), Madrid, Spain
| | - Juan C. Leza
- Department of Pharmacology and Toxicology, Faculty of Medicine, University Complutense Madrid (UCM), Madrid, Spain
- Biomedical Network Research Center of Mental Health (CIBERSAM), Institute of Health Carlos III, Madrid, Spain
- Neurochemistry Research Institute UCM, Hospital 12 de Octubre Research Institute (Imas12), Madrid, Spain
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37
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Wang M, Zhang Y, Li C, Chang W, Zhang L. The relationship between gut microbiota and COVID-19 progression: new insights into immunopathogenesis and treatment. Front Immunol 2023; 14:1180336. [PMID: 37205106 PMCID: PMC10185909 DOI: 10.3389/fimmu.2023.1180336] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/17/2023] [Indexed: 05/21/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a global health crisis. Increasing evidence underlines the key role of competent immune responses in resisting SARS-CoV-2 infection and manifests the disastrous consequence of host immune dysregulation. Elucidating the mechanisms responsible for deregulated host immunity in COVID-19 may provide a theoretical basis for further research on new treatment modalities. Gut microbiota comprises trillions of microorganisms colonizing the human gastrointestinal tract and has a vital role in immune homeostasis and the gut-lung crosstalk. Particularly, SARS-CoV-2 infection can lead to the disruption of gut microbiota equilibrium, a condition called gut dysbiosis. Due to its regulatory effect on host immunity, gut microbiota has recently received considerable attention in the field of SARS-CoV-2 immunopathology. Imbalanced gut microbiota can fuel COVID-19 progression through production of bioactive metabolites, intestinal metabolism, enhancement of the cytokine storm, exaggeration of inflammation, regulation of adaptive immunity and other aspects. In this review, we provide an overview of the alterations in gut microbiota in COVID-19 patients, and their effects on individuals' susceptibility to viral infection and COVID-19 progression. Moreover, we summarize currently available data on the critical role of the bidirectional regulation between intestinal microbes and host immunity in SARS-CoV-2-induced pathology, and highlight the immunomodulatory mechanisms of gut microbiota contributing to COVID-19 pathogenesis. In addition, we discuss the therapeutic benefits and future perspectives of microbiota-targeted interventions including faecal microbiota transplantation (FMT), bacteriotherapy and traditional Chinese medicine (TCM) in COVID-19 treatment.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
- *Correspondence: Man Wang, ; Chunmei Li,
| | - Yuan Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Chunmei Li
- Department of Radiology, Qingdao Municipal Hospital, Qingdao, China
- *Correspondence: Man Wang, ; Chunmei Li,
| | - Wenguang Chang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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38
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Xiang H, Liu QP. Alterations of the gut microbiota in coronavirus disease 2019 and its therapeutic potential. World J Gastroenterol 2022; 28:6689-6701. [PMID: 36620345 PMCID: PMC9813939 DOI: 10.3748/wjg.v28.i47.6689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/07/2022] [Accepted: 11/23/2022] [Indexed: 12/19/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a serious threat to global health. SARS-CoV-2 infects host cells primarily by binding to angiotensin-converting enzyme 2, which is coexpressed in alveolar type 2 cells and gut epithelial cells. It is known that COVID-19 often presents with gastrointestinal symptoms and gut dysbiosis, mainly characterized by an increase in opportunistic pathogens and a decrease in beneficial commensal bacteria. In recent years, multiple studies have comprehensively explored gut microbiota alterations in COVID-19 and highlighted the clinical correlation between dysbiosis and COVID-19. SARS-CoV-2 causes gastrointestinal infections and dysbiosis mainly through fecal-oral transmission and the circulatory and immune pathways. Studies have shown that the gut microbiota and its metabolites can regulate the immune response and modulate antiviral effects. In addition, the gut microbiota is closely related to gastrointestinal symptoms, such as diarrhea, a common gastrointestinal symptom among COVID-19. Therefore, the contribution of the gut microbiota in COVID-19 should not be overlooked. Strategies targeting the gut microbiota via probiotics, prebiotics and fecal microbiota transplantation should be considered to treat this patient population in the future. However, the specific alterations and mechanisms as well as the contributions of gut microbiota in COVID-19 should be urgently further explored.
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Affiliation(s)
- Hui Xiang
- Department of Infectious Disease, Chongqing University Three Gorges Hospital, Chongqing 404100, China
| | - Qi-Ping Liu
- Department of Pulmonary and Critical Care Medicine, Chongqing University Three Gorges Hospital, Chongqing 404100, China
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39
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Neag MA, Vulturar DM, Gherman D, Burlacu CC, Todea DA, Buzoianu AD. Gastrointestinal microbiota: A predictor of COVID-19 severity? World J Gastroenterol 2022; 28:6328-6344. [PMID: 36533107 PMCID: PMC9753053 DOI: 10.3748/wjg.v28.i45.6328] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/26/2022] [Accepted: 11/17/2022] [Indexed: 12/02/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by a severe acute respiratory syndrome coronavirus 2 infection, has raised serious concerns worldwide over the past 3 years. The severity and clinical course of COVID-19 depends on many factors (e.g., associated comorbidities, age, etc) and may have various clinical and imaging findings, which raises management concerns. Gut microbiota composition is known to influence respiratory disease, and respiratory viral infection can also influence gut microbiota. Gut and lung microbiota and their relationship (gut-lung axis) can act as modulators of inflammation. Modulating the intestinal microbiota, by improving its composition and diversity through nutraceutical agents, can have a positive impact in the prophylaxis/treatment of COVID-19.
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Affiliation(s)
- Maria Adriana Neag
- Department of Pharmacology, Toxicology and Clinical Pharmacology, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania
| | - Damiana-Maria Vulturar
- Department of Pneumology, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca 400332, Romania
| | - Diana Gherman
- Department of Radiology, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca 400347, Romania
| | - Codrin-Constantin Burlacu
- Faculty of Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca 400347, Romania
| | - Doina Adina Todea
- Department of Pneumology, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca 400332, Romania
| | - Anca Dana Buzoianu
- Department of Pharmacology, Toxicology and Clinical Pharmacology, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca 400337, Romania
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40
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Yadav A, Pandey R. Viral infectious diseases severity: co-presence of transcriptionally active microbes (TAMs) can play an integral role for disease severity. Front Immunol 2022; 13:1056036. [PMID: 36532032 PMCID: PMC9755851 DOI: 10.3389/fimmu.2022.1056036] [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] [Accepted: 11/21/2022] [Indexed: 12/04/2022] Open
Abstract
Humans have been challenged by infectious diseases for all of their recorded history, and are continually being affected even today. Next-generation sequencing (NGS) has enabled identification of, i) culture independent microbes, ii) emerging disease-causing pathogens, and iii) understanding of the genome architecture. This, in turn, has highlighted that pathogen/s are not a monolith, and thereby allowing for the differentiation of the wide-ranging disease symptoms, albeit infected by a primary pathogen. The conventional 'one disease - one pathogen' paradigm has been positively revisited by considering limited yet important evidence of the co-presence of multiple transcriptionally active microbes (TAMs), potential pathogens, in various infectious diseases, including the COVID-19 pandemic. The ubiquitous microbiota presence inside humans gives reason to hypothesize that the microbiome, especially TAMs, contributes to disease etiology. Herein, we discuss current evidence and inferences on the co-infecting microbes particularly in the diseases caused by the RNA viruses - Influenza, Dengue, and the SARS-CoV-2. We have highlighted that the specific alterations in the microbial taxonomic abundances (dysbiosis) is functionally connected to the exposure of primary infecting pathogen/s. The microbial presence is intertwined with the differential host immune response modulating differential disease trajectories. The microbiota-host interactions have been shown to modulate the host immune responses to Influenza and SARS-CoV-2 infection, wherein the active commensal microbes are involved in the generation of virus-specific CD4 and CD8 T-cells following the influenza virus infection. Furthermore, COVID-19 dysbiosis causes an increase in inflammatory cytokines such as IL-6, TNF-α, and IL-1β, which might be one of the important predisposing factors for severe infection. Through this article, we aim to provide a comprehensive view of functional microbiomes that can have a significant regulatory impact on predicting disease severity (mild, moderate and severe), as well as clinical outcome (survival and mortality). This can offer fresh perspectives on the novel microbial biomarkers for stratifying patients for severe disease symptoms, disease prevention and augmenting treatment regimens.
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Affiliation(s)
- Aanchal Yadav
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India,*Correspondence: Rajesh Pandey, ;
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41
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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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42
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Yin YS, Minacapelli CD, Parmar V, Catalano CC, Bhurwal A, Gupta K, Rustgi VK, Blaser MJ. Alterations of the fecal microbiota in relation to acute COVID-19 infection and recovery. MOLECULAR BIOMEDICINE 2022; 3:36. [PMID: 36437420 PMCID: PMC9702442 DOI: 10.1186/s43556-022-00103-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Abstract
People with acute COVID-19 due to SARS-CoV-2 infection experience a range of symptoms, but major factors contributing to severe clinical outcomes remain to be understood. Emerging evidence suggests associations between the gut microbiome and the severity and progression of COVID-19. To better understand the host-microbiota interactions in acute COVID-19, we characterized the intestinal microbiome of patients with active SARS-CoV-2 infection in comparison to recovered patients and uninfected healthy controls. We performed 16S rRNA sequencing of stool samples collected between May 2020 and January 2021 from 20 COVID-19-positive patients, 20 COVID-19-recovered subjects and 20 healthy controls. COVID-19-positive patients had altered microbiome community characteristics compared to the recovered and control subjects, as assessed by both α- and β-diversity differences. In COVID-19-positive patients, we observed depletion of Bacteroidaceae, Ruminococcaceae, and Lachnospiraceae, as well as decreased relative abundances of the genera Faecalibacterium, Adlercreutzia, and the Eubacterium brachy group. The enrichment of Prevotellaceae with COVID-19 infection continued after viral clearance; antibiotic use induced further gut microbiota perturbations in COVID-19-positive patients. In conclusion, we present evidence that acute COVID-19 induces gut microbiota dysbiosis with depletion of particular populations of commensal bacteria, a phenomenon heightened by antibiotic exposure, but the general effects do not persist post-recovery.
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Affiliation(s)
- Yue Sandra Yin
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Carlos D Minacapelli
- Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, NJ, USA.,Center for Liver Diseases and Liver Masses, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Veenat Parmar
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Carolyn C Catalano
- Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, NJ, USA.,Center for Liver Diseases and Liver Masses, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Abhishek Bhurwal
- Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, NJ, USA.,Center for Liver Diseases and Liver Masses, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Kapil Gupta
- Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, NJ, USA.,Center for Liver Diseases and Liver Masses, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Vinod K Rustgi
- Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, NJ, USA. .,Center for Liver Diseases and Liver Masses, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.
| | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA.
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Righi E, Lambertenghi L, Gorska A, Sciammarella C, Ivaldi F, Mirandola M, Sartor A, Tacconelli E. Impact of COVID-19 and Antibiotic Treatments on Gut Microbiome: A Role for Enterococcus spp. Biomedicines 2022; 10:2786. [PMID: 36359311 PMCID: PMC9687172 DOI: 10.3390/biomedicines10112786] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 08/29/2023] Open
Abstract
OBJECTIVE Several studies showed the substantial use of antibiotics and increased risk of antimicrobial resistant infections in patients with COVID-19. The impact of COVID-19-related treatments and antibiotics on gut dysbiosis has not been clarified. DESIGN The prospective cohort study included hospitalized COVID-19 patients (April-December 2020). The gut microbiome composition was analysed by 16S sequencing. The gut diversity and changes in opportunistic bacteria (OBs) or symbionts were analysed according to clinical parameters, laboratory markers of disease progression, type of non-antibiotic COVID-19 treatments (NACT) and type, WHO AWaRe group, and duration of antibiotic therapy (AT). RESULTS A total of 82 patients (mean age 66 ± 13 years, 70% males) were enrolled. The relative abundance of Enterococcus was significantly correlated with duration of hospitalization, intensive care unit stay, O2 needs, and D-dimer, ferritin, and IL-6 blood levels. The presence of Enterococcus showed the highest number of correlations with NACT, AT, and AT + NACT (e.g., hydroxychloroquine ± lopinavir/ritonavir) and increased relative abundance with AWaRe Watch/Reserve antibiotics, AT duration, and combinations. Abundance of Dorea, Agathobacter, Roseburia, and Barnesiella was negatively correlated with AT and corticosteroids use. Patients with increased IL-6, D-dimer, and ferritin levels receiving AT were more likely to show dysbiosis with increased abundance of Enterococcus and Bilophila bacteria and decreased abundance of Roseburia compared with those not receiving AT. CONCLUSION Microbiome diversity is affected by COVID-19 severity. In this context, antibiotic treatment may shift the gut microbiome composition towards OBs, particularly Enterococcus. The impact of treatment-driven dysbiosis on OBs infections and long-term consequences needs further study to define the role of gut homeostasis in COVID-19 recovery and inform targeted interventions.
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Affiliation(s)
- Elda Righi
- Infectious Diseases Unit, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | - Lorenza Lambertenghi
- Infectious Diseases Unit, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | - Anna Gorska
- Infectious Diseases Unit, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | - Concetta Sciammarella
- Infectious Diseases Unit, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | - Federico Ivaldi
- Infectious Diseases Unit, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | - Massimo Mirandola
- Infectious Diseases Unit, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
| | - Assunta Sartor
- Microbiology Unit, Udine University Hospital, 33100 Udine, Italy
| | - Evelina Tacconelli
- Infectious Diseases Unit, Department of Diagnostics and Public Health, University of Verona, 37134 Verona, Italy
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44
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Kaushik P, Kumari M, Singh NK, Suri A. The role of gut microbiota in etiopathogenesis of long COVID syndrome. Horm Mol Biol Clin Investig 2022:hmbci-2022-0079. [DOI: 10.1515/hmbci-2022-0079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/20/2022] [Indexed: 04/04/2023]
Affiliation(s)
- Priya Kaushik
- Biochemistry , SGT University , Gurugram , Haryana , India
| | | | | | - Arpita Suri
- Biochemistry , SGT University , Gurugram , Haryana , India
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45
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Li Q, Li N, Cai W, Xiao M, Liu B, Zeng F. Fermented natural product targeting gut microbiota regulate immunity and anti-inflammatory activity: A possible way to prevent COVID-19 in daily diet. J Funct Foods 2022; 97:105229. [PMID: 36034155 PMCID: PMC9393180 DOI: 10.1016/j.jff.2022.105229] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Low immune function makes the body vulnerable to being invaded by external bacteria or viruses, causing influenza and inflammation of various organs, and this trend is shifting to the young and middle-aged group. It has been pointed out that natural products fermented by probiotic have benign changes about their active ingredients in some studies, and it have shown strong nutritional value in anti-oxidation, anti-aging, regulating lipid metabolism, anti-inflammatory and improving immunity. In recent years, the gut microbiota plays a key role and has been extensively studied in improving immunity and anti-inflammation activity. By linking the relationship between natural products fermented by probiotic, gut microbiota, immunity, and inflammation, this review presents the modulating effects of probiotics and their fermented natural products on the body, including immunity-enhancing and anti-inflammatory activities by modulating gut microbiota, and it is discussed that the current understanding of its molecular mechanisms. It may become a possible way to prevent COVID-19 through consuming natural products fermented by probiotic in our daily diet.
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Affiliation(s)
- Quancen Li
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Na Li
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenwen Cai
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meifang Xiao
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Bin Liu
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- National Engineering Research Center of JUNCAO Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Feng Zeng
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- National Engineering Research Center of JUNCAO Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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46
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Seibert B, Cáceres CJ, Carnaccini S, Cardenas-Garcia S, Gay LC, Ortiz L, Geiger G, Rajao DS, Ottesen E, Perez DR. Pathobiology and dysbiosis of the respiratory and intestinal microbiota in 14 months old Golden Syrian hamsters infected with SARS-CoV-2. PLoS Pathog 2022; 18:e1010734. [PMID: 36279276 PMCID: PMC9632924 DOI: 10.1371/journal.ppat.1010734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 11/03/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS2) affected the geriatric population. Among research models, Golden Syrian hamsters (GSH) are one of the most representative to study SARS2 pathogenesis and host responses. However, animal studies that recapitulate the effects of SARS2 in the human geriatric population are lacking. To address this gap, we inoculated 14 months old GSH with a prototypic ancestral strain of SARS2 and studied the effects on virus pathogenesis, virus shedding, and respiratory and gastrointestinal microbiome changes. SARS2 infection led to high vRNA loads in the nasal turbinates (NT), lungs, and trachea as well as higher pulmonary lesions scores later in infection. Dysbiosis throughout SARS2 disease progression was observed in the pulmonary microbial dynamics with the enrichment of opportunistic pathogens (Haemophilus, Fusobacterium, Streptococcus, Campylobacter, and Johnsonella) and microbes associated with inflammation (Prevotella). Changes in the gut microbial community also reflected an increase in multiple genera previously associated with intestinal inflammation and disease (Helicobacter, Mucispirillum, Streptococcus, unclassified Erysipelotrichaceae, and Spirochaetaceae). Influenza A virus (FLUAV) pre-exposure resulted in slightly more pronounced pathology in the NT and lungs early on (3 dpc), and more notable changes in lungs compared to the gut microbiome dynamics. Similarities among aged GSH and the microbiome in critically ill COVID-19 patients, particularly in the lower respiratory tract, suggest that GSHs are a representative model to investigate microbial changes during SARS2 infection. The relationship between the residential microbiome and other confounding factors, such as SARS2 infection, in a widely used animal model, contributes to a better understanding of the complexities associated with the host responses during viral infections.
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Affiliation(s)
- Brittany Seibert
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - C. Joaquín Cáceres
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Silvia Carnaccini
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Stivalis Cardenas-Garcia
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - L. Claire Gay
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Lucia Ortiz
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Ginger Geiger
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Daniela S. Rajao
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
| | - Elizabeth Ottesen
- Department of Microbiology, University of Georgia, Athens, Georgia, United States of America
| | - Daniel R. Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, United States of America
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Ahmadi Badi S, Malek A, Paolini A, Rouhollahi Masoumi M, Seyedi SA, Amanzadeh A, Masotti A, Khatami S, Siadat SD. Downregulation of ACE, AGTR1, and ACE2 genes mediating SARS-CoV-2 pathogenesis by gut microbiota members and their postbiotics on Caco-2 cells. Microb Pathog 2022; 173:105798. [PMID: 36174833 PMCID: PMC9511898 DOI: 10.1016/j.micpath.2022.105798] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 12/23/2022]
Abstract
INTRODUCTION Coronavirus disease-2019 (COVID-19) is a complex infection caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can cause also gastrointestinal symptoms. There are various factors that determine the host susceptibility and severity of infection, including the renin-angiotensin system, the immune response, and the gut microbiota. In this regard, we aimed to investigate the gene expression of ACE, AGTR1, ACE2, and TMPRSS2, which mediate SARS-CoV-2 pathogenesis by Akkermansia muciniphila, Faecalibacterium prausnitzii, Bacteroides thetaiotaomicron, and Bacteroides fragilis on Caco-2 cells. Also, the enrichment analysis considering the studied genes was analyzed on raw data from the microarray analysis of COVID-19 patients. MATERIALS AND METHODS Caco-2 cells were treated with live, heat-inactivated form and cell free supernatants of A. muciniphila, F. prausnitzii, B. thetaiotaomicron and B. fragilis for overnight. After RNA extraction and cDNA synthesis, the expression of studied genes was assessed by RT-qPCR. DNA methylation of studied genes was analyzed by Partek® Genomics Suite® software on the GSE174818 dataset. We used GSE164805 and GSE166552 datasets from COVID-19 patients to perform enrichment analysis by considering the mentioned genes via GEO2R, DAVID. Finally, the related microRNAs to GO terms concerned on the studied genes were identified by miRPath. RESULTS The downregulation of ACE, AGTR1, and ACE2 genes by A. muciniphila, F. prausnitzii, B. thetaiotaomicron, and B. fragilis in live, heat-inactivated, and cell-free supernatants was reported for the first time. These genes had hypomethylated DNA status in COVID-19 patients' raw data. The highest fold enrichment in upregulated RAS pathways and immune responses belonged to ACE, AGTR1, and ACE2 by considering the protein-protein interaction network. The common miRNAs targeting the studied genes were reported as miR-124-3p and miR-26b-5p. In combination with our experimental data and bioinformatic analysis, we showed the potential of A. muciniphila, F. prausnitzii, B. thetaiotaomicron, and B. fragilis and postbiotics to reduce ACE, ATR1, and ACE2 expression, which are essential genes that drive upregulated biological processes in COVID-19 patients. CONCLUSION Accordingly, due to the potential of studied bacteria on the alteration of ACE, AGTR1, ACE2 genes expression, understanding their correlation with demonstrated miRNAs expression could be valuable. These findings suggest the importance of considering targeted gut microbiota intervention when designing the possible therapeutic strategy for controlling the COVID-19.
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Affiliation(s)
- Sara Ahmadi Badi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran; Mycobacteriology and Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran.
| | - Amin Malek
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran; Mycobacteriology and Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran.
| | - Alessandro Paolini
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories, V.le di San Paolo 15, 00146, Rome, Italy.
| | - Mahya Rouhollahi Masoumi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
| | - Seyed Amirhesam Seyedi
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran; Mycobacteriology and Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran.
| | - Amir Amanzadeh
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, Iran.
| | - Andrea Masotti
- Children's Hospital Bambino Gesù-IRCCS, Research Laboratories, V.le di San Paolo 15, 00146, Rome, Italy.
| | - Shohreh Khatami
- Department of Biochemistry, Pasteur Institute of Iran, Tehran, Iran.
| | - Seyed Davar Siadat
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran; Mycobacteriology and Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran.
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Mozaffari SA, Salehi A, Mousavi E, Zaman BA, Nassaj AE, Ebrahimzadeh F, Nasiri H, Valedkarimi Z, Adili A, Asemani G, Akbari M. SARS-CoV-2-associated gut microbiome alteration; A new contributor to colorectal cancer pathogenesis. Pathol Res Pract 2022; 239:154131. [PMID: 36191449 PMCID: PMC9477615 DOI: 10.1016/j.prp.2022.154131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/31/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022]
Abstract
The emergence of a novel coronavirus, COVID-19, in December 2019 led to a global pandemic with more than 170 million confirmed infections and more than 6 million deaths (by July 2022). Studies have shown that infection with SARS-CoV-2 in cancer patients has a higher mortality rate than in people without cancer. Here, we have reviewed the evidence showing that gut microbiota plays an important role in health and is linked to colorectal cancer development. Studies have shown that SARS-CoV-2 infection leads to a change in gut microbiota, which modify intestinal inflammation and barrier permeability and affects tumor-suppressor or oncogene genes, proposing SARS-CoV-2 as a potential contributor to CRC pathogenesis
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Affiliation(s)
- Shahrooz Amin Mozaffari
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Islamic Republic of Iran
| | - Ali Salehi
- Department of Oral and Maxillofacial Radiology, School of Dentistry, Islamic Azad University, Isfahan (Khorasgan) Branch, Isfahan, Islamic Republic of Iran
| | - Elnaz Mousavi
- Dental Sciences Research Center, Department of Endodontics, School of Dentistry, Guilan University of Medical Sciences, Rasht, Islamic Republic of Iran
| | - Burhan Abdullah Zaman
- Department of Basic Sciences, College of Pharmacy, University of Duhok, Duhok, Kurdistan Region, Iraq
| | - Ali Eslambol Nassaj
- Department of Endodontics, School of Dentistry, Kerman University of Medical Sciences, Kerman, Islamic Republic of Iran
| | - Farnoosh Ebrahimzadeh
- Department of Internal Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Islamic Republic of Iran
| | - Hadi Nasiri
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Islamic Republic of Iran
| | - Zahra Valedkarimi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Islamic Republic of Iran
| | - Ali Adili
- Senior Adult Oncology Department, Moffitt Cancer Center, University of South Florida, Tampa, USA; Department of Oncology, Tabriz University of Medical Sciences, Tabriz, Islamic Republic of Iran
| | - Ghazaleh Asemani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Islamic Republic of Iran
| | - Morteza Akbari
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Islamic Republic of Iran; Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Islamic Republic of Iran.
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Gut Microbiota and COVID-19: Potential Implications for Disease Severity. Pathogens 2022; 11:pathogens11091050. [PMID: 36145482 PMCID: PMC9503814 DOI: 10.3390/pathogens11091050] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/02/2022] [Accepted: 09/14/2022] [Indexed: 12/11/2022] Open
Abstract
The SARS-CoV-2 pandemic resulted in an unprecedented global crisis. SARS-CoV-2 primarily causes lung infection trough the binding of the virus with the ACE-2 cell receptor located on the surface of the alveolar epithelial cells. Notably, ACE-2 cell receptors are also expressed in the epithelial cells of the intestinal tract (GI). Recent data showed that the microbial communities of the GI might act as local and systematic inflammatory modulators. Gastrointestinal symptoms, including diarrhea, are frequently observed in infected individuals, and recent released data indicate that SARS-CoV-2 may also spread by fecal–oral transmission. Moreover, the gut microbiota’s ecosystem can regulate and be regulated by invading pathogens, including viruses, facilitating an effective immune response, which in turn results in less severe diseases. In this regard, increased SARS-CoV-2 mortality and morbidities appear to be frequently observed in elderly immunocompromised patients and in people with essential health problems, such as diabetes, who, indeed, tend to have a less diverse gut microbiota (dysbiosis). Therefore, it is important to understand how the interaction between the gut microbiota and SARS-CoV-2 might shape the intensity of the infection and different clinical outcomes. Here, we provide insights into the current knowledge of dysbiosis during SARS-CoV-2 infection and methods that may be used to re-establish a more correct microbiota composition.
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50
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Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes. Nat Commun 2022; 13:5235. [PMID: 36068270 PMCID: PMC9446638 DOI: 10.1038/s41467-022-32991-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/24/2022] [Indexed: 11/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), primarily a respiratory disease caused by infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is often accompanied by gastrointestinal symptoms. However, little is known about the relation between the human microbiome and COVID-19, largely due to the fact that most previous studies fail to provide high taxonomic resolution to identify microbes that likely interact with SARS-CoV-2 infection. Here we used whole-metagenome shotgun sequencing data together with assembly and binning strategies to reconstruct metagenome-assembled genomes (MAGs) from 514 COVID-19 related nasopharyngeal and fecal samples in six independent cohorts. We reconstructed a total of 11,584 medium-and high-quality microbial MAGs and obtained 5403 non-redundant MAGs (nrMAGs) with strain-level resolution. We found that there is a significant reduction of strain richness for many species in the gut microbiome of COVID-19 patients. The gut microbiome signatures can accurately distinguish COVID-19 cases from healthy controls and predict the progression of COVID-19. Moreover, we identified a set of nrMAGs with a putative causal role in the clinical manifestations of COVID-19 and revealed their functional pathways that potentially interact with SARS-CoV-2 infection. Finally, we demonstrated that the main findings of our study can be largely validated in three independent cohorts. The presented results highlight the importance of incorporating the human gut microbiome in our understanding of SARS-CoV-2 infection and disease progression. Here, using whole-metagenome shotgun sequencing data from patients with COVID-19 and controls, the authors reconstruct 11,584 microbial metagenome-assembled genomes (MAGs) including 5,403 non-redundant MAGs, revealing microbiota and metabolic pathways associations with SARS-CoV-2 infection at strain-level resolution.
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