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Moreno E, Ciordia S, Fátima SM, Jiménez D, Martínez-Sanz J, Vizcarra P, Ron R, Sánchez-Conde M, Bargiela R, Sanchez-Carrillo S, Moreno S, Corrales F, Ferrer M, Serrano-Villar S. Proteomic snapshot of saliva samples predicts new pathways implicated in SARS-CoV-2 pathogenesis. Clin Proteomics 2024; 21:37. [PMID: 38778280 PMCID: PMC11112864 DOI: 10.1186/s12014-024-09482-9] [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: 10/13/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Information on the microbiome's human pathways and active members that can affect SARS-CoV-2 susceptibility and pathogenesis in the salivary proteome is very scarce. Here, we studied a unique collection of samples harvested from April to June 2020 from unvaccinated patients. METHODS We compared 10 infected and hospitalized patients with severe (n = 5) and moderate (n = 5) coronavirus disease (COVID-19) with 10 uninfected individuals, including non-COVID-19 but susceptible individuals (n = 5) and non-COVID-19 and nonsusceptible healthcare workers with repeated high-risk exposures (n = 5). RESULTS By performing high-throughput proteomic profiling in saliva samples, we detected 226 unique differentially expressed (DE) human proteins between groups (q-value ≤ 0.05) out of 3376 unambiguously identified proteins (false discovery rate ≤ 1%). Major differences were observed between the non-COVID-19 and nonsusceptible groups. Bioinformatics analysis of DE proteins revealed human proteomic signatures related to inflammatory responses, central cellular processes, and antiviral activity associated with the saliva of SARS-CoV-2-infected patients (p-value ≤ 0.0004). Discriminatory biomarker signatures from human saliva include cystatins, protective molecules present in the oral cavity, calprotectins, involved in cell cycle progression, and histones, related to nucleosome functions. The expression levels of two human proteins related to protein transport in the cytoplasm, DYNC1 (p-value, 0.0021) and MAPRE1 (p-value, 0.047), correlated with angiotensin-converting enzyme 2 (ACE2) plasma activity. Finally, the proteomes of microorganisms present in the saliva samples showed 4 main microbial functional features related to ribosome functioning that were overrepresented in the infected group. CONCLUSION Our study explores potential candidates involved in pathways implicated in SARS-CoV-2 susceptibility, although further studies in larger cohorts will be necessary.
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Affiliation(s)
- Elena Moreno
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain.
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - Sergio Ciordia
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Santos Milhano Fátima
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Daniel Jiménez
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
| | - Javier Martínez-Sanz
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Pilar Vizcarra
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Raquel Ron
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Matilde Sánchez-Conde
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Rafael Bargiela
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Sergio Sanchez-Carrillo
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049, Madrid, Spain
- Centro de Biologia Molecular Severo Ochoa (CBM), CSIC-UAM, 28049, Madrid, Spain
| | - Santiago Moreno
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Facultad de Medicina, Universidad de Alcalá de Henares, 28801, Alcalá de Henares, Madrid, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049, Madrid, Spain
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
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Sun Z, Ning Z, Figeys D. The Landscape and Perspectives of the Human Gut Metaproteomics. Mol Cell Proteomics 2024; 23:100763. [PMID: 38608842 PMCID: PMC11098955 DOI: 10.1016/j.mcpro.2024.100763] [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: 11/14/2023] [Revised: 02/26/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024] Open
Abstract
The human gut microbiome is closely associated with human health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of the gut microbiome by analyzing the entire proteins present in microbial communities. Recent advancements in liquid chromatography and tandem mass spectrometry (LC-MS/MS) techniques have expanded the detection range of metaproteomics. However, the overall coverage of the proteome in metaproteomics is still limited. While metagenomics studies have revealed substantial microbial diversity and functional potential of the human gut microbiome, few studies have summarized and studied the human gut microbiome landscape revealed with metaproteomics. In this article, we present the current landscape of human gut metaproteomics studies by re-analyzing the identification results from 15 published studies. We quantified the limited proteome coverage in metaproteomics and revealed a high proportion of annotation coverage of metaproteomics-identified proteins. We conducted a preliminary comparison between the metaproteomics view and the metagenomics view of the human gut microbiome, identifying key areas of consistency and divergence. Based on the current landscape of human gut metaproteomics, we discuss the feasibility of using metaproteomics to study functionally unknown proteins and propose a whole workflow peptide-centric analysis. Additionally, we suggest enhancing metaproteomics analysis by refining taxonomic classification and calculating confidence scores, as well as developing tools for analyzing the interaction between taxonomy and function.
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Affiliation(s)
- Zhongzhi Sun
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Zhibin Ning
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
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Luo Y, Zhang Z, Ren J, Dou C, Wen J, Yang Y, Li X, Yan Z, Han Y. SARS-Cov-2 spike induces intestinal barrier dysfunction through the interaction between CEACAM5 and Galectin-9. Front Immunol 2024; 15:1303356. [PMID: 38686388 PMCID: PMC11056506 DOI: 10.3389/fimmu.2024.1303356] [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: 09/27/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
Background Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5), as a typical tumor marker, has been found to exert immunomodulatory effects in many diseases. We previously reported the clinical and molecular evidences supporting that SARS-Cov-2 infected the gastrointestinal (GI) tract and found a reduction of CEACAM5 in COVID-19 patients' feces which associated with gut dysbiosis. Yet the role of CEACAM5 in GI infection is ill-defined. Methods Mice models were established through intraperitoneally injecting with recombinant viral spike-Fc to mimic the intestinal inflammation. We collected duodenum, jejunum, ileum and colon samples after 6h, 2 days, 4 days and 7 days of spike-Fc or control-Fc injection to perform proteomic analysis. Blood was collected from healthy donors and peripheral blood mononuclear cells (PBMC) were separated by density gradient centrifugation, then CD4+ T cells were isolated with magnetic beads and co-cultured with Caco-2 cells. Results In addition to intestinal CEACAM5, the expression of tight junction and the percent of CD4+ T lymphocytes were significantly decreased in spike-Fc group compared to control (p < 0.05), accompanied with increased level of inflammatory factors. The KEGG analysis revealed differentially expressed proteins were mainly enriched in the coronavirus disease (COVID-19), tight junction, focal adhesion, adherens junction and PI3K-Akt signaling pathway. Protein-protein interaction (PPI) network analysis identified the interaction between CEACAM5 and Galectin-9 that was also verified by molecular docking and co-IP assay. We further confirmed a reduction of CEACAM5 in SARS-CoV-2 spike stimulated enterocytes could promote the expression of Galectin-9 protein in CD4+T cells. Then it gave rise to the increasing release of inflammatory factors and increased apoptosis of CD4+T cells by inhibition of PI3K/AKT/mTOR pathway. Ultimately intestinal barrier dysfunction happened. Conclusion Our results indicated that CEACAM5 overexpression and Galectin-9 knockdown played a protective role in intestinal barrier injury upon spike-Fc stimulation. Collectively, our findings identified firstly that SARS-CoV-2 spike induced intestinal barrier dysfunction through the interaction between CEACAM5 and Galectin-9. The result provides potential therapeutic targets in intestinal barrier dysfunction for treating severe COVID patients.
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Affiliation(s)
- Yingshu Luo
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Zhenling Zhang
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Jiangnan Ren
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Chunxu Dou
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Jiancheng Wen
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Yang Yang
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Xiaofeng Li
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Zhixiang Yan
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Yanzhi Han
- Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
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Chen L, Yin Z, Zhou D, Li X, Yu C, Luo C, Jin Y, Zhang L, Song J, Rasche L, Einsele H, Tu L, Zhou X, Bai T, Hou X. Lymphocyte and neutrophil count combined with intestinal bacteria abundance predict the severity of COVID-19. Microbiol Spectr 2024; 12:e0302723. [PMID: 38088542 PMCID: PMC10783053 DOI: 10.1128/spectrum.03027-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/06/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE The 2019 coronavirus disease (COVID-19) patients had a unique profile of gut bacteria. In this study, we characterized the intestinal bacteria in our COVID-19 cohorts and found that there was an increased incidence of severe cases in COVID-19 patients with decreased lymphocytes and increased neutrophils. Levels of lymphocytes and neutrophils and abundances of intestinal bacteria correlated with the severity of COVID-19.
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Affiliation(s)
- Liuying Chen
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhongwei Yin
- Division of Cardiology, Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dan Zhou
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xin Li
- Department of Paediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Cheng Yu
- Ultrasonic Department, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chang Luo
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Jin
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lei Zhang
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Song
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Leo Rasche
- Department of Internal Medicine II, University Hospital Würzburg, Julius-Maximilian University of Würzburg, Würzburg, Germany
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Julius-Maximilian University of Würzburg, Würzburg, Germany
| | - Lei Tu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiang Zhou
- Department of Internal Medicine II, University Hospital Würzburg, Julius-Maximilian University of Würzburg, Würzburg, Germany
| | - Tao Bai
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaohua Hou
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Marzano V, Mortera SL, Marangelo C, Piazzesi A, Rapisarda F, Pane S, Del Chierico F, Vernocchi P, Romani L, Campana A, Palma P, Putignani L. The metaproteome of the gut microbiota in pediatric patients affected by COVID-19. Front Cell Infect Microbiol 2023; 13:1327889. [PMID: 38188629 PMCID: PMC10766818 DOI: 10.3389/fcimb.2023.1327889] [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: 10/25/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction The gut microbiota (GM) play a significant role in the infectivity and severity of COVID-19 infection. However, the available literature primarily focuses on adult patients and it is known that the microbiota undergoes changes throughout the lifespan, with significant alterations occurring during infancy and subsequently stabilizing during adulthood. Moreover, children have exhibited milder symptoms of COVID-19 disease, which has been associated with the abundance of certain protective bacteria. Here, we examine the metaproteome of pediatric patients to uncover the biological mechanisms that underlie this protective effect of the GM. Methods We performed nanoliquid chromatography coupled with tandem mass spectrometry on a high resolution analytical platform, resulting in label free quantification of bacterial protein groups (PGs), along with functional annotations via COG and KEGG databases by MetaLab-MAG. Additionally, taxonomic assignment was possible through the use of the lowest common ancestor algorithm provided by Unipept software. Results A COVID-19 GM functional dissimilarity respect to healthy subjects was identified by univariate analysis. The alteration in COVID-19 GM function is primarily based on bacterial pathways that predominantly involve metabolic processes, such as those related to tryptophan, butanoate, fatty acid, and bile acid biosynthesis, as well as antibiotic resistance and virulence. Discussion These findings highlight the mechanisms by which the pediatric GM could contribute to protection against the more severe manifestations of the disease in children. Uncovering these mechanisms can, therefore, have important implications in the discovery of novel adjuvant therapies for severe COVID-19.
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Affiliation(s)
- Valeria Marzano
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Stefano Levi Mortera
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Chiara Marangelo
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Antonia Piazzesi
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Federica Rapisarda
- Research 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
| | - Federica Del Chierico
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Pamela Vernocchi
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Lorenza Romani
- Unit of Infectious Disease, Bambino Gesu’ Children’s Hospital, IRCCS, Rome, Italy
| | - Andrea Campana
- Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Paolo Palma
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiomics and Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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Mwangi VI, Netto RLA, Borba MGS, Santos GF, Lima GS, Machado LS, Yakubu MN, Val FFA, Sampaio VS, Sartim MA, Koolen HHF, Costa AG, Toméi MCM, Guimarães TP, Chaves AR, Vaz BG, Lacerda MVG, Monteiro WM, Gardinassi LG, Melo GC. Methylprednisolone therapy induces differential metabolic trajectories in severe COVID-19 patients. mSystems 2023; 8:e0072623. [PMID: 37874139 PMCID: PMC10734516 DOI: 10.1128/msystems.00726-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/17/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE The SARS-CoV-2 virus infection in humans induces significant inflammatory and systemic reactions and complications of which corticosteroids like methylprednisolone have been recommended as treatment. Our understanding of the metabolic and metabolomic pathway dysregulations while using intravenous corticosteroids in COVID-19 is limited. This study will help enlighten the metabolic and metabolomic pathway dysregulations underlying high daily doses of intravenous methylprednisolone in COVID-19 patients compared to those receiving placebo. The information on key metabolites and pathways identified in this study together with the crosstalk with the inflammation and biochemistry components may be used, in the future, to leverage the use of methylprednisolone in any future pandemics from the coronavirus family.
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Affiliation(s)
- Victor I. Mwangi
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
| | - Rebeca L. A. Netto
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
| | - Mayla G. S. Borba
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
| | - Gabriel F. Santos
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Gesiane S. Lima
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Lucas S. Machado
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Michael N. Yakubu
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
| | - Fernando F. A. Val
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Ciência da Saúde, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Ciências do Movimento Humano, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
| | - Vanderson S. Sampaio
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Instituto Todos pela Saúde, São Paulo, São Paulo, Brazil
| | - Marco A. Sartim
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Pró-reitoria de Pesquisa e Pós-graduação, Universidade Nilton Lins, Manaus, Amazonas, Brazil
| | - Hector H. F. Koolen
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Manaus, Amazonas, Brazil
| | - Allyson G. Costa
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, Amazonas, Brazil
- Escola de Enfermagem de Manaus, Universidade Federal do Amazonas (UFAM), Manaus, Amazonas, Brazil
- Programa de Pós-graduação em Ciências Aplicadas à Hematologia (PPGH-UEA/HEMOAM), Manaus, Amazonas, Brazil
| | - Maria C. M. Toméi
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás (UFG), Goiânia, Goiás, Brazil
| | - Tiago P. Guimarães
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás (UFG), Goiânia, Goiás, Brazil
| | - Andrea R. Chaves
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Boniek G. Vaz
- Laboratório de Cromatografia e Espectrometria de Massas, Instituto de Química, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Marcus V. G. Lacerda
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Instituto Leônidas & Maria Deane/Fundação Oswaldo Cruz (ILMD/Fiocruz Amazônia), Manaus, Amazonas, Brazil
| | - Wuelton M. Monteiro
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
| | - Luiz G. Gardinassi
- Instituto de Patologia Tropical e Saúde Pública, Universidade Federal de Goiás (UFG), Goiânia, Goiás, Brazil
| | - Gisely C. Melo
- Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas (UEA), Manaus, Amazonas, Brazil
- Fundação de Medicina Tropical Heitor Vieira Dourado (FMT-HVD), Manaus, Amazonas, Brazil
- Programa de Pós-graduação em Ciências Aplicadas à Hematologia (PPGH-UEA/HEMOAM), Manaus, Amazonas, Brazil
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Xiao Z, Pan M, Li X, Zhao C. Impact of SARS-CoV2 infection on gut microbiota dysbiosis. MICROBIOME RESEARCH REPORTS 2023; 3:7. [PMID: 38455085 PMCID: PMC10917619 DOI: 10.20517/mrr.2023.48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/12/2023] [Accepted: 11/28/2023] [Indexed: 03/09/2024]
Abstract
The composition and function of the gut microbiota constantly influence health. Disruptions in this delicate balance, termed gut microbiota dysbiosis, have been implicated in various adverse health events. As the largest global epidemic since 1918, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had devastating consequences. While the primary impact of Corona Virus Disease 2019 (COVID-19) has been on the respiratory system, a growing body of research has unveiled the significant involvement of the gastrointestinal tract as well. Emerging evidence underscores notable alterations in the gut microbiome of COVID-19 patients. In addition, the gut microbiome is also characterized by an abundance of opportunistic pathogens, which is related to disease manifestations of COVID-19 patients. The intricate bidirectional interaction between the respiratory mucosa and the gut microbiota, known as the gut-lung axis, emerges as a crucial player in the pathological immune response triggered by SARS-CoV-2. Here, we discuss microbiota-based gut characteristics of COVID-19 patients and the long-term consequences of gut microbiota dysregulation. These insights could potentially transform the development of long-term interventions for COVID-19, offering hope for improved outcomes and enhanced patient recovery.
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Affiliation(s)
- Zhenming Xiao
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College & National Clinical Research Center for Aging and Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Miaomiao Pan
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College & National Clinical Research Center for Aging and Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xinyao Li
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College & National Clinical Research Center for Aging and Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Chao Zhao
- Key Laboratory of Medical Molecular Virology, School of Basic Medical Sciences, Shanghai Medical College & National Clinical Research Center for Aging and Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200032, China
- Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, Shanghai Frontiers Science Center, Shanghai 200032, China
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Zhang F, Luna A, Tan T, Chen Y, Sander C, Guo T. COVIDpro: Database for Mining Protein Dysregulation in Patients with COVID-19. J Proteome Res 2023; 22:2847-2859. [PMID: 37555633 DOI: 10.1021/acs.jproteome.3c00092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
The ongoing pandemic of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 still has limited treatment options. Our understanding of the molecular dysregulations that occur in response to infection remains incomplete. We developed a web application COVIDpro (https://www.guomics.com/covidPro/) that includes proteomics data obtained from 41 original studies conducted in 32 hospitals worldwide, involving 3077 patients and covering 19 types of clinical specimens, predominantly plasma and serum. The data set encompasses 53 protein expression matrices, comprising a total of 5434 samples and 14,403 unique proteins. We identified a panel of proteins that exhibit significant dysregulation, enabling the classification of COVID-19 patients into severe and non-severe disease categories. The proteomic signatures achieved promising results in distinguishing severe cases, with a mean area under the curve of 0.87 and accuracy of 0.80 across five independent test sets. COVIDpro serves as a valuable resource for testing hypotheses and exploring potential targets for novel treatments in COVID-19 patients.
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Affiliation(s)
- Fangfei Zhang
- Fudan University, 220 Handan Road, Shanghai 200433, China
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province 310024, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China
| | - Augustin Luna
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, Cambridge, Massachusetts 02142, United States
| | - Tingting Tan
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province 310024, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China
| | - Yingdan Chen
- Westlake Omics (Hangzhou) Biotechnology Company Limited, Hangzhou, Zhejiang Province 310024, China
| | - Chris Sander
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, Cambridge, Massachusetts 02142, United States
| | - Tiannan Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province 310024, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou, Zhejiang 310030, China
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9
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Ascandari A, Aminu S, Safdi NEH, El Allali A, Daoud R. A bibliometric analysis of the global impact of metaproteomics research. Front Microbiol 2023; 14:1217727. [PMID: 37476667 PMCID: PMC10354264 DOI: 10.3389/fmicb.2023.1217727] [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: 05/05/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023] Open
Abstract
Background Metaproteomics is a subfield in meta-omics that is used to characterize the proteome of a microbial community. Despite its importance and the plethora of publications in different research area, scientists struggle to fully comprehend its functional impact on the study of microbiomes. In this study, bibliometric analyses are used to evaluate the current state of metaproteomic research globally as well as evaluate the specific contribution of Africa to this burgeoning research area. In this study, we use bibliometric analyses to evaluate the current state of metaproteomic research globally, identify research frontiers and hotspots, and further predict future trends in metaproteomics. The specific contribution of Africa to this research area was evaluated. Methods Relevant documents from 2004 to 2022 were extracted from the Scopus database. The documents were subjected to bibliometric analyses and visualization using VOS viewer and Biblioshiny package in R. Factors such as the trends in publication, country and institutional cooperation networks, leading scientific journals, author's productivity, and keywords analyses were conducted. The African publications were ranked using Field-Weighted Citation Impact (FWCI) scores. Results A total of 1,138 documents were included and the number of publications increased drastically from 2004 to 2022 with more publications (170) reported in 2021. In terms of publishers, Frontiers in Microbiology had the highest number of total publications (62). The United States of America (USA), Germany, China, and Canada, together with other European countries were the most productive. Institution-wise, the Helmholtz Zentrum für Umweltforschung, Germany had more publications while Max Plank Institute had the highest total collaborative link strength. Jehmlich N. was the most productive author whereas Hettich RL had the highest h-index of 63. Regarding Africa, only 2.2% of the overall publications were from the continent with more publication outputs from South Africa. More than half of the publications from the continent had an FWCI score ≥ 1. Conclusion The scientific outputs of metaproteomics are rapidly evolving with developed countries leading the way. Although Africa showed prospects for future progress, this could only be accelerated by providing funding, increased collaborations, and mentorship programs.
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Affiliation(s)
- AbdulAziz Ascandari
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Suleiman Aminu
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Nour El Houda Safdi
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Rachid Daoud
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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10
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Cheong KL, Chen S, Teng B, Veeraperumal S, Zhong S, Tan K. Oligosaccharides as Potential Regulators of Gut Microbiota and Intestinal Health in Post-COVID-19 Management. Pharmaceuticals (Basel) 2023; 16:860. [PMID: 37375807 DOI: 10.3390/ph16060860] [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: 04/30/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
The COVID-19 pandemic has had a profound impact worldwide, resulting in long-term health effects for many individuals. Recently, as more and more people recover from COVID-19, there is an increasing need to identify effective management strategies for post-COVID-19 syndrome, which may include diarrhea, fatigue, and chronic inflammation. Oligosaccharides derived from natural resources have been shown to have prebiotic effects, and emerging evidence suggests that they may also have immunomodulatory and anti-inflammatory effects, which could be particularly relevant in mitigating the long-term effects of COVID-19. In this review, we explore the potential of oligosaccharides as regulators of gut microbiota and intestinal health in post-COVID-19 management. We discuss the complex interactions between the gut microbiota, their functional metabolites, such as short-chain fatty acids, and the immune system, highlighting the potential of oligosaccharides to improve gut health and manage post-COVID-19 syndrome. Furthermore, we review evidence of gut microbiota with angiotensin-converting enzyme 2 expression for alleviating post-COVID-19 syndrome. Therefore, oligosaccharides offer a safe, natural, and effective approach to potentially improving gut microbiota, intestinal health, and overall health outcomes in post-COVID-19 management.
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Affiliation(s)
- Kit-Leong Cheong
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
| | - Shutong Chen
- Department of Biology, College of Science, Shantou University, Shantou 515063, China
| | - Bo Teng
- Department of Biology, College of Science, Shantou University, Shantou 515063, China
| | - Suresh Veeraperumal
- Department of Biology, College of Science, Shantou University, Shantou 515063, China
| | - Saiyi Zhong
- Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Provincial Science and Technology Innovation Center for Subtropical Fruit and Vegetable Processing, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang 524088, China
| | - Karsoon Tan
- Guangxi Key Laboratory of Beibu Gulf Biodiversity Conservation, Beibu Gulf University, Qinzhou 535000, China
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11
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Berezhnoy G, Bissinger R, Liu A, Cannet C, Schäfer H, Kienzle K, Bitzer M, Häberle H, Göpel S, Trautwein C, Singh Y. Maintained imbalance of triglycerides, apolipoproteins, energy metabolites and cytokines in long-term COVID-19 syndrome patients. Front Immunol 2023; 14:1144224. [PMID: 37228606 PMCID: PMC10203989 DOI: 10.3389/fimmu.2023.1144224] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 04/17/2023] [Indexed: 05/27/2023] Open
Abstract
Background Deep metabolomic, proteomic and immunologic phenotyping of patients suffering from an infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have matched a wide diversity of clinical symptoms with potential biomarkers for coronavirus disease 2019 (COVID-19). Several studies have described the role of small as well as complex molecules such as metabolites, cytokines, chemokines and lipoproteins during infection and in recovered patients. In fact, after an acute SARS-CoV-2 viral infection almost 10-20% of patients experience persistent symptoms post 12 weeks of recovery defined as long-term COVID-19 syndrome (LTCS) or long post-acute COVID-19 syndrome (PACS). Emerging evidence revealed that a dysregulated immune system and persisting inflammation could be one of the key drivers of LTCS. However, how these biomolecules altogether govern pathophysiology is largely underexplored. Thus, a clear understanding of how these parameters within an integrated fashion could predict the disease course would help to stratify LTCS patients from acute COVID-19 or recovered patients. This could even allow to elucidation of a potential mechanistic role of these biomolecules during the disease course. Methods This study comprised subjects with acute COVID-19 (n=7; longitudinal), LTCS (n=33), Recov (n=12), and no history of positive testing (n=73). 1H-NMR-based metabolomics with IVDr standard operating procedures verified and phenotyped all blood samples by quantifying 38 metabolites and 112 lipoprotein properties. Univariate and multivariate statistics identified NMR-based and cytokine changes. Results Here, we report on an integrated analysis of serum/plasma by NMR spectroscopy and flow cytometry-based cytokines/chemokines quantification in LTCS patients. We identified that in LTCS patients lactate and pyruvate were significantly different from either healthy controls (HC) or acute COVID-19 patients. Subsequently, correlation analysis in LTCS group only among cytokines and amino acids revealed that histidine and glutamine were uniquely attributed mainly with pro-inflammatory cytokines. Of note, triglycerides and several lipoproteins (apolipoproteins Apo-A1 and A2) in LTCS patients demonstrate COVID-19-like alterations compared with HC. Interestingly, LTCS and acute COVID-19 samples were distinguished mostly by their phenylalanine, 3-hydroxybutyrate (3-HB) and glucose concentrations, illustrating an imbalanced energy metabolism. Most of the cytokines and chemokines were present at low levels in LTCS patients compared with HC except for IL-18 chemokine, which tended to be higher in LTCS patients. Conclusion The identification of these persisting plasma metabolites, lipoprotein and inflammation alterations will help to better stratify LTCS patients from other diseases and could help to predict ongoing severity of LTCS patients.
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Affiliation(s)
- Georgy Berezhnoy
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Tübingen, Germany
| | - Rosi Bissinger
- Division of Endocrinology, Diabetology and Nephrology, Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
| | - Anna Liu
- Research Institute of Women’s Health, University of Tübingen, Tübingen, Germany
| | - Claire Cannet
- Bruker BioSpin, Applied Industrial and Clinical Division, Ettlingen, Germany
| | - Hartmut Schäfer
- Bruker BioSpin, Applied Industrial and Clinical Division, Ettlingen, Germany
| | - Katharina Kienzle
- Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
| | - Michael Bitzer
- Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
- Center for Personalized Medicine, University Hospital Tübingen, Tubingen, Germany
| | - Helene Häberle
- Department of Anesthesiology and Intensive Care Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Siri Göpel
- Department of Internal Medicine I, University Hospital Tübingen, Tübingen, Germany
| | - Christoph Trautwein
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, University of Tübingen, Tübingen, Germany
| | - Yogesh Singh
- Research Institute of Women’s Health, University of Tübingen, Tübingen, Germany
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- Next Generation Sequencing (NGS) Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
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12
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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: 75] [Impact Index Per Article: 75.0] [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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13
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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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14
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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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15
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Lin S, Li P, Qin J, Liu Q, Zhang J, Meng N, Jia C, Zhu K, Lv D, Sun L, Shang T, Lin Y, Niu W, Wang T. Exploring the key factors of schizophrenia relapse by integrating LC-MS/ 1H NMR metabolomics and weighted correlation network analysis. Clin Chim Acta 2023; 541:117252. [PMID: 36781041 DOI: 10.1016/j.cca.2023.117252] [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: 10/17/2022] [Revised: 02/08/2023] [Accepted: 02/09/2023] [Indexed: 02/13/2023]
Abstract
BACKGROUND Lack of comprehending key factors of schizophrenia relapse has impeded its effective treatment, indicating that the mechanism clarification and available intervention of schizophrenia relapse required further amelioration. METHOD Based on the integration of LC-MS and 1H NMR metabolomics, a weighted correlation network was established to screen pivotal factors of accelerating schizophrenia relapse. Then, the cluster most correlated with schizophrenia relapse was explored, and the biological function of cluster was investigated. Next, the key biomarker related to schizophrenia relapse was obtained through multiple algorithms. Moreover, the Lilikoi algorithm and correlation analysis were implemented to reveal the association between key biomarker and schizophrenia relapse. RESULT Results showed that 458 different forms of metabolites were identified for structuring the weighted correlation network. The module-trait correlation indicated that the turquoise module was the most highly correlated with schizophrenia relapse. Further, network analysis revealed that, in turquoise module, cluster 1 composed of 139 metabolites (involved in lipid metabolism and energy metabolism) was the most important subnetwork relevant to schizophrenia relapse. Finally, phenylalanylphenylalanine was recommended as the key biomarker related to schizophrenia relapse. Moreover, the correlation analysis indicated that phenylalanylphenylalanine might affect the progression of schizophrenia by intervening in energy metabolism. CONCLUSION In summary, critical factors of schizophrenia relapse have been revealed in our research, expounding the schizophrenia progression more systemically, which could shed some light on improving the intervention of schizophrenia relapse.
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Affiliation(s)
- Song Lin
- Basic Medical Science College, Qiqihar Medical University, Qiqihar, Heilongjiang Province 161006, China
| | - Ping Li
- School of Mental Health, Qiqihar Medical University, Qiqihar, Heilongjiang Province 161006, China
| | - Jinglei Qin
- Baiyupao Psychiatric Hospital of Harbin, Harbin, Heilongjiang Province 150000, China
| | - Qi Liu
- Research Institute of Medicine & Pharmacy, Qiqihar Medical University, Qiqihar, Heilongjiang Province 161006, China
| | - Jinling Zhang
- Research Institute of Medicine & Pharmacy, Qiqihar Medical University, Qiqihar, Heilongjiang Province 161006, China
| | - Nana Meng
- Basic Medical Science College, Qiqihar Medical University, Qiqihar, Heilongjiang Province 161006, China
| | - Cuicui Jia
- School of Mental Health, Qiqihar Medical University, Qiqihar, Heilongjiang Province 161006, China
| | - Kunjie Zhu
- Basic Medical Science College, Qiqihar Medical University, Qiqihar, Heilongjiang Province 161006, China
| | - Dan Lv
- School of Mental Health, Qiqihar Medical University, Qiqihar, Heilongjiang Province 161006, China
| | - Lei Sun
- School of Mental Health, Qiqihar Medical University, Qiqihar, Heilongjiang Province 161006, China
| | - Tinghuizi Shang
- School of Mental Health, Qiqihar Medical University, Qiqihar, Heilongjiang Province 161006, China
| | - Yan Lin
- Basic Medical Science College, Qiqihar Medical University, Qiqihar, Heilongjiang Province 161006, China
| | - Weipan Niu
- Baiyupao Psychiatric Hospital of Harbin, Harbin, Heilongjiang Province 150000, China
| | - Tianyang Wang
- School of Pharmacy, Qiqihar Medical University, Qiqihar, Heilongjiang Province 161006, China.
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16
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Bruzzone C, Conde R, Embade N, Mato JM, Millet O. Metabolomics as a powerful tool for diagnostic, pronostic and drug intervention analysis in COVID-19. Front Mol Biosci 2023; 10:1111482. [PMID: 36876049 PMCID: PMC9975567 DOI: 10.3389/fmolb.2023.1111482] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
COVID-19 currently represents one of the major health challenges worldwide. Albeit its infectious character, with onset affectation mainly at the respiratory track, it is clear that the pathophysiology of COVID-19 has a systemic character, ultimately affecting many organs. This feature enables the possibility of investigating SARS-CoV-2 infection using multi-omic techniques, including metabolomic studies by chromatography coupled to mass spectrometry or by nuclear magnetic resonance (NMR) spectroscopy. Here we review the extensive literature on metabolomics in COVID-19, that unraveled many aspects of the disease including: a characteristic metabotipic signature associated to COVID-19, discrimination of patients according to severity, effect of drugs and vaccination treatments and the characterization of the natural history of the metabolic evolution associated to the disease, from the infection onset to full recovery or long-term and long sequelae of COVID.
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Affiliation(s)
- Chiara Bruzzone
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bilbao, Bizkaia, Spain
| | - Ricardo Conde
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bilbao, Bizkaia, Spain
| | - Nieves Embade
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bilbao, Bizkaia, Spain
| | - José M. Mato
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bilbao, Bizkaia, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Oscar Millet
- Precision Medicine and Metabolism Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bilbao, Bizkaia, Spain
- CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
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17
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Yang F, Chen Y, Xiao Y, Jiang H, Jiang Z, Yang M, Li M, Su Y, Yan Z, Lin Y, Li D. pH-sensitive molybdenum (Mo)-based polyoxometalate nanoclusters have therapeutic efficacy in inflammatory bowel disease by counteracting ferroptosis. Pharmacol Res 2023; 188:106645. [PMID: 36610695 DOI: 10.1016/j.phrs.2023.106645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/01/2023] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
Current therapeutic drugs for ulcerative colitis (UC) remained inadequate due to drug dependence and unacceptable adverse events. Reactive oxygen species (ROS) played a critical role in the occurrence and development of UC, which most likely benefited from treatment in scavenging ROS. In this study, we developed a pH-sensitive molybdenum-based polyoxometalate (POM) nanocluster, which might contribute to site specific colonic delivery and enhance systemic efficacy of UC treatment. Our results demonstrated that POM displayed robust ROS scavenging ability in vitro. POM could significantly alleviate the enteric symptoms and inflammatory indicators in DSS-induced UC mouse models. Flow cytometry showed an effective diminishment of macrophages, neutrophils and T cells infiltration after POM administration in UC models. Also, for the first time, we demonstrated that POM interfered with metabolic pathway associated to oxidative stress and partially improved the abnormal production of intestinal metabolites in UC to some extent. Benefiting from the ROS scavenging ability, POM attenuated ferroptosis in DSS induced UC, as evidenced by increase of GSH, down-expression of GPX4 and improvement in mitochondrial morphological changes. Meanwhile, there were no side effects on normal tissues. Thus, our powerful therapeutic effects pioneered the application of POM for safer and more effective POM-based UC therapy.
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Affiliation(s)
- Fan Yang
- Department of Nuclear Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China
| | - Yuechuan Chen
- Department of Nuclear Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China
| | - Yitai Xiao
- Department of Nuclear Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China
| | - Hailong Jiang
- Department of Nuclear Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Center for Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China
| | - Zebo Jiang
- Department of Nuclear Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China
| | - Meilin Yang
- Department of Nuclear Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China
| | - Mengzhu Li
- Department of Nuclear Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China
| | - Yonghui Su
- Department of Gastrointestinal Surgery, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China.
| | - Zhixiang Yan
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, Guangdong Province 519000, China.
| | - Yong Lin
- Department of Psychiatry, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China.
| | - Dan Li
- Department of Nuclear Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China; Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong Province 519000, China.
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18
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Baldanzi G, Purghè B, Ragnoli B, Sainaghi PP, Rolla R, Chiocchetti A, Manfredi M, Malerba M. Circulating Peptidome Is Strongly Altered in COVID-19 Patients. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:1564. [PMID: 36674321 PMCID: PMC9865723 DOI: 10.3390/ijerph20021564] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 05/30/2023]
Abstract
Whilst the impact of coronavirus disease 2019 (COVID-19) on the host proteome, metabolome, and lipidome has been largely investigated in different bio-fluids, to date, the circulating peptidome remains unexplored. Thus, the present study aimed to apply an untargeted peptidomic approach to provide insight into alterations of circulating peptides in the development and severity of SARS-CoV-2 infection. The circulating peptidome from COVID-19 severe and mildly symptomatic patients and negative controls was characterized using LC-MS/MS analysis for identification and quantification purposes. Database search and statistical analysis allowed a complete characterization of the plasma peptidome and the detection of the most significant modulated peptides that were impacted by the infection. Our results highlighted not only that peptide abundance inversely correlates with disease severity, but also the involvement of biomolecules belonging to inflammatory, immune-response, and coagulation proteins/processes. Moreover, our data suggested a possible involvement of changes in protein degradation patterns. In the present research, for the first time, the untargeted peptidomic approach enabled the identification of circulating peptides potentially playing a crucial role in the progression of COVID-19.
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Affiliation(s)
- Gianluca Baldanzi
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | - Beatrice Purghè
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | | | - Pier Paolo Sainaghi
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Internal and Emergency Medicine Department, Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
| | - Roberta Rolla
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy
| | - Annalisa Chiocchetti
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, 28100 Novara, Italy
- Department of Health Sciences, University of Piemonte Orientale, 28100 Novara, Italy
| | - Marcello Manfredi
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Center for Translational Research on Autoimmune and Allergic Diseases, University of Piemonte Orientale, 28100 Novara, Italy
| | - Mario Malerba
- Department of Translational Medicine, University of Piemonte Orientale, 28100 Novara, Italy
- Respiratory Unit, Sant’Andrea Hospital, 13100 Vercelli, Italy
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19
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Zhou B, Pang X, Wu J, Liu T, Wang B, Cao H. Gut microbiota in COVID-19: new insights from inside. Gut Microbes 2023; 15:2201157. [PMID: 37078497 PMCID: PMC10120564 DOI: 10.1080/19490976.2023.2201157] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/04/2023] [Indexed: 04/21/2023] Open
Abstract
The epidemic of coronavirus disease-19 (COVID-19) has grown to be a global health threat. Gastrointestinal symptoms are thought to be common clinical manifestations apart from a series of originally found respiratory symptoms. The human gut harbors trillions of microorganisms that are indispensable for complex physiological processes and homeostasis. Growing evidence demonstrate that gut microbiota alteration is associated with COVID-19 progress and severity, and post-COVID-19 syndrome, characterized by decrease of anti-inflammatory bacteria like Bifidobacterium and Faecalibacterium and enrichment of inflammation-associated microbiota including Streptococcus and Actinomyces. Therapeutic strategies such as diet, probiotics/prebiotics, herb, and fecal microbiota transplantation have shown positive effects on relieving clinical symptoms. In this article, we provide and summarize the recent evidence about the gut microbiota and their metabolites alterations during and after COVID-19 infection and focus on potential therapeutic strategies targeting gut microbiota. Understanding the connections between intestinal microbiota and COVID-19 would provide new insights into COVID-19 management in the future.
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Affiliation(s)
- Bingqian Zhou
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Xiaoqi Pang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Jingyi Wu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Tianyu Liu
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
| | - Hailong Cao
- Department of Gastroenterology and Hepatology, General Hospital, Tianjin Medical University, National Key Clinical Specialty, Tianjin Institute of Digestive Diseases, Tianjin Key Laboratory of Digestive Diseases, Tianjin, China
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He S, Wu K, Cheng Z, He M, Hu R, Fan N, Shen L, Li Q, Fan H, Tong Y. Long COVID: The latest manifestations, mechanisms, and potential therapeutic interventions. MedComm (Beijing) 2022; 3:e196. [PMID: 36514781 PMCID: PMC9732402 DOI: 10.1002/mco2.196] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 12/14/2022] Open
Abstract
COVID-19 caused by SARS-CoV-2 infection affects humans not only during the acute phase of the infection, but also several weeks to 2 years after the recovery. SARS-CoV-2 infects a variety of cells in the human body, including lung cells, intestinal cells, vascular endothelial cells, olfactory epithelial cells, etc. The damages caused by the infections of these cells and enduring immune response are the basis of long COVID. Notably, the changes in gene expression caused by viral infection can also indirectly contribute to long COVID. We summarized the occurrences of both common and uncommon long COVID, including damages to lung and respiratory system, olfactory and taste deficiency, damages to myocardial, renal, muscle, and enduring inflammation. Moreover, we provided potential treatments for long COVID symptoms manifested in different organs and systems, which were based on the pathogenesis and the associations between symptoms in different organs. Importantly, we compared the differences in symptoms and frequency of long COVID caused by breakthrough infection after vaccination and infection with different variants of concern, in order to provide a comprehensive understanding of the characteristics of long COVID and propose improvement for tackling COVID-19.
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Affiliation(s)
- Shi‐ting He
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Kexin Wu
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Zixuan Cheng
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Mengjie He
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Ruolan Hu
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Ning Fan
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Lin Shen
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Qirui Li
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Huahao Fan
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
| | - Yigang Tong
- College of Life Science and TechnologyBeijing University of Chemical TechnologyBeijingChina
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21
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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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22
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Zhang F, Luna A, Tan T, Chen Y, Sander C, Guo T. COVIDpro: Database for mining protein dysregulation in patients with COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.27.509819. [PMID: 36203550 PMCID: PMC9536031 DOI: 10.1101/2022.09.27.509819] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Background The ongoing pandemic of the coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) still has limited treatment options partially due to our incomplete understanding of the molecular dysregulations of the COVID-19 patients. We aimed to generate a repository and data analysis tools to examine the modulated proteins underlying COVID-19 patients for the discovery of potential therapeutic targets and diagnostic biomarkers. Methods We built a web server containing proteomic expression data from COVID-19 patients with a toolset for user-friendly data analysis and visualization. The web resource covers expert-curated proteomic data from COVID-19 patients published before May 2022. The data were collected from ProteomeXchange and from select publications via PubMed searches and aggregated into a comprehensive dataset. Protein expression by disease subgroups across projects was compared by examining differentially expressed proteins. We also visualize differentially expressed pathways and proteins. Moreover, circulating proteins that differentiated severe cases were nominated as predictive biomarkers. Findings We built and maintain a web server COVIDpro ( https://www.guomics.com/covidPro/ ) containing proteomics data generated by 41 original studies from 32 hospitals worldwide, with data from 3077 patients covering 19 types of clinical specimens, the majority from plasma and sera. 53 protein expression matrices were collected, for a total of 5434 samples and 14,403 unique proteins. Our analyses showed that the lipopolysaccharide-binding protein, as identified in the majority of the studies, was highly expressed in the blood samples of patients with severe disease. A panel of significantly dysregulated proteins was identified to separate patients with severe disease from non-severe disease. Classification of severe disease based on these proteomic signatures on five test sets reached a mean AUC of 0.87 and ACC of 0.80. Interpretation COVIDpro is an online database with an integrated analysis toolkit. It is a unique and valuable resource for testing hypotheses and identifying proteins or pathways that could be targeted by new treatments of COVID-19 patients. Funding National Key R&D Program of China: Key PDPM technologies (2021YFA1301602, 2021YFA1301601, 2021YFA1301603), Zhejiang Provincial Natural Science Foundation for Distinguished Young Scholars (LR19C050001), Hangzhou Agriculture and Society Advancement Program (20190101A04), National Natural Science Foundation of China (81972492) and National Science Fund for Young Scholars (21904107), National Resource for Network Biology (NRNB) from the National Institute of General Medical Sciences (NIGMS-P41 GM103504). Research in context Evidence before this study: Although an increasing number of therapies against COVID-19 are being developed, they are still insufficient, especially with the rise of new variants of concern. This is partially due to our incomplete understanding of the disease’s mechanisms. As data have been collected worldwide, several questions are now worth addressing via meta-analyses. Most COVID-19 drugs function by targeting or affecting proteins. Effectiveness and resistance to therapeutics can be effectively assessed via protein measurements. Empowered by mass spectrometry-based proteomics, protein expression has been characterized in a variety of patient specimens, including body fluids (e.g., serum, plasma, urea) and tissue (i.e., formalin-fixed and paraffin-embedded (FFPE)). We expert-curated proteomic expression data from COVID-19 patients published before May 2022, from the largest proteomic data repository ProteomeXhange as well as from literature search engines. Using this resource, a COVID-19 proteome meta-analysis could provide useful insights into the mechanisms of the disease and identify new potential drug targets.Added value of this study: We integrated many published datasets from patients with COVID-19 from 11 nations, with over 3000 patients and more than 5434 proteome measurements. We collected these datasets in an online database, and generated a toolbox to easily explore, analyze, and visualize the data. Next, we used the database and its associated toolbox to identify new proteins of diagnostic and therapeutic value for COVID-19 treatment. In particular, we identified a set of significantly dysregulated proteins for distinguishing severe from non-severe patients using serum samples.Implications of all the available evidence: COVIDpro will support the navigation and analysis of patterns of dysregulated proteins in various COVID-19 clinical specimens for identification and verification of protein biomarkers and potential therapeutic targets.
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23
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Fobofou SA, Savidge T. Microbial metabolites: cause or consequence in gastrointestinal disease? Am J Physiol Gastrointest Liver Physiol 2022; 322:G535-G552. [PMID: 35271353 PMCID: PMC9054261 DOI: 10.1152/ajpgi.00008.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 01/31/2023]
Abstract
Systems biology studies have established that changes in gastrointestinal microbiome composition and function can adversely impact host physiology. Notable diseases synonymously associated with dysbiosis include inflammatory bowel diseases, cancer, metabolic disorders, and opportunistic and recurrent pathogen infections. However, there is a scarcity of mechanistic data that advances our understanding of taxonomic correlations with pathophysiological host-microbiome interactions. Generally, to survive a hostile gut environment, microbes are highly metabolically active and produce trans-kingdom signaling molecules to interact with competing microorganisms and the host. These specialized metabolites likely play important homeostatic roles, and identifying disease-specific taxa and their effector pathways can provide better strategies for diagnosis, treatment, and prevention, as well as the discovery of innovative therapeutics. The signaling role of microbial biotransformation products such as bile acids, short-chain fatty acids, polysaccharides, and dietary tryptophan is increasingly recognized, but little is known about the identity and function of metabolites that are synthesized by microbial biosynthetic gene clusters, including ribosomally synthesized and posttranslationally modified peptides (RiPPs), nonribosomal peptides (NRPs), polyketides (PKs), PK-NRP hybrids, and terpenes. Here we consider how bioactive natural products directly encoded by the human microbiome can contribute to the pathophysiology of gastrointestinal disease, cancer, autoimmune, antimicrobial-resistant bacterial and viral infections (including COVID-19). We also present strategies used to discover these compounds and the biological activities they exhibit, with consideration of therapeutic interventions that could emerge from understanding molecular causation in gut microbiome research.
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Affiliation(s)
- Serge Alain Fobofou
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas
| | - Tor Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
- Department of Pathology, Texas Children's Microbiome Center, Texas Children's Hospital, Houston, Texas
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24
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Cortes GM, Marcialis MA, Bardanzellu F, Corrias A, Fanos V, Mussap M. Inflammatory Bowel Disease and COVID-19: How Microbiomics and Metabolomics Depict Two Sides of the Same Coin. Front Microbiol 2022; 13:856165. [PMID: 35391730 PMCID: PMC8981987 DOI: 10.3389/fmicb.2022.856165] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/21/2022] [Indexed: 12/11/2022] Open
Abstract
The integrity of the gastrointestinal tract structure and function is seriously compromised by two pathological conditions sharing, at least in part, several pathogenetic mechanisms: inflammatory bowel diseases (IBD) and coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. IBD and COVID-19 are marked by gut inflammation, intestinal barrier breakdown, resulting in mucosal hyperpermeability, gut bacterial overgrowth, and dysbiosis together with perturbations in microbial and human metabolic pathways originating changes in the blood and fecal metabolome. This review compared the most relevant metabolic and microbial alterations reported from the literature in patients with IBD with those in patients with COVID-19. In both diseases, gut dysbiosis is marked by the prevalence of pro-inflammatory bacterial species and the shortfall of anti-inflammatory species; most studies reported the decrease in Firmicutes, with a specific decrease in obligately anaerobic producers short-chain fatty acids (SCFAs), such as Faecalibacterium prausnitzii. In addition, Escherichia coli overgrowth has been observed in IBD and COVID-19, while Akkermansia muciniphila is depleted in IBD and overexpressed in COVID-19. In patients with COVID-19, gut dysbiosis continues after the clearance of the viral RNA from the upper respiratory tract and the resolution of clinical symptoms. Finally, we presented and discussed the impact of gut dysbiosis, inflammation, oxidative stress, and increased energy demand on metabolic pathways involving key metabolites, such as tryptophan, phenylalanine, histidine, glutamine, succinate, citrate, and lipids.
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Affiliation(s)
- Gian Mario Cortes
- Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Monserrato, Italy
| | - Maria Antonietta Marcialis
- Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Monserrato, Italy
| | - Flaminia Bardanzellu
- Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Monserrato, Italy
| | - Angelica Corrias
- Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Monserrato, Italy
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Monserrato, Italy
| | - Michele Mussap
- Laboratory Medicine, Department of Surgical Sciences, School of Medicine, University of Cagliari, Monserrato, Italy
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25
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Farsi Y, Tahvildari A, Arbabi M, Vazife F, Sechi LA, Shahidi Bonjar AH, Jamshidi P, Nasiri MJ, Mirsaeidi M. Diagnostic, Prognostic, and Therapeutic Roles of Gut Microbiota in COVID-19: A Comprehensive Systematic Review. Front Cell Infect Microbiol 2022; 12:804644. [PMID: 35310853 PMCID: PMC8930898 DOI: 10.3389/fcimb.2022.804644] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/07/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction The Coronavirus Disease 2019 (COVID-19) pandemic caused by Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) emerged in late December 2019. Considering the important role of gut microbiota in maturation, regulation, and induction of the immune system and subsequent inflammatory processes, it seems that evaluating the composition of gut microbiota in COVID-19 patients compared with healthy individuals may have potential value as a diagnostic and/or prognostic biomarker for the disease. Also, therapeutic interventions affecting gut microbial flora may open new horizons in the treatment of COVID-19 patients and accelerating their recovery. Methods A systematic search was conducted for relevant studies published from December 2019 to December 2021 using Pubmed/Medline, Embase, and Scopus. Articles containing the following keywords in titles or abstracts were selected: "SARS-CoV-2" or "COVID-19" or "Coronavirus Disease 19" and "gastrointestinal microbes" or "dysbiosis" or "gut microbiota" or "gut bacteria" or "gut microbes" or "gastrointestinal microbiota". Results Out of 1,668 studies, 22 articles fulfilled the inclusion criteria and a total of 1,255 confirmed COVID-19 patients were examined. All included studies showed a significant association between COVID-19 and gut microbiota dysbiosis. The most alteration in bacterial composition of COVID-19 patients was depletion in genera Ruminococcus, Alistipes, Eubacterium, Bifidobacterium, Faecalibacterium, Roseburia, Fusicathenibacter, and Blautia and enrichment of Eggerthella, Bacteroides, Actinomyces, Clostridium, Streptococcus, Rothia, and Collinsella. Also, some gut microbiome alterations were associated with COVID-19 severity and poor prognosis including the increment of Bacteroides, Parabacteroides, Clostridium, Bifidobacterium, Ruminococcus, Campylobacter, Rothia, Corynebacterium, Megasphaera, Enterococcus, and Aspergillus spp. and the decrement of Roseburia, Eubacterium, Lachnospira, Faecalibacterium, and the Firmicutes/Bacteroidetes ratio. Conclusion Our study showed a significant change of gut microbiome composition in COVID-19 patients compared with healthy individuals. This great extent of impact has proposed the gut microbiota as a potential diagnostic, prognostic, and therapeutic strategy for COVID-19. There is much evidence about this issue, and it is expected to be increased in near future.
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Affiliation(s)
- Yeganeh Farsi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Azin Tahvildari
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahta Arbabi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fateme Vazife
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leonardo A. Sechi
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Struttura Complessa (SC), Microbiologia e Virologia, Azienda Ospedaliera Universitaria, Sassari, Italy
| | - Amir Hashem Shahidi Bonjar
- Clinician Scientist of Dental Materials and Restorative Dentistry, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Parnian Jamshidi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Mirsaeidi
- Division of Pulmonary and Critical Care, College of Medicine-Jacksonville, University of Florida, Jacksonville, FL, United States
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