1
|
Kopera K, Gromowski T, Wydmański W, Skonieczna-Żydecka K, Muszyńska A, Zielińska K, Wierzbicka-Woś A, Kaczmarczyk M, Kadaj-Lipka R, Cembrowska-Lech D, Januszkiewicz K, Kotfis K, Witkiewicz W, Nalewajska M, Feret W, Marlicz W, Łoniewski I, Łabaj PP, Rydzewska G, Kosciolek T. Gut microbiome dynamics and predictive value in hospitalized COVID-19 patients: a comparative analysis of shallow and deep shotgun sequencing. Front Microbiol 2024; 15:1342749. [PMID: 38962119 PMCID: PMC11219902 DOI: 10.3389/fmicb.2024.1342749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 05/20/2024] [Indexed: 07/05/2024] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has led to a wide range of clinical presentations, with respiratory symptoms being common. However, emerging evidence suggests that the gastrointestinal (GI) tract is also affected, with angiotensin-converting enzyme 2, a key receptor for SARS-CoV-2, abundantly expressed in the ileum and colon. The virus has been detected in GI tissues and fecal samples, even in cases with negative results of the reverse transcription polymerase chain reaction in the respiratory tract. GI symptoms have been associated with an increased risk of ICU admission and mortality. The gut microbiome, a complex ecosystem of around 40 trillion bacteria, plays a crucial role in immunological and metabolic pathways. Dysbiosis of the gut microbiota, characterized by a loss of beneficial microbes and decreased microbial diversity, has been observed in COVID-19 patients, potentially contributing to disease severity. We conducted a comprehensive gut microbiome study in 204 hospitalized COVID-19 patients using both shallow and deep shotgun sequencing methods. We aimed to track microbiota composition changes induced by hospitalization, link these alterations to clinical procedures (antibiotics administration) and outcomes (ICU referral, survival), and assess the predictive potential of the gut microbiome for COVID-19 prognosis. Shallow shotgun sequencing was evaluated as a cost-effective diagnostic alternative for clinical settings. Our study demonstrated the diverse effects of various combinations of clinical parameters, microbiome profiles, and patient metadata on the precision of outcome prognostication in patients. It indicates that microbiological data possesses greater reliability in forecasting patient outcomes when contrasted with clinical data or metadata. Furthermore, we established that shallow shotgun sequencing presents a viable and cost-effective diagnostic alternative to deep sequencing within clinical environments.
Collapse
Affiliation(s)
- Katarzyna Kopera
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Tomasz Gromowski
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of General Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Witold Wydmański
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Faculty of Mathematics and Computer Science, Jagiellonian University, Kraków, Poland
| | | | - Agata Muszyńska
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Kinga Zielińska
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | | | - Mariusz Kaczmarczyk
- Sanprobi Sp. z o.o. Sp. k., Szczecin, Poland
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, Szczecin, Poland
| | - Roland Kadaj-Lipka
- Department of Internal Medicine and Gastroenterology, Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
| | - Danuta Cembrowska-Lech
- Department of Biochemical Science, Pomeranian Medical University, Szczecin, Poland
- Sanprobi Sp. z o.o. Sp. k., Szczecin, Poland
| | | | - Katarzyna Kotfis
- Department of Anesthesiology, Intensive Care and Pain Management, Pomeranian Medical University, Szczecin, Poland
| | | | | | - Wiktoria Feret
- Clinical Department of Nephrology, Transplantology and Internal Medicine, Pomeranian Medical University, Szczecin, Poland
| | - Wojciech Marlicz
- Sanprobi Sp. z o.o. Sp. k., Szczecin, Poland
- Department of Gastroenterology, Pomeranian Medical University, Szczecin, Poland
| | - Igor Łoniewski
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Biochemical Science, Pomeranian Medical University, Szczecin, Poland
- Sanprobi Sp. z o.o. Sp. k., Szczecin, Poland
| | - Paweł P. Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Grażyna Rydzewska
- Department of Internal Medicine and Gastroenterology, Central Clinical Hospital of the Ministry of Interior and Administration, Warsaw, Poland
| | - Tomasz Kosciolek
- Małopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| |
Collapse
|
2
|
Chen Y, Chen C. Gut microbiota, inflammatory proteins and COVID-19: a Mendelian randomisation study. Front Immunol 2024; 15:1406291. [PMID: 38803488 PMCID: PMC11128586 DOI: 10.3389/fimmu.2024.1406291] [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: 03/24/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
Background The human gut microbiota has been identified as a potentially important factor influencing the development of COVID-19. It is believed that the disease primarily affects the organism through inflammatory pathways. With the aim of improving early diagnosis and targeted therapy, it is crucial to identify the specific gut microbiota associated with COVID-19 and to gain a deeper understanding of the underlying processes. The present study sought to investigate the potential causal relationship between the gut microbiota and COVID-19, and to determine the extent to which inflammatory proteins act as mediators in this relationship. Methods Bidirectional mendelian randomization (MR) and Two-step mediated MR analyses were applied to examine causative associations among 196 gut microbiota, 91 inflammatory proteins and COVID-19. The main analytical method used in the MR was the random effects inverse variance weighted (IVW) method. This was complemented by the Bayesian weighted Mendelian randomization (BWMR) method, which was utilized to test the hypothesis of MR. In order for the results to be deemed reliable, statistical significance was required for both methods. Validation was then carried out using an external dataset, and further meta-analyses were conducted to authenticate that the association was reliable. Results Results of our research indicated that seven gut microbiota were actively associated to the COVID-19 risk. Five inflammatory proteins were associated with COVID-19 risk, of which three were positively and two were negatively identified with COVID-19. Further validation was carried out using sensitivity analyses. Mediated MR results revealed that CCL2 was a possible mediator of causality of family Bifidobacteriaceae and order Bifidobacteriales with COVID-19, mediating at a ratio of 12.73%. Conclusion Suggesting a genetic causation between specific gut microbiota and COVID-19, our present research emphasizes the underlying mediating role of CCL2, an inflammatory factor, and contributes to a deeper understanding of the mechanism of action underlying COVID-19.
Collapse
Affiliation(s)
- Yuling Chen
- Department of Clinical Laboratory, Nanchong Central Hospital (Nanchong Hospital of Beijing Anzhen Hospital, Capital Medical University), The Second Clinical Medical College of North Sichuan Medical College, Nanchong, Sichuan, China
| | - Chang Chen
- Medical Department, Nanchong Guoning Mental Health Hospital, Nanchong, Sichuan, China
| |
Collapse
|
3
|
Galeeva JS, Fedorov DE, Starikova EV, Manolov AI, Pavlenko AV, Selezneva OV, Klimina KM, Veselovsky VA, Morozov MD, Yanushevich OO, Krikheli NI, Levchenko OV, Andreev DN, Sokolov FS, Fomenko AK, Devkota MK, Andreev NG, Zaborovskiy AV, Bely PA, Tsaregorodtsev SV, Evdokimov VV, Maev IV, Govorun VM, Ilina EN. Microbial Signatures in COVID-19: Distinguishing Mild and Severe Disease via Gut Microbiota. Biomedicines 2024; 12:996. [PMID: 38790958 PMCID: PMC11118803 DOI: 10.3390/biomedicines12050996] [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: 04/14/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has significantly impacted global healthcare, underscoring the importance of exploring the virus's effects on infected individuals beyond treatments and vaccines. Notably, recent findings suggest that SARS-CoV-2 can infect the gut, thereby altering the gut microbiota. This study aimed to analyze the gut microbiota composition differences between COVID-19 patients experiencing mild and severe symptoms. We conducted 16S rRNA metagenomic sequencing on fecal samples from 49 mild and 43 severe COVID-19 cases upon hospital admission. Our analysis identified a differential abundance of specific bacterial species associated with the severity of the disease. Severely affected patients showed an association with Enterococcus faecium, Akkermansia muciniphila, and others, while milder cases were linked to Faecalibacterium prausnitzii, Alistipes putredinis, Blautia faecis, and additional species. Furthermore, a network analysis using SPIEC-EASI indicated keystone taxa and highlighted structural differences in bacterial connectivity, with a notable disruption in the severe group. Our study highlights the diverse impacts of SARS-CoV-2 on the gut microbiome among both mild and severe COVID-19 patients, showcasing a spectrum of microbial responses to the virus. Importantly, these findings align, to some extent, with observations from other studies on COVID-19 gut microbiomes, despite variations in methodologies. The findings from this study, based on retrospective data, establish a foundation for future prospective research to confirm the role of the gut microbiome as a predictive biomarker for the severity of COVID-19.
Collapse
Affiliation(s)
- Julia S. Galeeva
- Research Institute for Systems Biology and Medicine, Department of Mathematical Biology and Bioinformatics, Moscow 117246, Russia; (D.E.F.); (E.V.S.); (A.I.M.); (A.V.P.)
| | - Dmitry E. Fedorov
- Research Institute for Systems Biology and Medicine, Department of Mathematical Biology and Bioinformatics, Moscow 117246, Russia; (D.E.F.); (E.V.S.); (A.I.M.); (A.V.P.)
| | - Elizaveta V. Starikova
- Research Institute for Systems Biology and Medicine, Department of Mathematical Biology and Bioinformatics, Moscow 117246, Russia; (D.E.F.); (E.V.S.); (A.I.M.); (A.V.P.)
| | - Alexander I. Manolov
- Research Institute for Systems Biology and Medicine, Department of Mathematical Biology and Bioinformatics, Moscow 117246, Russia; (D.E.F.); (E.V.S.); (A.I.M.); (A.V.P.)
| | - Alexander V. Pavlenko
- Research Institute for Systems Biology and Medicine, Department of Mathematical Biology and Bioinformatics, Moscow 117246, Russia; (D.E.F.); (E.V.S.); (A.I.M.); (A.V.P.)
| | - Oksana V. Selezneva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (O.V.S.); (K.M.K.); (V.A.V.); (M.D.M.)
| | - Ksenia M. Klimina
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (O.V.S.); (K.M.K.); (V.A.V.); (M.D.M.)
| | - Vladimir A. Veselovsky
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (O.V.S.); (K.M.K.); (V.A.V.); (M.D.M.)
| | - Maxim D. Morozov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (O.V.S.); (K.M.K.); (V.A.V.); (M.D.M.)
| | - Oleg O. Yanushevich
- Department of Clinical Dentistry, Moscow State University of Medicine and Dentistry, Moscow 127473, Russia; (O.O.Y.); (N.I.K.); (O.V.L.); (D.N.A.); (F.S.S.); (A.K.F.); (M.K.D.); (N.G.A.); (A.V.Z.); (P.A.B.); (S.V.T.); (V.V.E.); (I.V.M.); (V.M.G.)
| | - Natella I. Krikheli
- Department of Clinical Dentistry, Moscow State University of Medicine and Dentistry, Moscow 127473, Russia; (O.O.Y.); (N.I.K.); (O.V.L.); (D.N.A.); (F.S.S.); (A.K.F.); (M.K.D.); (N.G.A.); (A.V.Z.); (P.A.B.); (S.V.T.); (V.V.E.); (I.V.M.); (V.M.G.)
| | - Oleg V. Levchenko
- Department of Clinical Dentistry, Moscow State University of Medicine and Dentistry, Moscow 127473, Russia; (O.O.Y.); (N.I.K.); (O.V.L.); (D.N.A.); (F.S.S.); (A.K.F.); (M.K.D.); (N.G.A.); (A.V.Z.); (P.A.B.); (S.V.T.); (V.V.E.); (I.V.M.); (V.M.G.)
| | - Dmitry N. Andreev
- Department of Clinical Dentistry, Moscow State University of Medicine and Dentistry, Moscow 127473, Russia; (O.O.Y.); (N.I.K.); (O.V.L.); (D.N.A.); (F.S.S.); (A.K.F.); (M.K.D.); (N.G.A.); (A.V.Z.); (P.A.B.); (S.V.T.); (V.V.E.); (I.V.M.); (V.M.G.)
| | - Filipp S. Sokolov
- Department of Clinical Dentistry, Moscow State University of Medicine and Dentistry, Moscow 127473, Russia; (O.O.Y.); (N.I.K.); (O.V.L.); (D.N.A.); (F.S.S.); (A.K.F.); (M.K.D.); (N.G.A.); (A.V.Z.); (P.A.B.); (S.V.T.); (V.V.E.); (I.V.M.); (V.M.G.)
| | - Aleksey K. Fomenko
- Department of Clinical Dentistry, Moscow State University of Medicine and Dentistry, Moscow 127473, Russia; (O.O.Y.); (N.I.K.); (O.V.L.); (D.N.A.); (F.S.S.); (A.K.F.); (M.K.D.); (N.G.A.); (A.V.Z.); (P.A.B.); (S.V.T.); (V.V.E.); (I.V.M.); (V.M.G.)
| | - Mikhail K. Devkota
- Department of Clinical Dentistry, Moscow State University of Medicine and Dentistry, Moscow 127473, Russia; (O.O.Y.); (N.I.K.); (O.V.L.); (D.N.A.); (F.S.S.); (A.K.F.); (M.K.D.); (N.G.A.); (A.V.Z.); (P.A.B.); (S.V.T.); (V.V.E.); (I.V.M.); (V.M.G.)
| | - Nikolai G. Andreev
- Department of Clinical Dentistry, Moscow State University of Medicine and Dentistry, Moscow 127473, Russia; (O.O.Y.); (N.I.K.); (O.V.L.); (D.N.A.); (F.S.S.); (A.K.F.); (M.K.D.); (N.G.A.); (A.V.Z.); (P.A.B.); (S.V.T.); (V.V.E.); (I.V.M.); (V.M.G.)
| | - Andrey V. Zaborovskiy
- Department of Clinical Dentistry, Moscow State University of Medicine and Dentistry, Moscow 127473, Russia; (O.O.Y.); (N.I.K.); (O.V.L.); (D.N.A.); (F.S.S.); (A.K.F.); (M.K.D.); (N.G.A.); (A.V.Z.); (P.A.B.); (S.V.T.); (V.V.E.); (I.V.M.); (V.M.G.)
| | - Petr A. Bely
- Department of Clinical Dentistry, Moscow State University of Medicine and Dentistry, Moscow 127473, Russia; (O.O.Y.); (N.I.K.); (O.V.L.); (D.N.A.); (F.S.S.); (A.K.F.); (M.K.D.); (N.G.A.); (A.V.Z.); (P.A.B.); (S.V.T.); (V.V.E.); (I.V.M.); (V.M.G.)
| | - Sergei V. Tsaregorodtsev
- Department of Clinical Dentistry, Moscow State University of Medicine and Dentistry, Moscow 127473, Russia; (O.O.Y.); (N.I.K.); (O.V.L.); (D.N.A.); (F.S.S.); (A.K.F.); (M.K.D.); (N.G.A.); (A.V.Z.); (P.A.B.); (S.V.T.); (V.V.E.); (I.V.M.); (V.M.G.)
| | - Vladimir V. Evdokimov
- Department of Clinical Dentistry, Moscow State University of Medicine and Dentistry, Moscow 127473, Russia; (O.O.Y.); (N.I.K.); (O.V.L.); (D.N.A.); (F.S.S.); (A.K.F.); (M.K.D.); (N.G.A.); (A.V.Z.); (P.A.B.); (S.V.T.); (V.V.E.); (I.V.M.); (V.M.G.)
| | - Igor V. Maev
- Department of Clinical Dentistry, Moscow State University of Medicine and Dentistry, Moscow 127473, Russia; (O.O.Y.); (N.I.K.); (O.V.L.); (D.N.A.); (F.S.S.); (A.K.F.); (M.K.D.); (N.G.A.); (A.V.Z.); (P.A.B.); (S.V.T.); (V.V.E.); (I.V.M.); (V.M.G.)
| | - Vadim M. Govorun
- Department of Clinical Dentistry, Moscow State University of Medicine and Dentistry, Moscow 127473, Russia; (O.O.Y.); (N.I.K.); (O.V.L.); (D.N.A.); (F.S.S.); (A.K.F.); (M.K.D.); (N.G.A.); (A.V.Z.); (P.A.B.); (S.V.T.); (V.V.E.); (I.V.M.); (V.M.G.)
| | - Elena N. Ilina
- Department of Clinical Dentistry, Moscow State University of Medicine and Dentistry, Moscow 127473, Russia; (O.O.Y.); (N.I.K.); (O.V.L.); (D.N.A.); (F.S.S.); (A.K.F.); (M.K.D.); (N.G.A.); (A.V.Z.); (P.A.B.); (S.V.T.); (V.V.E.); (I.V.M.); (V.M.G.)
| |
Collapse
|
4
|
Wang M, Lkhagva E, Kim S, Zhai C, Islam MM, Kim HJ, Hong ST. The gut microbe pair of Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270 confers complete protection against SARS-CoV-2 infection by activating CD8+ T cell-mediated immunity. Gut Microbes 2024; 16:2342497. [PMID: 38635321 PMCID: PMC11028030 DOI: 10.1080/19490976.2024.2342497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
Despite the potential protective role of the gut microbiome against COVID-19, specific microbes conferring resistance to COVID-19 have not yet been identified. In this work, we aimed to identify and validate gut microbes at the species level that provide protection against SARS-CoV-2 infection. To identify gut microbes conferring protection against COVID-19, we conducted a fecal microbiota transplantation (FMT) from an individual with no history of COVID-19 infection or immunization into a lethal COVID-19 hamster model. FMT from this COVID-19-resistant donor resulted in significant phenotypic changes related to COVID-19 sensitivity in the hamsters. Metagenomic analysis revealed distinct differences in the gut microbiome composition among the hamster groups, leading to the identification of two previously unknown bacterial species: Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270, both associated with COVID-19 resistance. Subsequently, we conducted a proof-of-concept confirmation animal experiment adhering to Koch's postulates. Oral administration of this gut microbe pair, Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270, to the hamsters provided complete protection against SARS-CoV-2 infection through the activation of CD8+ T cell mediated immunity. The prophylactic efficacy of the gut microbe pair against SARS-CoV-2 infection was comparable to, or even superior to, current mRNA vaccines. This strong prophylactic efficacy suggests that the gut microbe pair could be developed as a host-directed universal vaccine for all betacoronaviruses, including potential future emerging viruses.
Collapse
Affiliation(s)
- Mingda Wang
- Department of Biomedical Sciences, Jeonbuk National University Medical School, Jeollabuk-Do, South Korea
- Department of Critical Care Medicine, Shandong Provincial Hospital affiliated with Shandong First Medical University, Jinan, China
| | - Enkhchimeg Lkhagva
- Department of Biomedical Sciences, Jeonbuk National University Medical School, Jeollabuk-Do, South Korea
| | - Sura Kim
- Department of Biomedical Sciences, Jeonbuk National University Medical School, Jeollabuk-Do, South Korea
| | - Chongkai Zhai
- Department of Biomedical Sciences, Jeonbuk National University Medical School, Jeollabuk-Do, South Korea
- College of Food and Drugs, Luoyang Polytechnic, Animal Diseases and Public Health Engineering Research Center of Henan Province, Luoyang, Henan Province, China
| | - Md Minarul Islam
- Department of Biomedical Sciences, Jeonbuk National University Medical School, Jeollabuk-Do, South Korea
| | - Hyeon J. Kim
- BioLabs-LA at the Lundquist Institute for Bio Medical Innovation at Harbor UCLA, SNJ Pharma Inc, Torrance, CA, USA
| | - Seong-Tshool Hong
- Department of Biomedical Sciences, Jeonbuk National University Medical School, Jeollabuk-Do, South Korea
| |
Collapse
|
5
|
Ma J, Zhu Z, Yishajiang Y, Alarjani KM, Hong L, Luo L. Role of gut microbiota and inflammatory factors in acute respiratory distress syndrome: a Mendelian randomization analysis. Front Microbiol 2023; 14:1294692. [PMID: 38173678 PMCID: PMC10761488 DOI: 10.3389/fmicb.2023.1294692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/29/2023] [Indexed: 01/05/2024] Open
Abstract
Background Acute respiratory distress syndrome (ARDS) is a serious lung ailment marked by significant inflammation and damage in the alveoli and capillaries of the lungs. Recent research suggests a strong correlation between the onset and advancement of ARDS and an imbalance in the gut microbiota (GM). Methods In this investigation, Mendelian randomization (MR) analysis was utilized, drawing on data from publicly accessible genome-wide association studies. The primary focus was on examining the interplay between GM, inflammatory factors (IFs) and ARDS. Instrumental variables were established through genetic modifications of GM and IFs. Various statistical analysis methods including the inverse-variance weighted model, MR-Egger method and Wald ratio test were applied for comprehensive data analysis. Results Eight bacterial taxa within the GM demonstrated a potential causal link with development of ARDS. Notably, the phylum Actinobacteria and the genus Intestinibacter exhibited a negative association with the risk of ARDS. However, Erysipelotrichales (id. 2,148), Victivallis (id. 2,256), Ruminococcaceae UCG014 (id. 11,371), Eubacterium ruminantium group (id. 11,340), Erysipelotrichaceae (id. 2,149) and Erysipelotrichia (id. 2,147) demonstrated a positive association with ARDS risk. Additionally, the study identified a potential causal relationship between the inflammatory factors interleukin-16 and C-C motif chemokine 3 with the occurrence of ARDS. Conclusion This study strongly suggests that the interaction between gut microbiota (GM) and inflammatory factors (IFs) significantly contributes to the pathogenesis of acute respiratory distress syndrome (ARDS). This underscores their crucial involvement in both the initiation and advancement of this severe lung disorder.
Collapse
Affiliation(s)
- Jiawei Ma
- Department of Critical Care Medicine, Jiangnan University Medical Center, Wuxi, China
- Department of Critical Care Medicine, Aheqi County People's Hospital, Xinjiang, China
| | - Zigang Zhu
- Department of Critical Care Medicine, Jiangnan University Medical Center, Wuxi, China
| | | | - Khaloud Mohammed Alarjani
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Lei Hong
- Institute of Clinical Medicine Research, The Affiliated Suzhou Science and Technology Town Hospital of Nanjing Medical University, Suzhou, China
| | - Liang Luo
- Department of Critical Care Medicine, Jiangnan University Medical Center, Wuxi, China
| |
Collapse
|
6
|
He KY, Lei XY, Zhang L, Wu DH, Li JQ, Lu LY, Laila UE, Cui CY, Xu ZX, Jian YP. Development and management of gastrointestinal symptoms in long-term COVID-19. Front Microbiol 2023; 14:1278479. [PMID: 38156008 PMCID: PMC10752947 DOI: 10.3389/fmicb.2023.1278479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023] Open
Abstract
Background Emerging evidence reveals that SARS-CoV-2 possesses the capability to disrupt the gastrointestinal (GI) homeostasis, resulting in the long-term symptoms such as loss of appetite, diarrhea, gastroesophageal reflux, and nausea. In the current review, we summarized recent reports regarding the long-term effects of COVID-19 (long COVID) on the gastrointestine. Objective To provide a narrative review of abundant clinical evidence regarding the development and management of long-term GI symptoms in COVID-19 patients. Results Long-term persistent digestive symptoms are exhibited in a majority of long-COVID patients. SARS-CoV-2 infection of intestinal epithelial cells, cytokine storm, gut dysbiosis, therapeutic drugs, psychological factors and exacerbation of primary underlying diseases lead to long-term GI symptoms in COVID-19 patients. Interventions like probiotics, prebiotics, fecal microbiota transplantation, and antibiotics are proved to be beneficial in preserving intestinal microecological homeostasis and alleviating GI symptoms. Conclusion Timely diagnosis and treatment of GI symptoms in long-COVID patients hold great significance as they may contribute to the mitigation of severe conditions and ultimately lead to the improvement of outcomes of the patients.
Collapse
Affiliation(s)
- Kai-Yue He
- School of Life Sciences, Henan University, Kaifeng, China
| | - Xin-Yuan Lei
- School of Life Sciences, Henan University, Kaifeng, China
| | - Lei Zhang
- School of Life Sciences, Henan University, Kaifeng, China
| | - Dan-Hui Wu
- School of Life Sciences, Henan University, Kaifeng, China
| | - Jun-Qi Li
- School of Life Sciences, Henan University, Kaifeng, China
| | - Li-Yuan Lu
- School of Life Sciences, Henan University, Kaifeng, China
| | - Umm E. Laila
- School of Life Sciences, Henan University, Kaifeng, China
| | - Cui-Yun Cui
- Department of Blood Transfusion, Henan Provincial People’s Hospital, Zhengzhou, Henan, China
| | - Zhi-Xiang Xu
- School of Life Sciences, Henan University, Kaifeng, China
| | - Yong-Ping Jian
- School of Life Sciences, Henan University, Kaifeng, China
| |
Collapse
|
7
|
Fan R, Liu S, Sun N, Yang Y, Deng X, Hu B, Sun C, Wen C, Li H, Cheng D, Huang C, Hou P, Zhang T. Gut microbiota composition is associated with disease severity and host immune responses in COVID-19. Front Cell Infect Microbiol 2023; 13:1274690. [PMID: 38149007 PMCID: PMC10749918 DOI: 10.3389/fcimb.2023.1274690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/21/2023] [Indexed: 12/28/2023] Open
Abstract
Background Human gut microbiota play a crucial role in the immune response of the host to respiratory viral infection. However, evidence regarding the association between the gut microbiome, host immune responses, and disease severity in coronavirus disease 2019 (COVID-19) remains insufficient. Methods To better comprehend the interactions between the host and gut microbiota in COVID-19, we conducted 16S rRNA sequencing and characterized the gut microbiome compositions in stool samples from 40 COVID-19 patients and 33 non-pneumonia controls. We assessed several hematological parameters to determine the immune status. Results We found that the gut microbial composition was significantly changed in COVID-19 patients, which was characterized by increased opportunistic pathogens and decreased commensal bacteria. The frequency of prevalent opportunistic pathogens Enterococcus and Lactobacillus increased, especially in severe patients; yet the abundance of butyrate-producing bacteria, Faecalibacterium, Roseburia, and Anaerostipes, decreased significantly, and Faecalibacterium prausnitzii might help discriminate severe patients from moderate patients and non-pneumonia people. Furthermore, we then obtained a correlation map between the clinical characteristics of COVID-19 and severity-related gut microbiota. We observed a notable correlation between the abundance of Enterococcus faecium and abnormal neutrophil or lymphocyte percentage in all COVID-19 patients. Faecalibacterium was positively correlated with lymphocyte counts, while negatively correlated with neutrophil percentage. Conclusion These results suggested that the gut microbiome could have a potential function in regulating host immune responses and impacting the severity or consequences of diseases.
Collapse
Affiliation(s)
- Ruyue Fan
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Shuai Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Shandong Key Laboratory of Infectious Respiratory Disease, Jinan, Shandong, China
| | - Na Sun
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Ying Yang
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Xia Deng
- School of Public Healthy, Weifang Medical University, Weifang, Shandong, China
| | - Bin Hu
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Changhua Sun
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Chengli Wen
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Hui Li
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Dong Cheng
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Chuanjun Huang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
- Shandong Key Laboratory of Infectious Respiratory Disease, Jinan, Shandong, China
| | - Peibin Hou
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| | - Tianliang Zhang
- Shandong Center for Disease Control and Prevention, Jinan, Shandong, China
- Shandong Provincial Key Laboratory of Infectious Diseases Control and Prevention, Jinan, Shandong, China
| |
Collapse
|
8
|
Moreno-Corona NC, López-Ortega O, Pérez-Martínez CA, Martínez-Castillo M, De Jesús-González LA, León-Reyes G, León-Juárez M. Dynamics of the Microbiota and Its Relationship with Post-COVID-19 Syndrome. Int J Mol Sci 2023; 24:14822. [PMID: 37834270 PMCID: PMC10573029 DOI: 10.3390/ijms241914822] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Coronavirus disease (COVID-19) is an infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which can be asymptomatic or present with multiple organ dysfunction. Many infected individuals have chronic alterations associated with neuropsychiatric, endocrine, gastrointestinal, and musculoskeletal symptoms, even several months after disease onset, developing long-COVID or post-acute COVID-19 syndrome (PACS). Microbiota dysbiosis contributes to the onset and progression of many viral diseases, including COVID-19 and post-COVID-19 manifestations, which could serve as potential diagnostic and prognostic biomarkers. This review aimed to discuss the most recent findings on gut microbiota dysbiosis and its relationship with the sequelae of PACS. Elucidating these mechanisms could help develop personalized and non-invasive clinical strategies to identify individuals at a higher risk of experiencing severe disease progression or complications associated with PACS. Moreover, the review highlights the importance of targeting the gut microbiota composition to avoid dysbiosis and to develop possible prophylactic and therapeutic measures against COVID-19 and PACS in future studies.
Collapse
Affiliation(s)
- Nidia Carolina Moreno-Corona
- Laboratory of Human Lymphohematopoiesis, Imagine Institute, INSERM UMR 1163, Université de Paris, 75015 Paris, France;
| | - Orestes López-Ortega
- Université Paris Cité, INSERM UMR-S1151, CNRS UMR-S8253, Institute Necker Enfants Malades, 75015 Paris, France;
| | | | - Macario Martínez-Castillo
- Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico;
| | | | - Guadalupe León-Reyes
- Laboratorio de Nutrigenética y Nutrigenómica, Instituto Nacional de Medicina Genómica (INMEGEN), México City 16610, Mexico;
| | - Moisés León-Juárez
- Laboratorio de Virología Perinatal y Diseño Molecular de Antígenos y Biomarcadores, Departamento de Inmunobioquímica, Instituto Nacional de Perinatología, Mexico City 11000, Mexico
| |
Collapse
|
9
|
Taufer CR, Rampelotto PH. The Role of Bifidobacterium in COVID-19: A Systematic Review. Life (Basel) 2023; 13:1847. [PMID: 37763251 PMCID: PMC10532519 DOI: 10.3390/life13091847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
The COVID-19 pandemic, caused by the SARS-CoV-2 virus, mainly causes respiratory and intestinal symptoms and changes in the microbiota of patients. We performed a systematic search in major databases using "Bifidobacterium" and "COVID-19" or "SARS-CoV-2" as key terms to assess the relationship of the genus to COVID-19. After the selection steps, 25 articles were analyzed. Of these, eighteen were observational, and seven were interventional articles that evaluated the use of Bifidobacterium alone or in mix as probiotics for additional treatment of patients with COVID-19. All stages and severities were contemplated, including post-COVID-19 patients. Overall, Bifidobacterium was associated with both protective effects and reduced abundance in relation to the disease. The genus has been found to be abundant in some cases and linked to disease severity. The studies evaluating the use of Bifidobacterium as probiotics have demonstrated the potential of this genus in reducing symptoms, improving pulmonary function, reducing inflammatory markers, alleviating gastrointestinal symptoms, and even contributing to better control of mortality. In summary, Bifidobacterium may offer protection against COVID-19 through its ability to modulate the immune response, reduce inflammation, compete with pathogenic microbes, and maintain gut barrier function. The findings provide valuable insights into the relationship between the disease and the genus Bifidobacterium, highlighting the potential of microbiota modulation in the treatment of COVID-19.
Collapse
Affiliation(s)
- Clarissa Reginato Taufer
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Pabulo Henrique Rampelotto
- Bioinformatics and Biostatistics Core Facility, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
- Graduate Program in Biological Sciences: Pharmacology and Therapeutics, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| |
Collapse
|
10
|
Hwang IC, Vasquez R, Song JH, Engstrand L, Valeriano VD, Kang DK. Alterations in the gut microbiome and its metabolites are associated with the immune response to mucosal immunization with Lactiplantibacillus plantarum-displaying recombinant SARS-CoV-2 spike epitopes in mice. Front Cell Infect Microbiol 2023; 13:1242681. [PMID: 37705931 PMCID: PMC10495993 DOI: 10.3389/fcimb.2023.1242681] [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: 06/19/2023] [Accepted: 08/11/2023] [Indexed: 09/15/2023] Open
Abstract
Lactic acid bacteria (LAB) expressing foreign antigens have great potential as mucosal vaccines. Our previous study reported that recombinant Lactiplantibacillus plantarum SK156 displaying SARS-CoV-2 spike S1 epitopes elicited humoral and cell-mediated immune responses in mice. Here, we further examined the effect of the LAB-based mucosal vaccine on gut microbiome composition and function, and gut microbiota-derived metabolites. Forty-nine (49) female BALB/c mice were orally administered L. plantarum SK156-displaying SARS-CoV-2 spike S1 epitopes thrice (at 14-day intervals). Mucosal immunization considerably altered the gut microbiome of mice by enriching the abundance of beneficial gut bacteria, such as Muribaculaceae, Mucispirillum, Ruminococcaceae, Alistipes, Roseburia, and Clostridia vadinBB60. Moreover, the predicted function of the gut microbiome showed increased metabolic pathways for amino acids, energy, carbohydrates, cofactors, and vitamins. The fecal concentration of short-chain fatty acids, especially butyrate, was also altered by mucosal immunization. Notably, alterations in gut microbiome composition, function, and butyrate levels were positively associated with the immune response to the vaccine. Our results suggest that the gut microbiome and its metabolites may have influenced the immunogenicity of the LAB-based SARS-CoV-2 vaccine.
Collapse
Affiliation(s)
- In-Chan Hwang
- Department of Animal Biotechnology, Dankook University, Cheonan, Republic of Korea
| | - Robie Vasquez
- Department of Animal Biotechnology, Dankook University, Cheonan, Republic of Korea
| | - Ji Hoon Song
- Department of Animal Biotechnology, Dankook University, Cheonan, Republic of Korea
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Valerie Diane Valeriano
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Dae-Kyung Kang
- Department of Animal Biotechnology, Dankook University, Cheonan, Republic of Korea
| |
Collapse
|
11
|
Li Z, Zhu G, Lei X, Tang L, Kong G, Shen M, Zhang L, Song L. Genetic support of the causal association between gut microbiome and COVID-19: a bidirectional Mendelian randomization study. Front Immunol 2023; 14:1217615. [PMID: 37483615 PMCID: PMC10360131 DOI: 10.3389/fimmu.2023.1217615] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
Background The association between gut microbiome and coronavirus disease 2019 (COVID-19) has attracted much attention, but its causality remains unclear and requires more direct evidence. Methods In this study, we conducted the bidirectional Mendelian randomization (MR) analysis to assess the causal association between gut microbiome and COVID-19 based on the summary statistics data of genome-wide association studies (GWASs). Over 1.8 million individuals with three COVID-19 phenotypes (severity, hospitalization and infection) were included. And 196 bacterial taxa from phylum to genus were analyzed. The inverse-variance weighted (IVW) analysis was chosen as the primary method. Besides, false discovery rate (FDR) correction of p-value was used. To test the robustness of the causal relationships with p-FDR < 0.05, sensitivity analyses including the secondary MR analyses, horizontal pleiotropy test, outliers test, and "leave-one-out" analysis were conducted. Results In the forward MR, we found that 3, 8, and 10 bacterial taxa had suggestive effects on COVID-19 severity, hospitalization and infection, respectively. The genus Alloprevotella [odds ratio (OR) = 1.67; 95% confidence interval (95% CI), 1.32-2.11; p = 1.69×10-5, p-FDR = 2.01×10-3] was causally associated with a higher COVID-19 severity risk. In the reverse MR, COVID-19 severity, hospitalization and infection had suggestive effects on the abundance of 4, 8 and 10 bacterial taxa, respectively. COVID-19 hospitalization causally increased the abundance of the phylum Bacteroidetes (OR = 1.13; 95% CI, 1.04-1.22; p = 3.02×10-3; p-FDR = 2.72×10-2). However, secondary MR analyses indicated that the result of COVID-19 hospitalization on the phylum Bacteroidetes required careful consideration. Conclusion Our study revealed the causal association between gut microbiome and COVID-19 and highlighted the role of "gut-lung axis" in the progression of COVID-19.
Collapse
Affiliation(s)
- Zengbin Li
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- China-Australia Joint Research Center for Infectious Diseases, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Guixian Zhu
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Xiangye Lei
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- China-Australia Joint Research Center for Infectious Diseases, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Liqiong Tang
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Guangyao Kong
- National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Mingwang Shen
- China-Australia Joint Research Center for Infectious Diseases, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, China
| | - Lei Zhang
- China-Australia Joint Research Center for Infectious Diseases, School of Public Health, Xi’an Jiaotong University Health Science Center, Xi’an, China
- Melbourne Sexual Health Centre, Alfred Health, Melbourne, VIC, Australia
- Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Lingqin Song
- Department of Oncology, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| |
Collapse
|
12
|
Tong J, Chen Y, He M, Wang W, Wang Y, Li N, Xia Q. The triangle relationship between human genome, gut microbiome, and COVID-19: opening of a Pandora's box. Front Microbiol 2023; 14:1190939. [PMID: 37455722 PMCID: PMC10344606 DOI: 10.3389/fmicb.2023.1190939] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
Since the pandemic started, the coronavirus disease 2019 (COVID-19) has spread worldwide. In patients with COVID-19, the gut microbiome (GM) has been supposed to be closely related to the progress of the disease. The gut microbiota composition and human genetic variation are also connected in COVID-19 patients, assuming a triangular relationship between the genome, GM, and COVID-19. Here, we reviewed the recent developments in the study of the relationship between gut microbiota and COVID-19. The keywords "COVID-19," "microbiome," and "genome" were used to search the literature in the PubMed database. We first found that the composition of the GM in COVID-19 patients varies according to the severity of the illness. Most obviously, Candida albicans abnormally increased while the probiotic Bifidobacterium decreased in severe cases of COVID-19. Interestingly, clinical studies have consistently emphasized that the family Lachnospiraceae plays a critical role in patients with COVID-19. Additionally, we have demonstrated the impact of microbiome-related genes on COVID-19. Specially, we focused on angiotensin-converting enzyme 2's dual functions in SARS-CoV-2 infection and gut microbiota alternation. In summary, these studies showed that the diversity of GMs is closely connected to COVID-19. A triangular relationship exists between COVID-19, the human genome, and the gut flora, suggesting that human genetic variations may offer a chance for a precise diagnosis of COVID-19, and the important relationships between genetic makeup and microbiome regulation may affect the therapy of COVID-19.
Collapse
Affiliation(s)
- Jie Tong
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, China
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Yuran Chen
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Mei He
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Wenjing Wang
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Yiyang Wang
- College of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, China
| | - Na Li
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, China
- Department of Tropical Diseases, The Second Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Qianfeng Xia
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine, Hainan Medical University, Haikou, China
- Department of Tropical Diseases, The Second Affiliated Hospital of Hainan Medical University, Haikou, China
| |
Collapse
|
13
|
Zhang F, Lau RI, Liu Q, Su Q, Chan FKL, Ng SC. Gut microbiota in COVID-19: key microbial changes, potential mechanisms and clinical applications. Nat Rev Gastroenterol Hepatol 2023; 20:323-337. [PMID: 36271144 PMCID: PMC9589856 DOI: 10.1038/s41575-022-00698-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/22/2022] [Indexed: 01/14/2023]
Abstract
The gastrointestinal tract is involved in coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The gut microbiota has important roles in viral entry receptor angiotensin-converting enzyme 2 (ACE2) expression, immune homeostasis, and crosstalk between the gut and lungs, the 'gut-lung axis'. Emerging preclinical and clinical studies indicate that the gut microbiota might contribute to COVID-19 pathogenesis and disease outcomes; SARS-CoV-2 infection was associated with altered intestinal microbiota and correlated with inflammatory and immune responses. Here, we discuss the cutting-edge evidence on the interactions between SARS-CoV-2 infection and the gut microbiota, key microbial changes in relation to COVID-19 severity and host immune dysregulations with the possible underlying mechanisms, and the conceivable consequences of the pandemic on the human microbiome and post-pandemic health. Finally, potential modulatory strategies of the gut microbiota are discussed. These insights could shed light on the development of microbiota-based interventions for COVID-19.
Collapse
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.
| |
Collapse
|
14
|
Shang W, Zhang S, Qian H, Pan X, Huang S, Wen Z, Liu J, Chen D. Association of gut microbiota with COVID-19 susceptibility and severity: A two-sample Mendelian randomization study. J Med Virol 2023; 95:e28734. [PMID: 37185856 DOI: 10.1002/jmv.28734] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/17/2023] [Accepted: 04/06/2023] [Indexed: 05/17/2023]
Abstract
Evidence supports the observational associations of gut microbiota with the risk of COVID-19; however, it is unclear whether these associations reflect a causal relationship. This study investigated the association of gut microbiota with COVID-19 susceptibility and severity. Data were obtained from a large-scale gut microbiota data set (n = 18 340) and the COVID-19 Host Genetics Initiative (n = 2 942 817). Causal effects were estimated with inverse variance weighted (IVW), MR-Egger, and weighted median, and sensitivity analyses were implemented with Cochran's Q test, MR-Egger intercept test, MR-PRESSO, leave-one-out analysis, and funnel plots. For COVID-19 susceptibility, IVW estimates suggested that Gammaproteobacteria (odds ratio [OR] = 0.94, 95% confidence interval [CI], 0.89-0.99, p = 0.0295] and Streptococcaceae (OR = 0.95, 95% CI, 0.92-1.00, p = 0.0287) had a reduced risk, while Negativicutes (OR = 1.05, 95% CI, 1.01-1.10, p = 0.0302), Selenomonadales (OR = 1.05, 95% CI, 1.01-1.10, p = 0.0302), Bacteroides (OR = 1.06, 95% CI, 1.01-1.12, p = 0.0283), and Bacteroidaceae (OR = 1.06, 95% CI, 1.01-1.12, p = 0.0283) were associated with an increased risk (all p < 0.05, nominally significant). For COVID-19 severity, Subdoligranulum (OR = 0.80, 95% CI, 0.69-0.92, p = 0.0018), Cyanobacteria (OR = 0.85, 95% CI, 0.76-0.96, p = 0.0062), Lactobacillales (OR = 0.87, 95% CI, 0.76-0.98, p = 0.0260), Christensenellaceae (OR = 0.87, 95% CI, 0.77-0.99, p = 0.0384), Tyzzerella3 (OR = 0.89, 95% CI, 0.81-0.97, p = 0.0070), and RuminococcaceaeUCG011 (OR = 0.91, 95% CI, 0.83-0.99, p = 0.0247) exhibited negative correlations, while RikenellaceaeRC9 (OR = 1.09, 95% CI, 1.01-1.17, p = 0.0277), LachnospiraceaeUCG008 (OR = 1.12, 95% CI, 1.00-1.26, p = 0.0432), and MollicutesRF9 (OR = 1.14, 95% CI, 1.01-1.29, p = 0.0354) exhibited positive correlations (all p < 0.05, nominally significant). Sensitivity analyses validated the robustness of the above associations. These findings suggest that gut microbiota might influence the susceptibility and severity of COVID-19 in a causal way, thus providing novel insights into the gut microbiota-mediated development mechanism of COVID-19.
Collapse
Affiliation(s)
- Weifeng Shang
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sheng Zhang
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hang Qian
- Anhui Medical University, Hefei, China
| | - Xiaojun Pan
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sisi Huang
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenliang Wen
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiao Liu
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dechang Chen
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Abstract
Coronavirus disease 2019 (COVID-19) severity has been associated with alterations of the gut microbiota. However, the relationship between gut microbiome alterations and COVID-19 prognosis remains elusive. Here, we performed a genome-resolved metagenomic analysis on fecal samples from 300 in-hospital COVID-19 patients, collected at the time of admission. Among the 2,568 high quality metagenome-assembled genomes (HQMAGs), redundancy analysis identified 33 HQMAGs which showed differential distribution among mild, moderate, and severe/critical severity groups. Co-abundance network analysis determined that the 33 HQMAGs were organized as two competing guilds. Guild 1 harbored more genes for short-chain fatty acid biosynthesis, and fewer genes for virulence and antibiotic resistance, compared with Guild 2. Based on average abundance difference between the two guilds, the guild-level microbiome index (GMI) classified patients from different severity groups (average AUROC [area under the receiver operating curve] = 0.83). Moreover, age-adjusted partial Spearman's correlation showed that GMIs at admission were correlated with 8 clinical parameters, which are predictors for COVID-19 prognosis, on day 7 in hospital. In addition, GMI at admission was associated with death/discharge outcome of the critical patients. We further validated that GMI was able to consistently classify patients with different COVID-19 symptom severities in different countries and differentiated COVID-19 patients from healthy subjects and pneumonia controls in four independent data sets. Thus, this genome-based guild-level signature may facilitate early identification of hospitalized COVID-19 patients with high risk of more severe outcomes at time of admission. IMPORTANCE Previous reports on the associations between COVID-19 and gut microbiome have been constrained by taxonomic-level analysis and overlook the interaction between microbes. By applying a genome-resolved, reference-free, guild-based metagenomic analysis, we demonstrated that the relationship between gut microbiota and COVID-19 is genome-specific instead of taxon-specific or even species-specific. Moreover, the COVID-19-associated genomes were not independent but formed two competing guilds, with Guild 1 potentially beneficial and Guild 2 potentially more detrimental to the host based on comparative genomic analysis. The dominance of Guild 2 over Guild 1 at time of admission was associated with hospitalized COVID-19 patients at high risk for more severe outcomes. Moreover, the guild-level microbiome signature is not only correlated with the symptom severity of COVID-19 patients, but also differentiates COVID-19 patients from pneumonia controls and healthy subjects across different studies. Here, we showed the possibility of using genome-resolved and guild-level microbiome signatures to identify hospitalized COVID-19 patients with a high risk of more severe outcomes at the time of admission.
Collapse
|
17
|
Association between Gut Microbiota and SARS-CoV-2 Infection and Vaccine Immunogenicity. Microorganisms 2023; 11:microorganisms11020452. [PMID: 36838417 PMCID: PMC9961186 DOI: 10.3390/microorganisms11020452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023] Open
Abstract
Gut microbiota is increasingly recognized to play a pivotal role in various human physiological functions and diseases. Amidst the COVID-19 pandemic, research has suggested that dysbiosis of the gut microbiota is also involved in the development and severity of COVID-19 symptoms by regulating SARS-CoV-2 entry and modulating inflammation. Previous studies have also suggested that gut microbiota and their metabolites could have immunomodulatory effects on vaccine immunogenicity, including influenza vaccines and oral rotavirus vaccines. In light of these observations, it is possible that gut microbiota plays a role in influencing the immune responses to COVID-19 vaccinations via similar mechanisms including effects of lipopolysaccharides, flagellin, peptidoglycan, and short-chain fatty acids. In this review, we give an overview of the current understanding on the role of the gut microbiota in COVID-19 manifestations and vaccine immunogenicity. We then discuss the limitations of currently published studies on the associations between gut microbiota and COVID-19 vaccine outcomes. Future research directions shall be focused on the development of microbiota-based interventions on improving immune response to SARS-CoV-2 infection and vaccinations.
Collapse
|
18
|
SeyedAlinaghi S, Afzalian A, Pashaei Z, Varshochi S, Karimi A, Mojdeganlou H, Mojdeganlou P, Razi A, Ghanadinezhad F, Shojaei A, Amiri A, Dashti M, Ghasemzadeh A, Dadras O, Mehraeen E, Afsahi AM. Gut microbiota and COVID-19: A systematic review. Health Sci Rep 2023; 6:e1080. [PMID: 36721396 PMCID: PMC9881458 DOI: 10.1002/hsr2.1080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/24/2022] [Accepted: 01/11/2023] [Indexed: 01/28/2023] Open
Abstract
Background and Aims Alteration in humans' gut microbiota was reported in patients infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The gut and upper respiratory tract (URT) microbiota harbor a dynamic and complex population of microorganisms and have strong interaction with host immune system homeostasis. However, our knowledge about microbiota and its association with SARS-CoV-2 is still limited. We aimed to systematically review the effects of gut microbiota on the SARS-CoV-2 infection and its severity and the impact that SARS-CoV-2 could have on the gut microbiota. Methods We searched the keywords in the online databases of Web of Science, Scopus, PubMed, and Cochrane on December 31, 2021. After duplicate removal, we performed the screening process in two stages; title/abstract and then full-text screening. The data of the eligible studies were extracted into a pre-designed word table. This study adhered to the PRISMA checklist and Newcastle-Ottawa Scale Bias Assessment tool. Results Sixty-three publications were included in this review. Our study shows that among COVID-19 patients, particularly moderate to severe cases, the gut and lung microbiota was different compared to healthy individuals. In addition, the severity, and viral load of COVID-19 disease would probably also be influenced by the gut, and lung microbiota's composition. Conclusion Our study concludes that there was a significant difference in the composition of the URT, and gut microbiota in COVID-19 patients compared to the general healthy individuals, with an increase in opportunistic pathogens. Further, research is needed to investigate the probable bidirectional association of COVID-19 and human microbiome.
Collapse
Affiliation(s)
- SeyedAhmad SeyedAlinaghi
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Arian Afzalian
- School of MedicineTehran University of Medical SciencesTehranIran
| | - Zahra Pashaei
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Sanaz Varshochi
- School of MedicineTehran University of Medical SciencesTehranIran
| | - Amirali Karimi
- School of MedicineTehran University of Medical SciencesTehranIran
| | | | | | - Armin Razi
- School of MedicineTehran University of Medical SciencesTehranIran
| | | | - Alireza Shojaei
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Ava Amiri
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran
| | - Mohsen Dashti
- Department of RadiologyTabriz University of Medical SciencesTabrizIran
| | | | - Omid Dadras
- Iranian Research Center for HIV/AIDS, Iranian Institute for Reduction of High Risk BehaviorsTehran University of Medical SciencesTehranIran,Department of Global Public Health and Primary CareUniversity of BergenBergenNorway
| | - Esmaeil Mehraeen
- Department of Health Information TechnologyKhalkhal University of Medical SciencesKhalkhalIran
| | - Amir Masoud Afsahi
- Department of RadiologyUniversity of California, San Diego (UCSD)CaliforniaUSA
| |
Collapse
|
19
|
Gradisteanu Pircalabioru G, Grigore GA, Czobor Barbu I, Chifiriuc MC, Savu O. Impact of COVID-19 on the Microbiome and Inflammatory Status of Type 2 Diabetes Patients. Biomedicines 2023; 11:biomedicines11010179. [PMID: 36672688 PMCID: PMC9856008 DOI: 10.3390/biomedicines11010179] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/12/2023] Open
Abstract
The severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) pandemic has advanced our understanding of the host-microbiome-virus interplay. Several studies in various geographical regions report that SARS-CoV-2 infection disrupts the intestinal microbiota, allowing pathogenic bacteria such as Enterobacteriaceae to thrive, and triggering more severe disease outcomes. Here, we profile the microbiota of 30 individuals, 15 healthy controls and 15 type 2 diabetes (T2D) patients, before and after coronavirus disease 2019 (COVID-19). Despite similar viral loads in both patients and controls, SARS-CoV-2 infection led to exacerbated microbiome changes in T2D patients, characterized by higher levels of Enterobacteriaceae, loss of butyrate producers and an enrichment in fungi such as Candida spp. and Aspergillus spp. Several members of the microbiota were associated with more severe clinical and inflammatory (IL-8 and IL-17) parameters. Future studies to delineate the connection between cytokine release and microbiota disturbances will enhance our understanding of whether these microbial shifts directly impact the cytokine storm in COVID-19 patients or whether they are consecutive to the critical disease.
Collapse
Affiliation(s)
- Gratiela Gradisteanu Pircalabioru
- Research Institute of University of Bucharest (ICUB), 050095 Bucharest, Romania
- Academy of Romanian Scientists, 050045 Bucharest, Romania
- Correspondence:
| | - Georgiana Alexandra Grigore
- Academy of Romanian Scientists, 050045 Bucharest, Romania
- Faculty of Biology, University of Bucharest, 050095 Bucharesti, Romania
| | - Ilda Czobor Barbu
- Academy of Romanian Scientists, 050045 Bucharest, Romania
- Faculty of Biology, University of Bucharest, 050095 Bucharesti, Romania
| | - Mariana-Carmen Chifiriuc
- Research Institute of University of Bucharest (ICUB), 050095 Bucharest, Romania
- Academy of Romanian Scientists, 050045 Bucharest, Romania
- Faculty of Biology, University of Bucharest, 050095 Bucharesti, Romania
- Romanian Academy, 010071 Bucharest, Romania
| | - Octavian Savu
- “N.C. Paulescu” National Institute of Diabetes, Nutrition and Metabolic Diseases, 020042 Bucharest, Romania
- Department of Doctoral School, “Carol Davila” University of Medicine and Pharmacy, 5th District, 050474 Bucharest, Romania
| |
Collapse
|
20
|
Brown EL, Essigmann HT, Hoffman KL, Alexander AS, Newmark M, Jiang ZD, Suescun J, Schiess MC, Hanis CL, DuPont HL. IgA-Biome Profiles Correlate with Clinical Parkinson's Disease Subtypes. JOURNAL OF PARKINSON'S DISEASE 2023; 13:501-513. [PMID: 37212075 PMCID: PMC10357173 DOI: 10.3233/jpd-230066] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/18/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Parkinson's disease is a heterogeneous neurodegenerative disorder with distinctive gut microbiome patterns suggesting that interventions targeting the gut microbiota may prevent, slow, or reverse disease progression and severity. OBJECTIVE Because secretory IgA (SIgA) plays a key role in shaping the gut microbiota, characterization of the IgA-Biome of individuals classified into either the akinetic rigid (AR) or tremor dominant (TD) Parkinson's disease clinical subtypes was used to further define taxa unique to these distinct clinical phenotypes. METHODS Flow cytometry was used to separate IgA-coated and -uncoated bacteria from stool samples obtained from AR and TD patients followed by amplification and sequencing of the V4 region of the 16 S rDNA gene on the MiSeq platform (Illumina). RESULTS IgA-Biome analyses identified significant alpha and beta diversity differences between the Parkinson's disease phenotypes and the Firmicutes/Bacteroides ratio was significantly higher in those with TD compared to those with AR. In addition, discriminant taxa analyses identified a more pro-inflammatory bacterial profile in the IgA+ fraction of those with the AR clinical subclass compared to IgA-Biome analyses of those with the TD subclass and with the taxa identified in the unsorted control samples. CONCLUSION IgA-Biome analyses underscores the importance of the host immune response in shaping the gut microbiome potentially affecting disease progression and presentation. In the present study, IgA-Biome analyses identified a unique proinflammatory microbial signature in the IgA+ fraction of those with AR that would have otherwise been undetected using conventional microbiome analysis approaches.
Collapse
Affiliation(s)
- Eric L. Brown
- Center for Infectious Diseases, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA
| | - Heather T. Essigmann
- Center for Infectious Diseases, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Zhi-Dong Jiang
- Center for Infectious Diseases, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA
| | - Jessika Suescun
- Department of Neurology/UTMOVE University of Texas McGovern Medical School, Houston, TX, USA
| | - Mya C. Schiess
- Department of Neurology/UTMOVE University of Texas McGovern Medical School, Houston, TX, USA
| | - Craig L. Hanis
- Human Genetics Center, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA
| | - Herbert L. DuPont
- Center for Infectious Diseases, Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, TX, USA
- Kelsey Research Foundation, Houston, TX, USA
- Department of Internal Medicine, University of Texas McGovern Medical School, Houston, TX, USA
| |
Collapse
|
21
|
Yin YS, Minacapelli CD, Parmar V, Catalano CC, Bhurwal A, Gupta K, Rustgi VK, Blaser MJ. Alterations of the fecal microbiota in relation to acute COVID-19 infection and recovery. MOLECULAR BIOMEDICINE 2022; 3:36. [PMID: 36437420 PMCID: PMC9702442 DOI: 10.1186/s43556-022-00103-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Abstract
People with acute COVID-19 due to SARS-CoV-2 infection experience a range of symptoms, but major factors contributing to severe clinical outcomes remain to be understood. Emerging evidence suggests associations between the gut microbiome and the severity and progression of COVID-19. To better understand the host-microbiota interactions in acute COVID-19, we characterized the intestinal microbiome of patients with active SARS-CoV-2 infection in comparison to recovered patients and uninfected healthy controls. We performed 16S rRNA sequencing of stool samples collected between May 2020 and January 2021 from 20 COVID-19-positive patients, 20 COVID-19-recovered subjects and 20 healthy controls. COVID-19-positive patients had altered microbiome community characteristics compared to the recovered and control subjects, as assessed by both α- and β-diversity differences. In COVID-19-positive patients, we observed depletion of Bacteroidaceae, Ruminococcaceae, and Lachnospiraceae, as well as decreased relative abundances of the genera Faecalibacterium, Adlercreutzia, and the Eubacterium brachy group. The enrichment of Prevotellaceae with COVID-19 infection continued after viral clearance; antibiotic use induced further gut microbiota perturbations in COVID-19-positive patients. In conclusion, we present evidence that acute COVID-19 induces gut microbiota dysbiosis with depletion of particular populations of commensal bacteria, a phenomenon heightened by antibiotic exposure, but the general effects do not persist post-recovery.
Collapse
Affiliation(s)
- Yue Sandra Yin
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Carlos D Minacapelli
- Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, NJ, USA.,Center for Liver Diseases and Liver Masses, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Veenat Parmar
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Carolyn C Catalano
- Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, NJ, USA.,Center for Liver Diseases and Liver Masses, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Abhishek Bhurwal
- Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, NJ, USA.,Center for Liver Diseases and Liver Masses, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Kapil Gupta
- Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, NJ, USA.,Center for Liver Diseases and Liver Masses, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Vinod K Rustgi
- Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, NJ, USA. .,Center for Liver Diseases and Liver Masses, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.
| | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA.
| |
Collapse
|
22
|
Di Pierro F, Iqtadar S, Mumtaz SU, Bertuccioli A, Recchia M, Zerbinati N, Khan A. Clinical Effects of Streptococcus salivarius K12 in Hospitalized COVID-19 Patients: Results of a Preliminary Study. Microorganisms 2022; 10:microorganisms10101926. [PMID: 36296202 PMCID: PMC9609702 DOI: 10.3390/microorganisms10101926] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/21/2022] [Accepted: 09/24/2022] [Indexed: 11/30/2022] Open
Abstract
Anatomical and physiological considerations indicate that the oral cavity is a primary source of the lung microbiota community, and recent studies have shown that the microbiota in the lungs contributes to immunological homeostasis, potentially altering the organ’s susceptibility to viral infection, including SARS-CoV-2. It has been proposed that, in the case of viral infection, lung Gram-negative bacteria could promote the cytokine cascade with a better performance than a microbiota mainly constituted by Gram-positive bacteria. Recent observations also suggest that Prevotella-rich oral microbiotas would dominate the oral cavity of SARS-CoV-2-infected patients. In comparison, Streptococcus-rich microbiotas would dominate the oral cavity of healthy people. To verify if the modulation of the oral microbiota could have an impact on the current coronavirus disease, we administered for 14 days a well-recognized and oral-colonizing probiotic (S. salivarius K12) to hospitalized COVID-19 patients. The preliminary results of our randomized and controlled trial seem to prove the potential role of this oral strain in improving the course of the main markers of pathology, as well as its ability to apparently reduce the death rate from COVID-19. Although in a preliminary and only circumstantial way, our results seem to confirm the hypothesis of a direct involvement of the oral microbiota in the construction of a lung microbiota whose taxonomic structure could modulate the inflammatory processes generated at the pulmonary and systemic level by a viral infection.
Collapse
Affiliation(s)
- Francesco Di Pierro
- Scientific & Research Department, Velleja Research, 20100 Milan, Italy
- Digestive Endoscopy, Fondazione Poliambulanza, 25133 Brescia, Italy
- Correspondence: ; Tel.: +39-0523-510848; Fax: +39-0523-511894
| | - Somia Iqtadar
- Department of Medicine, King Edward Medical University, Lahore 54000, Pakistan
| | - Sami Ullah Mumtaz
- Department of Medicine, King Edward Medical University, Lahore 54000, Pakistan
| | - Alexander Bertuccioli
- Department of Biomolecular Sciences (DISB), University of Urbino, 61029 Urbino, Italy
| | - Martino Recchia
- Medistat, Unità di Epidemiologia Clinica e Biostatistica, 20100 Milan, Italy
| | - Nicola Zerbinati
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| | - Amjad Khan
- Nuffield Division of Clinical and Laboratory Sciences (NDCLS), Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
| |
Collapse
|
23
|
Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes. Nat Commun 2022; 13:5235. [PMID: 36068270 PMCID: PMC9446638 DOI: 10.1038/s41467-022-32991-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/24/2022] [Indexed: 11/14/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19), primarily a respiratory disease caused by infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is often accompanied by gastrointestinal symptoms. However, little is known about the relation between the human microbiome and COVID-19, largely due to the fact that most previous studies fail to provide high taxonomic resolution to identify microbes that likely interact with SARS-CoV-2 infection. Here we used whole-metagenome shotgun sequencing data together with assembly and binning strategies to reconstruct metagenome-assembled genomes (MAGs) from 514 COVID-19 related nasopharyngeal and fecal samples in six independent cohorts. We reconstructed a total of 11,584 medium-and high-quality microbial MAGs and obtained 5403 non-redundant MAGs (nrMAGs) with strain-level resolution. We found that there is a significant reduction of strain richness for many species in the gut microbiome of COVID-19 patients. The gut microbiome signatures can accurately distinguish COVID-19 cases from healthy controls and predict the progression of COVID-19. Moreover, we identified a set of nrMAGs with a putative causal role in the clinical manifestations of COVID-19 and revealed their functional pathways that potentially interact with SARS-CoV-2 infection. Finally, we demonstrated that the main findings of our study can be largely validated in three independent cohorts. The presented results highlight the importance of incorporating the human gut microbiome in our understanding of SARS-CoV-2 infection and disease progression. Here, using whole-metagenome shotgun sequencing data from patients with COVID-19 and controls, the authors reconstruct 11,584 microbial metagenome-assembled genomes (MAGs) including 5,403 non-redundant MAGs, revealing microbiota and metabolic pathways associations with SARS-CoV-2 infection at strain-level resolution.
Collapse
|
24
|
Probiotics in the Management of Mental and Gastrointestinal Post-COVID Symptomes. J Clin Med 2022; 11:jcm11175155. [PMID: 36079082 PMCID: PMC9457065 DOI: 10.3390/jcm11175155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/17/2022] [Accepted: 08/29/2022] [Indexed: 01/30/2023] Open
Abstract
Patients with “post-COVID” syndrome manifest with a variety of signs and symptoms that continue/develop after acute COVID-19. Among the most common are gastrointestinal (GI) and mental symptoms. The reason for symptom occurrence lies in the SARS-CoV-2 capability of binding to exact receptors, among other angiotensin converting enzyme 2 (ACE2) receptors in gastrointestinal lining and neuropilin-1 (NRP-1) in the nervous system, which leads to loss of gastrointestinal and blood-brain barriers integrity and function. The data are mounting that SARS-CoV-2 can trigger systemic inflammation and lead to disruption of gut-brain axis (GBA) and the development of disorders of gut brain interaction (DGBIs). Functional dyspepsia (FD) and irritable bowel syndrome (IBS) are the most common DGBIs syndromes. On the other hand, emotional disorders have also been demonstrated as DGBIs. Currently, there are no official recommendations or recommended procedures for the use of probiotics in patients with COVID-19. However, it can be assumed that many doctors, pharmacists, and patients will want to use a probiotic in the treatment of this disease. In such cases, strains with documented activity should be used. There is a constant need to plan and conduct new trials on the role of probiotics and verify their clinical efficacy for counteracting the negative consequences of COVID-19 pandemic. Quality control is another important but often neglected aspect in trials utilizing probiotics in various clinical entities. It determines the safety and efficacy of probiotics, which is of utmost importance in patients with post-acute COVID-19 syndrome.
Collapse
|
25
|
Immunomodulatory Effects of Probiotics on COVID-19 Infection by Targeting the Gut–Lung Axis Microbial Cross-Talk. Microorganisms 2022; 10:microorganisms10091764. [PMID: 36144365 PMCID: PMC9505869 DOI: 10.3390/microorganisms10091764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 01/08/2023] Open
Abstract
The ecosystem of the human gastrointestinal tract, named gut microbiota, represents the most thoroughly mapped ecosystem. Perturbations on bacterial populations cause dysbiosis, a condition correlated to a wide range of autoimmune, neurological, metabolic, cardiovascular, and respiratory diseases. The lungs have their flora, which are directly related to the gut flora via bidirectional communication allowing the transport of microbial metabolites and toxins produced by intestinal bacteria through the circulation and lymphatic system. This mutual microbial cross-talk communication called the gut–lung axis modulates the immune and inflammatory response to infections. COVID-19 causes dysbiosis, altered intestinal permeability, and bacterial translocation. Dysbiosis, through the gut–lung axis, promotes hyper-inflammation, exacerbates lung damage, and worsens clinical outcomes. Preclinical and clinical studies have shown that probiotics can regulate cytokine secretion, thus affecting both nonspecific and specific immunity. Probiotics act by blocking the virus from invading and proliferating in host cells, by stimulating the immune response, and by suppressing the activation of NLRP3 inflammasome. Herein, we reviewed the evidence from preclinical and clinical studies evaluating the effect of probiotics administration on the immune response to COVID-19 infection by targeting the gut–lung axis microbial cross-talk.
Collapse
|
26
|
Li S, Zhou Y, Yan D, Wan Y. An Update on the Mutual Impact between SARS-CoV-2 Infection and Gut Microbiota. Viruses 2022; 14:1774. [PMID: 36016396 PMCID: PMC9415881 DOI: 10.3390/v14081774] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/02/2022] [Accepted: 08/11/2022] [Indexed: 12/15/2022] Open
Abstract
The gut microbiota is essential for good health. It has also been demonstrated that the gut microbiota can regulate immune responses against respiratory tract infections. Since the outbreak of the COVID-19 pandemic, accumulating evidence suggests that there is a link between the severity of COVID-19 and the alteration of one's gut microbiota. The composition of gut microbiota can be profoundly affected by COVID-19 and vice versa. Here, we summarize the observations of the mutual impact between SARS-CoV-2 infection and gut microbiota composition. We discuss the consequences and mechanisms of the bi-directional interaction. Moreover, we also discuss the immune cross-reactivity between SARS-CoV-2 and commensal bacteria, which represents a previously overlooked connection between COVID-19 and commensal gut bacteria. Finally, we summarize the progress in managing COVID-19 by utilizing microbial interventions.
Collapse
Affiliation(s)
- Shaoshuai Li
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
- Shanghai Public Health Clinical Center, Department of Laboratory Medicine, Shanghai 201508, China
- Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, School of Basic Medicine, Jiamusi University, Jiamusi 154000, China
| | - Yang Zhou
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Dongmei Yan
- Key Laboratory of Microecology-Immune Regulatory Network and Related Diseases, School of Basic Medicine, Jiamusi University, Jiamusi 154000, China
| | - Yanmin Wan
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, China
- Shanghai Public Health Clinical Center, Department of Radiology, Shanghai 201508, China
| |
Collapse
|
27
|
Gang J, Wang H, Xue X, Zhang S. Microbiota and COVID-19: Long-term and complex influencing factors. Front Microbiol 2022; 13:963488. [PMID: 36033885 PMCID: PMC9417543 DOI: 10.3389/fmicb.2022.963488] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/25/2022] [Indexed: 01/08/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). According to the World Health Organization statistics, more than 500 million individuals have been infected and more than 6 million deaths have resulted worldwide. Although COVID-19 mainly affects the respiratory system, considerable evidence shows that the digestive, cardiovascular, nervous, and reproductive systems can all be involved. Angiotensin-converting enzyme 2 (AEC2), the target of SARS-CoV-2 invasion of the host is mainly distributed in the respiratory and gastrointestinal tract. Studies found that microbiota contributes to the onset and progression of many diseases, including COVID-19. Here, we firstly conclude the characterization of respiratory, gut, and oral microbial dysbiosis, including bacteria, fungi, and viruses. Then we explore the potential mechanisms of microbial involvement in COVID-19. Microbial dysbiosis could influence COVID-19 by complex interactions with SARS-CoV-2 and host immunity. Moreover, microbiota may have an impact on COVID-19 through their metabolites or modulation of ACE2 expression. Subsequently, we generalize the potential of microbiota as diagnostic markers for COVID-19 patients and its possible association with post-acute COVID-19 syndrome (PACS) and relapse after recovery. Finally, we proposed directed microbiota-targeted treatments from the perspective of gut microecology such as probiotics and prebiotics, fecal transplantation and antibiotics, and other interventions such as traditional Chinese medicine, COVID-19 vaccines, and ACE2-based treatments.
Collapse
Affiliation(s)
- Jiaqi Gang
- Department of Emergency, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Department of Oncology, Xiuwu County People’s Hospital, Jiaozuo, China
| | - Haiyu Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangsheng Xue
- Department of Oncology, Xiuwu County People’s Hospital, Jiaozuo, China
- *Correspondence: Xiangsheng Xue,
| | - Shu Zhang
- Department of Emergency, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Shu Zhang,
| |
Collapse
|
28
|
Sencio V, Benech N, Robil C, Deruyter L, Heumel S, Machelart A, Sulpice T, Lamazière A, Grangette C, Briand F, Sokol H, Trottein F. Alteration of the gut microbiota's composition and metabolic output correlates with COVID-19-like severity in obese NASH hamsters. Gut Microbes 2022; 14:2100200. [PMID: 35830432 PMCID: PMC9291689 DOI: 10.1080/19490976.2022.2100200] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Obese patientss with nonalcoholic steatohepatitis (NASH) are particularly prone to developing severe forms of coronavirus disease 19 (COVID-19). The gut-to-lung axis is critical during viral infections of the respiratory tract, and a change in the gut microbiota's composition might have a critical role in disease severity. Here, we investigated the consequences of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on the gut microbiota in the context of obesity and NASH. To this end, we set up a nutritional model of obesity with dyslipidemia and NASH in the golden hamster, a relevant preclinical model of COVID-19. Relative to lean non-NASH controls, obese NASH hamsters develop severe inflammation of the lungs and liver. 16S rRNA gene profiling showed that depending on the diet, SARS-CoV-2 infection induced various changes in the gut microbiota's composition. Changes were more prominent and transient at day 4 post-infection in lean animals, alterations still persisted at day 10 in obese NASH animals. A targeted, quantitative metabolomic analysis revealed changes in the gut microbiota's metabolic output, some of which were diet-specific and regulated over time. Our results showed that specifically diet-associated taxa are correlated with disease parameters. Correlations between infection variables and diet-associated taxa highlighted a number of potentially protective or harmful bacteria in SARS-CoV-2-infected hamsters. In particular, some taxa in obese NASH hamsters (e.g. Blautia and Peptococcus) were associated with pro-inflammatory parameters in both the lungs and the liver. These taxon profiles and their association with specific disease markers suggest that microbial patterns might influence COVID-19 outcomes.
Collapse
Affiliation(s)
- Valentin Sencio
- CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, Inserm, Lille, France,UMR 9017, Centre National de la Recherche Scientifique (CNRS), Lille, France,Institut National de la Santé et de la Recherche Médicale (Inserm) U1019, Lille, France,Centre Hospitalier Universitaire de Lille, Lille, France,Institut Pasteur de Lille, Lille, France
| | - Nicolas Benech
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1019, Lille, France,Institut Pasteur de Lille, Lille, France
| | - Cyril Robil
- CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, Inserm, Lille, France,UMR 9017, Centre National de la Recherche Scientifique (CNRS), Lille, France,Institut National de la Santé et de la Recherche Médicale (Inserm) U1019, Lille, France,Centre Hospitalier Universitaire de Lille, Lille, France,Institut Pasteur de Lille, Lille, France
| | - Lucie Deruyter
- CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, Inserm, Lille, France,UMR 9017, Centre National de la Recherche Scientifique (CNRS), Lille, France,Institut National de la Santé et de la Recherche Médicale (Inserm) U1019, Lille, France,Centre Hospitalier Universitaire de Lille, Lille, France,Institut Pasteur de Lille, Lille, France
| | - Séverine Heumel
- CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, Inserm, Lille, France,UMR 9017, Centre National de la Recherche Scientifique (CNRS), Lille, France,Institut National de la Santé et de la Recherche Médicale (Inserm) U1019, Lille, France,Centre Hospitalier Universitaire de Lille, Lille, France,Institut Pasteur de Lille, Lille, France
| | - Arnaud Machelart
- CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, Inserm, Lille, France,UMR 9017, Centre National de la Recherche Scientifique (CNRS), Lille, France,Institut National de la Santé et de la Recherche Médicale (Inserm) U1019, Lille, France,Centre Hospitalier Universitaire de Lille, Lille, France,Institut Pasteur de Lille, Lille, France
| | | | - Antonin Lamazière
- Inserm, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology department, Sorbonne Université, Paris, France,Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France
| | - Corinne Grangette
- CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, Inserm, Lille, France,UMR 9017, Centre National de la Recherche Scientifique (CNRS), Lille, France,Institut National de la Santé et de la Recherche Médicale (Inserm) U1019, Lille, France,Centre Hospitalier Universitaire de Lille, Lille, France,Institut Pasteur de Lille, Lille, France
| | | | - Harry Sokol
- Inserm, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, Gastroenterology department, Sorbonne Université, Paris, France,Paris Center for Microbiome Medicine, Fédération Hospitalo-Universitaire, Paris, France,UMR1319 Micalis & AgroParisTech, Institut National de la Recherche Agronomique (INRAE), Jouy en Josas, France
| | - François Trottein
- CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, Inserm, Lille, France,UMR 9017, Centre National de la Recherche Scientifique (CNRS), Lille, France,Institut National de la Santé et de la Recherche Médicale (Inserm) U1019, Lille, France,Centre Hospitalier Universitaire de Lille, Lille, France,Institut Pasteur de Lille, Lille, France,CONTACT François Trottein Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, LilleF-59000France
| |
Collapse
|
29
|
Mizutani T, Ishizaka A, Koga M, Tsutsumi T, Yotsuyanagi H. Role of Microbiota in Viral Infections and Pathological Progression. Viruses 2022; 14:950. [PMID: 35632692 PMCID: PMC9144409 DOI: 10.3390/v14050950] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 02/04/2023] Open
Abstract
Viral infections are influenced by various microorganisms in the environment surrounding the target tissue, and the correlation between the type and balance of commensal microbiota is the key to establishment of the infection and pathogenicity. Some commensal microorganisms are known to resist or promote viral infection, while others are involved in pathogenicity. It is also becoming evident that the profile of the commensal microbiota under normal conditions influences the progression of viral diseases. Thus, to understand the pathogenesis underlying viral infections, it is important to elucidate the interactions among viruses, target tissues, and the surrounding environment, including the commensal microbiota, which should have different relationships with each virus. In this review, we outline the role of microorganisms in viral infections. Particularly, we focus on gaining an in-depth understanding of the correlations among viral infections, target tissues, and the surrounding environment, including the commensal microbiota and the gut virome, and discussing the impact of changes in the microbiota (dysbiosis) on the pathological progression of viral infections.
Collapse
Affiliation(s)
- Taketoshi Mizutani
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
| | - Aya Ishizaka
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
| | - Michiko Koga
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
| | - Takeya Tsutsumi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
| | - Hiroshi Yotsuyanagi
- Division of Infectious Diseases, Advanced Clinical Research Center, the Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan; (A.I.); (M.K.); (T.T.); (H.Y.)
- Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| |
Collapse
|
30
|
Suskun C, Kilic O, Yilmaz Ciftdogan D, Guven S, Karbuz A, Ozkaya Parlakay A, Kara Y, Kacmaz E, Sahin A, Boga A, Kizmaz Isancli D, Gulhan B, Kanik-Yuksek S, Kiral E, Bozan G, Arslanoglu MO, Kizil MC, Dinleyici M, Us T, Varis A, Kaya M, Vandenplas Y, Dinleyici EC. Intestinal microbiota composition of children with infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and multisystem inflammatory syndrome (MIS-C). Eur J Pediatr 2022; 181:3175-3191. [PMID: 35585256 PMCID: PMC9117086 DOI: 10.1007/s00431-022-04494-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/28/2022] [Accepted: 04/30/2022] [Indexed: 02/07/2023]
Abstract
UNLABELLED Microbiota composition may play a role in the development, prognosis, or post-infection of COVID-19. There are studies evaluating the microbiota composition at the time of diagnosis and during the course of COVID-19, especially in adults, while studies in children are limited and no study available in children with multisystem inflammatory syndrome in children (MIS-C). This study was planned to compare intestinal microbiota composition in children diagnosed with MIS-C and acute COVID-19 infection with healthy children. In this prospective multicenter study, 25 children diagnosed with MIS-C, 20 with COVID-19 infection, and 19 healthy children were included. Intestinal microbiota composition was evaluated by 16 s rRNA gene sequencing. We observed changes of diversity, richness, and composition of intestinal microbiota in MIS-C cases compared to COVID-19 cases and in the healthy controls. The Shannon index was higher in the MIS-C group than the healthy controls (p < 0.01). At phylum level, in the MIS-C group, a significantly higher relative abundance of Bacteroidetes and lower abundance of Firmicutes was found compared to the control group. Intestinal microbiota composition changed in MIS-C cases compared to COVID-19 and healthy controls, and Faecalibacterium prausnitzii decreased; Bacteroides uniformis, Bacteroides plebeius, Clostridium ramosum, Eubacterium dolichum, Eggerthella lenta, Bacillus thermoamylovorans, Prevotella tannerae, and Bacteroides coprophilus were dominant in children with MIS-C. At species level, we observed decreased Faecalibacterium prausnitzii, and increased Eubacterium dolichum, Eggerthella lenta, and Bacillus thermoamylovorans in children with MIS-C and increased Bifidobacterium adolescentis and Dorea formicigenerasus in the COVID-19 group. Our study is the first to evaluate the microbiota composition in MIS-C cases. There is a substantial change in the composition of the gut microbiota: (1) reduction of F. prausnitzii in children with MIS-C and COVID-19; (2) an increase of Eggerthella lenta which is related with autoimmunity; and (3) the predominance of E. dolichum is associated with metabolic dysfunctions and obesity in children with MIS-C. CONCLUSIONS Alterations of the intestinal microbiota might be part of pathogenesis of predisposing factor for MIS-C. It would be beneficial to conduct more extensive studies on the cause-effect relationship of these changes in microbiota composition and their effects on long-term prognosis. WHAT IS KNOWN • Microbiota composition may play a role in the development, prognosis, or post-infection of COVID-19. • However, the number of studies on children is limited, and no study on multisystem inflammatory syndrome in children is currently available (MIS-C). WHAT IS NEW • In individuals with MIS-C, the composition of the gut microbiota changed dramatically. • Decreased Faecalibacterium prausnitzii have been observed, increased Eggerthella lenta, which was previously linked to autoimmunity, and predominance of Eubacterium dolichum which was linked to metabolic dysfunction and obesity.
Collapse
Affiliation(s)
- Cansu Suskun
- grid.164274.20000 0004 0596 2460Department of Pediatrics, Eskisehir Osmangazi University Faculty of Medicine, Eskisehir, TR-26040 Turkey
| | - Omer Kilic
- grid.164274.20000 0004 0596 2460Department of Pediatric Infectious Disease, Eskisehir Osmangazi University Faculty of Medicine, Eskisehir, Turkey
| | - Dilek Yilmaz Ciftdogan
- grid.411795.f0000 0004 0454 9420Department of Pediatric Infectious Disease, Izmir Katip Celebi University Faculty of Medicine, Izmir, Turkey
| | - Sirin Guven
- grid.414850.c0000 0004 0642 8921Department of Pediatrics, Prof. Dr Ilhan Varank Training and Research Hospital, Istanbul, Turkey
| | - Adem Karbuz
- Department of Pediatric Infectious Disease, Dr. Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Aslinur Ozkaya Parlakay
- grid.512925.80000 0004 7592 6297Yildirim Beyazit University Faculty of Medicine Department of Pediatric Infectious Disease, Ankara City Hospital Department of Pediatric Infectious Disease, Ankara, Turkey
| | - Yalcın Kara
- grid.164274.20000 0004 0596 2460Department of Pediatric Infectious Disease, Eskisehir Osmangazi University Faculty of Medicine, Eskisehir, Turkey
| | - Ebru Kacmaz
- grid.164274.20000 0004 0596 2460Pediatric Intensive Care Unit, Eskisehir Osmangazi University Faculty of Medicine, Eskisehir, Turkey
| | - Aslihan Sahin
- grid.411795.f0000 0004 0454 9420Department of Pediatric Infectious Disease, Izmir Katip Celebi University Faculty of Medicine, Izmir, Turkey
| | - Aysun Boga
- grid.414850.c0000 0004 0642 8921Department of Pediatrics, Prof. Dr Ilhan Varank Training and Research Hospital, Istanbul, Turkey
| | - Didem Kizmaz Isancli
- Department of Pediatric Infectious Disease, Dr. Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Belgin Gulhan
- grid.512925.80000 0004 7592 6297Department of Pediatric Infectious Disease, Ankara City Hospital, Ankara, Turkey
| | - Saliha Kanik-Yuksek
- grid.512925.80000 0004 7592 6297Department of Pediatric Infectious Disease, Ankara City Hospital, Ankara, Turkey
| | - Eylem Kiral
- grid.164274.20000 0004 0596 2460Pediatric Intensive Care Unit, Eskisehir Osmangazi University Faculty of Medicine, Eskisehir, Turkey
| | - Gurkan Bozan
- grid.164274.20000 0004 0596 2460Pediatric Intensive Care Unit, Eskisehir Osmangazi University Faculty of Medicine, Eskisehir, Turkey
| | - Mehmet Ozgür Arslanoglu
- grid.164274.20000 0004 0596 2460Pediatric Intensive Care Unit, Eskisehir Osmangazi University Faculty of Medicine, Eskisehir, Turkey
| | - Mahmut Can Kizil
- grid.164274.20000 0004 0596 2460Department of Pediatric Infectious Disease, Eskisehir Osmangazi University Faculty of Medicine, Eskisehir, Turkey
| | - Meltem Dinleyici
- grid.164274.20000 0004 0596 2460Department of Social Pediatrics, Eskisehir Osmangazi University Faculty of Medicine, Eskisehir, Turkey
| | - Tercan Us
- grid.164274.20000 0004 0596 2460Department of Microbiology, Eskisehir Osmangazi University Faculty of Medicine, Eskisehir, Turkey
| | | | | | - Yvan Vandenplas
- grid.8767.e0000 0001 2290 8069KidZ Health Castle, UZ Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Ener Cagri Dinleyici
- grid.164274.20000 0004 0596 2460Department of Pediatrics, Eskisehir Osmangazi University Faculty of Medicine, Eskisehir, TR-26040 Turkey
| |
Collapse
|