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Naveen KV, Saravanakumar K, Sathiyaseelan A, MubarakAli D, Wang MH. Human Fungal Infection, Immune Response, and Clinical Challenge-a Perspective During COVID-19 Pandemic. Appl Biochem Biotechnol 2022; 194:4244-4257. [PMID: 35648275 PMCID: PMC9156836 DOI: 10.1007/s12010-022-03979-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2022] [Indexed: 12/15/2022]
Abstract
Fungi are a small but important part of the human microbiota and several fungi are familiar to the immune system, yet certain can cause infections in immunocompromised hosts and referred as opportunistic pathogens. The fungal coinfections in COVID-19 hosts with predisposing conditions and immunosuppressive medications are posing higher severity and death. The immunological counteraction (innate/adaptive immunity) is triggered when the PRRs on the host cells recognize the fungal PAMPs. However, in simultaneous infections (COVID-19 and fungal coinfection), the synergism of TLR and NLR may hyperactivate the immune cells which dramatically increase the cytokine level and generate cytokine storm. Fungal colonization in the human gut assists the development of microbiome assembly, ecology, and shaping immune response. However, SARS-CoV-2 infection represented unstable mycobiomes and long-term dysbiosis in a large proportion in COVID-19 patients. Normally, amphotericin B is considered as first-line treatment for invasive fungal infection. So, amphotericin B therapy is recommended in COVID-19 hosts with serious fungal infections. Still, the long-term corticosteroid supplementation prescribed in case of severe pneumonia and lower oxygen levels may result in systemic fungal infection in COVID-19 patients, eventually limiting the lifesaving benefits of available medications. Also, due to the evolution of fungal resistance to available antibiotics, the current treatments are becoming ineffective. Therefore, this review summarizes the concerns, needed to deal with the impending crises.
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Affiliation(s)
- Kumar Vishven Naveen
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, 200-701, Republic of Korea
| | - Kandasamy Saravanakumar
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, 200-701, Republic of Korea
| | - Anbazhagan Sathiyaseelan
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, 200-701, Republic of Korea
| | - Davoodbasha MubarakAli
- School of Life Sciences, B.S. Abdur Rahman Crescent Institute of Science and Technology, Chennai, Tamil Nadu, 600048, India
| | - Myeong-Hyeon Wang
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, 200-701, Republic of Korea.
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102
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Reis RM, Carlo HL, dos Santos RL, Sabella FM, Parisotto TM, de Carvalho FG. Possible Relationship Between the Oral and Gut Microbiome, Caries Development, and Obesity in Children During the COVID-19 Pandemic. FRONTIERS IN ORAL HEALTH 2022; 3:887765. [PMID: 35711624 PMCID: PMC9196306 DOI: 10.3389/froh.2022.887765] [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: 03/02/2022] [Accepted: 04/28/2022] [Indexed: 11/28/2022] Open
Abstract
The COVID-19 pandemic has brought health damage and socioeconomic disruptions, together with lifestyle disorders around the world. Children are one of the most commonly affected, mainly due to social isolation and changes in eating habits and physical activities. This way, the risk of weight gain and obesity is possibly enhanced, as well as poor oral hygiene conditions and early childhood caries (ECC) development during the lockdown. In children under 6 years of age, ECC is defined as carious lesions in one or more primary teeth, with or without cavitation. Importantly, alterations in the oral microbiome caused by changes in children lifestyles have much more than a local impact on oral tissues, interplaying with the gut microbiome and influencing systemic environments. Recent studies have been exploring the oral health conditions, eating habits, and weight gain in the childhood population during the COVID-19 pandemic; however, there is a lack of information concerning the association among oral and gut microbiome, dental caries, and obesity in the COVID-19 era. In this context, this review aimed at analyzing a possible relationship between the oral and gut microbiome, caries, and obesity in children during the COVID-19 pandemic.
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Affiliation(s)
- Ranam Moreira Reis
- Department of Dentistry, Federal University of Juiz de Fora, Governador Valadares, Brazil
| | - Hugo Lemes Carlo
- Department of Dentistry, Federal University of Juiz de Fora, Governador Valadares, Brazil
| | | | - Fernanda Maria Sabella
- Laboratory of Clinical and Molecular Microbiology, São Francisco University, Bragança Paulista, Brazil
| | - Thaís Manzano Parisotto
- Laboratory of Clinical and Molecular Microbiology, São Francisco University, Bragança Paulista, Brazil
| | - Fabíola Galbiatti de Carvalho
- Department of Dentistry, Federal University of Juiz de Fora, Governador Valadares, Brazil
- *Correspondence: Fabíola Galbiatti de Carvalho
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103
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Jalodia R, Antoine D, Braniff RG, Dutta RK, Ramakrishnan S, Roy S. Opioid-Use, COVID-19 Infection, and Their Neurological Implications. Front Neurol 2022; 13:884216. [PMID: 35677336 PMCID: PMC9169980 DOI: 10.3389/fneur.2022.884216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/25/2022] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an imminent threat to human health and public safety. ACE2 and transmembrane serine protease 2 proteins on host cells provide the viral entry point to SARS-CoV-2. Although SARS-CoV-2 mainly infects the respiratory system, there have been reports of viral neurotropism and central nervous system injury as indicated by plasma biomarkers, including neurofilament light chain protein and glial fibrillary acidic protein. Even with a small proportion of infections leading to neurological manifestation, the overall number remains high. Common neurological manifestations of SARS-CoV-2 infection include anosmia, ageusia, encephalopathy, and stroke, which are not restricted to only the most severe infection cases. Opioids and opioid antagonists bind to the ACE2 receptor and thereby have been hypothesized to have therapeutic potential in treating COVID-19. However, in the case of other neurotropic viral infections such as human immunodeficiency virus (HIV), opioid use has been established to exacerbate HIV-mediated central nervous system pathogenesis. An analysis of electronic health record data from more than 73 million patients shows that people with Substance Use Disorders are at higher risk of contracting COVID-19 and suffer worse consequences then non-users. Our in-vivo and in-vitro unpublished studies show that morphine treatment causes increased expression of ACE2 in murine lung and brain tissue as early as 24 h post treatment. At the same time, we also observed morphine and lipopolysaccharides treatment lead to a synergistic increase in ACE2 expression in the microglial cell line, SIM-A9. This data suggests that opioid treatment may potentially increase neurotropism of SARS-CoV-2 infection. We have previously shown that opioids induce gut microbial dysbiosis. Similarly, gut microbiome alterations have been reported with SARS-CoV-2 infection and may play a role in predicting COVID-19 disease severity. However, there are no studies thus far linking opioid-mediated dysbiosis with the severity of neuron-specific COVID-19 infection.
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Affiliation(s)
| | | | | | | | | | - Sabita Roy
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
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104
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SARS CoV-2-Induced Viral Sepsis: The Role of Gut Barrier Dysfunction. Microorganisms 2022; 10:microorganisms10051050. [PMID: 35630492 PMCID: PMC9143860 DOI: 10.3390/microorganisms10051050] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 12/13/2022] Open
Abstract
A considerable proportion of patients with severe COVID-19 meet Sepsis-3 criteria and share common pathophysiological mechanisms of multiorgan injury with bacterial sepsis, in absence of secondary bacterial infections, a process characterized as “viral sepsis”. The intestinal barrier exerts a central role in the pathophysiological sequence of events that lead from SARS-CoV-2 infection to severe systemic complications. Accumulating evidence suggests that SARS-CoV-2 disrupts the integrity of the biological, mechanical and immunological gut barrier. Specifically, microbiota diversity and beneficial bacteria population are reduced, concurrently with overgrowth of pathogenic bacteria (dysbiosis). Enterocytes’ tight junctions (TJs) are disrupted, and the apoptotic death of intestinal epithelial cells is increased leading to increased gut permeability. In addition, mucosal CD4(+) and CD8(+) T cells, Th17 cells, neutrophils, dendritic cells and macrophages are activated, and T-regulatory cells are decreased, thus promoting an overactivated immune response, which further injures the intestinal epithelium. This dysfunctional gut barrier in SARS-CoV-2 infection permits the escape of luminal bacteria, fungi and endotoxin to normally sterile extraintestinal sites and the systemic circulation. Pre-existing gut barrier dysfunction and endotoxemia in patients with comorbidities including cardiovascular disease, obesity, diabetes and immunosuppression predisposes to aggravated endotoxemia. Bacterial and endotoxin translocation promote the systemic inflammation and immune activation, which characterize the SARS-CoV-2 induced “viral sepsis” syndrome associated with multisystemic complications of severe COVID-19.
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105
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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.
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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
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106
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The therapeutic effect of Xuanbai Chengqi Decoction on chronic obstructive pulmonary disease with excessive heat in the lung and fu-organs based on gut and lung microbiota as well as metabolic profiles. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1198:123250. [DOI: 10.1016/j.jchromb.2022.123250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/03/2022] [Accepted: 04/07/2022] [Indexed: 12/29/2022]
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107
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Yang Z, Liu Y, Wang L, Lin S, Dai X, Yan H, Ge Z, Ren Q, Wang H, Zhu F, Wang S. Traditional Chinese medicine against COVID-19: Role of the gut microbiota. Biomed Pharmacother 2022; 149:112787. [PMID: 35279010 PMCID: PMC8901378 DOI: 10.1016/j.biopha.2022.112787] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/26/2022] [Accepted: 03/02/2022] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is an acute respiratory infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and it has become a public health concern worldwide. In addition to respiratory symptoms, some COVID‑19 patients also show various gastrointestinal symptoms and even consider gastrointestinal symptoms to be the first manifestation. A large amount of evidence has shown that SARS-CoV-2 infection could disrupt the gut microbiota balance, and disorders of the gut microbiota could aggravate the condition of COVID-19 patients. Therefore, maintaining the gut microbiota balance is expected to become a potential new therapeutic target for treating COVID-19. Traditional Chinese medicine (TCM) has significant effects in all stages of the prevention and treatment of COVID-19. It can adjust the gut microbiota and is an ideal intestinal microecological regulator. This review summarizes the advantages and clinical efficacy of TCM in the treatment of COVID-19 and expounds on the relationship between TCM and the gut microbiota, the relationship between COVID-19 and the gut microbiota, the mechanism of gut microbiota disorders induced by SARS-CoV-2, the relationship between cytokine storms and the gut microbiota, and the role and mechanism of TCM in preventing and treating COVID-19 by regulating the gut microbiota to provide new research ideas for TCM in the prevention and treatment of COVID-19.
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Affiliation(s)
- Zhihua Yang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yangxi Liu
- Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300381, China
| | - Lin Wang
- Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300381, China
| | - Shanshan Lin
- Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300381, China
| | - Xiangdong Dai
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Institute of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Haifeng Yan
- The First Affiliated Hospital of Henan University of Traditional Chinese Medicine, Zhengzhou, Henan 450000, China
| | - Zhao Ge
- Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300381, China
| | - Qiuan Ren
- Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300381, China
| | - Hui Wang
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300381, China
| | - Feng Zhu
- Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Shuping Wang
- Characteristic Medical Center of Chinese People's Armed Police Force, Tianjin 300162, China.
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108
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Jing Y, Wang J, Zhang H, Yang K, Li J, Zhao T, Liu J, Wu J, Chen Y. Alterations of Urinary Microbial Metabolites and Immune Indexes Linked With COVID-19 Infection and Prognosis. Front Immunol 2022; 13:841739. [PMID: 35422810 PMCID: PMC9001849 DOI: 10.3389/fimmu.2022.841739] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/23/2022] [Indexed: 11/13/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has evolved into an established global pandemic. Metabolomic studies in COVID-19 patients is worth exploring for further available screening methods. In our study, we recruited a study cohort of 350 subjects comprising 248 COVID-19 patients (161 non-severe cases, 60 asymptomatic cases, and 27 severe cases) and 102 healthy controls (HCs), and herein present data with respect to their demographic features, urinary metabolome, immunological indices, and follow-up health status. We found that COVID-19 resulted in alterations of 39 urinary, mainly microbial, metabolites. Using random forest analysis, a simplified marker panel including three microbial metabolites (oxoglutaric acid, indoxyl, and phenylacetamide) was constructed (AUC=0.963, 95% CI, 0.930-0.983), which exhibited higher diagnostic performance than immune feature-based panels between COVID-19 and HC groups (P<0.0001). Meanwhile, we observed that urine metabolic markers enabled discriminating asymptomatic patients (ASY) from HCs (AUC = 0.981, 95% CI, 0.946-0.996), and predicting the incidence of high-risk sequalae in COVID-19 individuals (AUC=0.931, 95% CI, 0.877-0.966). Co-expression network analysis showed that 13 urinary microbial metabolites (e.g., oxoglutaric acid) were significantly correlated with alterations of CD4+, CD3+, and CD8+ T-cells, as well as IFN-γ, IL-2 and IL-4 levels, suggesting close interactions between microbial metabolites and host immune dysregulation in COVID-19. Taken together, our findings indicate that urinary metabolites may have promising potential for screening of COVID-19 in different application scenarios, and provide a new entry point to understand the microbial metabolites and related immune dysfunction in COVID-19.
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Affiliation(s)
- Yixian Jing
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Jing Wang
- Department of Clinical Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Haiyan Zhang
- Department of Clinical Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Kun Yang
- Department of Clinical Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Jungang Li
- Department of Clinical Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Ting Zhao
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
| | - Jiaxiu Liu
- Department of Clinical Laboratory, Chongqing Public Health Medical Center, Chongqing, China
| | - Jing Wu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China.,National Health Commission of the People's Republic of China (NHC) Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yaokai Chen
- Division of Infectious Diseases, Chongqing Public Health Medical Center, Chongqing, China
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109
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Asai N, Kato H, Mikamo H. The pathophysiological mechanisms of COVID-19 and host immunity, with emphasis on the dysbiosis of the lung and gut microbiomes and pregnancy. Respir Investig 2022; 60:496-502. [PMID: 35422403 PMCID: PMC8977498 DOI: 10.1016/j.resinv.2022.03.002] [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: 11/23/2021] [Revised: 02/27/2022] [Accepted: 03/07/2022] [Indexed: 11/24/2022]
Abstract
The coronavirus 2019 (COVID-19) pandemic is a health and economic crisis. It has also highlighted human relational problems, such as racism and conflicts between nations. Although vaccination programs against the severe respiratory syndrome coronavirus 2 (SARS-CoV-2) have started worldwide, the pandemic is ongoing, and people are struggling. The mechanism of disease severity in COVID-19 is multifactorial, complicated, and affected by viral pathogenesis. For example, monocyte dysfunction due to aging and respiratory and gut dysbiosis influence the host's immunity against SARS-CoV-2 including helper T-cell imbalance and viral clearance reduction, leading to accelerated disease progression in older patients or those with underlying diseases. The different immune responses against SARS-CoV-2 also contribute to various radiological findings, including that of acute respiratory distress syndrome, which is associated with high mortality, especially in patients susceptible to disease progression. We aimed to review the pathophysiological mechanisms involved in COVID-19, with emphasis on the altered microbiome in the lung and gut, and the different radiological findings in different patient groups, such as younger adults and pregnant women.
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110
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Guo XJ, Jiang T, Ma XX, Hu XJ, Huang JB, Cui LT, Cui J, Yao XH, Shi YL, Li J, Guo ZL, Lou JD, Liang MC, Fu HY, Yuan P, Liu JY, Tu LP, Xu JT. Relationships Between Diurnal Changes of Tongue Coating Microbiota and Intestinal Microbiota. Front Cell Infect Microbiol 2022; 12:813790. [PMID: 35433494 PMCID: PMC9008461 DOI: 10.3389/fcimb.2022.813790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/02/2022] [Indexed: 11/29/2022] Open
Abstract
The oral cavity and the intestine are the main distribution locations of human digestive bacteria. Exploring the relationships between the tongue coating and gut microbiota, the influence of the diurnal variations of the tongue coating microbiota on the intestinal microbiota can provide a reference for the development of the disease diagnosis and monitoring, as well as the medication time. In this work, a total of 39 healthy college students were recruited. We collected their tongue coating microbiota which was collected before and after sleep and fecal microbiota. The diurnal variations of tongue coating microbiota are mainly manifested on the changes in diversity and relative abundance. There are commensal bacteria in the tongue coating and intestines, especially Prevotella which has the higher proportion in both sites. The relative abundance of Prevotella in the tongue coating before sleep has a positive correlation with intestinal Prevotella; the r is 0.322 (p < 0.05). Bacteroides in the intestine had the most bacteria associated with the tongue coating and had the highest correlation coefficient with Veillonella in the oral cavity, which was 0.468 (p < 0.01). These results suggest that the abundance of the same flora in the two sites may have a common change trend. The SourceTracker results show that the proportion of intestinal bacteria sourced from tongue coating is less than 1%. It indicates that oral flora is difficult to colonize in the intestine in healthy people. This will provide a reference for the study on the oral and intestinal microbiota in diseases.
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Affiliation(s)
- Xiao-jing Guo
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Tao Jiang
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Xu-xiang Ma
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Xiao-juan Hu
- Shanghai Collaborative Innovation Center of Health Service in Traditional Chinese Medicine (TCM), Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Jing-bin Huang
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Long-tao Cui
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Ji Cui
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Xing-hua Yao
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Yu-lin Shi
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Jun Li
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Zhi-ling Guo
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Jin-di Lou
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Meng-chen Liang
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Hong-yuan Fu
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Pei Yuan
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Jia-yi Liu
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
| | - Li-ping Tu
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
- *Correspondence: Li-ping Tu, ; Jia-tuo Xu,
| | - Jia-tuo Xu
- Basic Medical College, Shanghai University of Traditional Chinese Medicine (TCM), Shanghai, China
- *Correspondence: Li-ping Tu, ; Jia-tuo Xu,
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111
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Yang T, Jiang Y, Tang J, Chang G, Zhao W, Hou S, Chen G. Comparison of Cecal Microbiota and Performance Indices Between Lean-Type and Fatty-Type Pekin Ducks. Front Microbiol 2022; 13:820569. [PMID: 35350611 PMCID: PMC8957900 DOI: 10.3389/fmicb.2022.820569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Fatty-type (FT) Pekin ducks exhibit higher lipid deposition than lean-type (LT) ducks. The gut microbiota plays an important role in modulating fat metabolism. We compared the growth performance, slaughter performance, and cecal microbiota of FT and LT Pekin ducks and analyzed the role of cecal microbiota in lipid deposition in Pekin ducks. A total of 140 1-day-old FT and LT Pekin ducks with similar body weights were randomly assigned to 10 cages, with 14 ducks in each replicate. All ducks were fed commercial diets from 28 to 42 days of age. Results showed that the average body weight and feed intake of FT ducks were higher than those of LT ducks. The breast muscle and eviscerated percentages of LT ducks were higher than those of FT ducks; the abdominal fat and sebum percentages of LT ducks were lower than those of FT ducks at 6 weeks of age (P < 0.01). 16S DNA sequencing of the cecal microbiota revealed that the bacterial abundance differed between FT and LT ducks at 4 and 6 weeks of age. The abundance of Firmicutes was higher, while that of Fusobacteria and Fusobacterium was lower in LT ducks than in FT ducks at 4 weeks of age. The abundance of Spirochaetes was higher, while that of Firmicutes and Bacteroides was lower in LT ducks than in FT ducks at 6 weeks of age. The abundance of Spirochaetes and Brachyspira in LT ducks was higher at 6 weeks than at 4 weeks of age. Interestingly, the abundance of Firmicutes and Bacteroides in FT ducks was higher at 6 weeks of age than at 4 weeks of age, while that of Fusobacteria and Fusobacterium was lower at 6 weeks than at 4 weeks of age. Linear discriminant analysis effect size analysis showed that Spirochaetes, Brachyspira, Alistipes, Campylobacter, Megamonas, Butyricicoccus, and Fusobacteria may be involved in the fat metabolism pathway as specific markers. We reveal the differences in microbial abundance in the cecal microbiota between FT and LT Pekin ducks and provide an insight into the role of cecal microbiota in lipid deposition in Pekin ducks.
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Affiliation(s)
- Tingshuo Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, Yangzhou, China
| | - Yong Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, Yangzhou, China
| | - Jing Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, Yangzhou, China
| | - Wenming Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, Yangzhou, China
| | - Shuisheng Hou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Key Laboratory for Animal Genetics & Molecular Breeding of Jiangsu Province, Yangzhou, China
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Roles of oral microbiota and oral-gut microbial transmission in hypertension. J Adv Res 2022; 43:147-161. [PMID: 36585105 PMCID: PMC9811375 DOI: 10.1016/j.jare.2022.03.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 01/07/2023] Open
Abstract
INTRODUCTION Considerable evidence has linked periodontitis (PD) to hypertension (HTN), but the nature behind this connection is unclear. Dysbiosis of oral microbiota leading to PD is known to aggravate different systematic diseases, but the alteration of oral microbiota in HTN and their impacts on blood pressure (BP) remains to be discovered. OBJECTIVES To characterize the alterations of oral and gut microbiota and their roles in HTN. METHODS We performed a cross-sectional (95 HTN participants and 39 controls) and a 6-month follow-up study (52 HTN participants and 26 controls) to analyze the roles of oral and gut microbiota in HTN. Saliva, subgingival plaques, and feces were collected for 16S rRNA gene sequencing or metagenomic analysis. C57BL/6J mice were pretreated with antibiotics to deplete gut microbiota, and then transplanted with human saliva by gavage to test the impacts of abnormal oral-gut microbial transmission on HTN. RESULTS BP in participants with PD was higher than no PD in both cross-sectional and follow-up cohort. Relative abundances of 14 salivary genera, 15 subgingival genera and 10 gut genera significantly altered in HTN and those of 7 salivary genera, 12 subgingival genera and 6 gut genera significantly correlated with BP. Sixteen species under 5 genera were identified as oral-gut transmitters, illustrating the presence of oral-gut microbial transmission in HTN. Veillonella was a frequent oral-gut transmitter stably enriched in HTN participants of both cross-sectional and follow-up cohorts. Saliva from HTN participants increased BP in hypertensive mice. Human saliva-derived Veillonella successfully colonized in mouse gut, more abundantly under HTN condition. CONCLUSIONS PD and oral microbiota are strongly associated with HTN, likely through oral-gut transmission of microbes. Ectopic colonization of saliva-derived Veillonella in the gut may aggravate HTN. Therefore, precise manipulations of oral microbiota and/or oral-gut microbial transmission may be useful strategies for better prevention and treatment of HTN.
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113
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Shi YL, He MZ, Han MZ, Gui HY, Wang P, Yu JL, Ge YL, Sun Y, Huang SH. Characterization of Altered Oropharyngeal Microbiota in Hospitalized Patients With Mild SARS-CoV-2 Infection. Front Cell Infect Microbiol 2022; 12:824578. [PMID: 35372134 PMCID: PMC8965315 DOI: 10.3389/fcimb.2022.824578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/08/2022] [Indexed: 12/19/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) remains a serious emerging global health problem, and little is known about the role of oropharynx commensal microbes in infection susceptibility and severity. Here, we present the oropharyngeal microbiota characteristics identified by full-length 16S rRNA gene sequencing through the NANOPORE platform of oropharynx swab specimens from 10 mild COVID-19 patients and 10 healthy controls. Our results revealed a distinct oropharyngeal microbiota composition in mild COVID-19 patients, characterized by enrichment of opportunistic pathogens such as Peptostreptococcus anaerobius and Pseudomonas stutzeri and depletion of Sphingomonas yabuuchiae, Agrobacterium sullae, and Pseudomonas veronii. Based on the relative abundance of the oropharyngeal microbiota at the species level, we built a microbial classifier to distinguish COVID-19 patients from healthy controls, in which P. veronii, Pseudomonas fragi, and S. yabuuchiae were identified as the most prominent signatures for their depletion in the COVID-19 group. Several members of the genus Campylobacter, especially Campylobacter fetus and Campylobacter rectus, which were highly enriched in COVID-19 patients with higher severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and showed a significant correlation with disease status and several routine clinical blood indicators, indicate that several bacteria may transform into opportunistic pathogen in COVID-19 patients when facing the challenges of viral infection. We also found the diver taxa Streptococcus anginosus and Streptococcus alactolyticus in the network of disease patients, suggesting that these oropharynx microbiota alterations may impact COVID-19 severity by influencing the microbial association patterns. In conclusion, the low sample size of SARS-CoV-2 infection patients (n = 10) here makes these results tentative; however, we have provided the overall characterization that oropharyngeal microbiota alterations and microbial correlation patterns were associated with COVID-19 severity in Anhui Province.
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Affiliation(s)
- Yong-Lin Shi
- Anhui Provincial Centers for Disease Control and Prevention, Hefei, China
| | - Mao-Zhang He
- Department of Microbiology, The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Mao-Zhen Han
- School of Life Sciences, Anhui Medical University, Hefei, China
| | - Hong-Ya Gui
- Department of Microbiology, The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Peng Wang
- Anhui Provincial Centers for Disease Control and Prevention, Hefei, China
| | - Jun-Ling Yu
- Anhui Provincial Centers for Disease Control and Prevention, Hefei, China
| | - Ying-Lu Ge
- Anhui Provincial Centers for Disease Control and Prevention, Hefei, China
| | - Yong Sun
- Anhui Provincial Centers for Disease Control and Prevention, Hefei, China
- *Correspondence: Sheng-Hai Huang, ; Yong Sun,
| | - Sheng-Hai Huang
- Department of Microbiology, The Key Laboratory of Microbiology and Parasitology of Anhui Province, The Key Laboratory of Zoonoses of High Institutions in Anhui, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
- School of Life Sciences, Anhui Medical University, Hefei, China
- *Correspondence: Sheng-Hai Huang, ; Yong Sun,
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114
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Schwab G, Palmieri M, Zerbinati RM, Sarmento DJS, Reis T, Ortega KL, Kano IT, Caixeta RAV, Hasséus B, Sapkota D, Junges R, Giannecchini S, Costa ALF, Jales SMCP, Lindoso JAL, Gallo CB, Braz-Silva PH. Lack of direct association between oral mucosal lesions and SARS-CoV- 2 in a cohort of patients hospitalised with COVID-19. J Oral Microbiol 2022; 14:2047491. [PMID: 35295979 PMCID: PMC8920376 DOI: 10.1080/20002297.2022.2047491] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background COVID-19 is a disease affecting various human organs and systems, in which the virus seeks to interact with angiotensin-converting enzyme 2 receptors. These receptors are present in the oral cavity, but the direct relationship between such an interaction and possible oral manifestations of COVID-19 is still unclear. Aim The present study evaluated oral manifestations in a cohort of COVID-19 patients during the period of hospitalisation. Methods In total, 154 patients presenting moderate-to-severe forms of COVID-19 had their oral mucosa examined twice a week until the final outcome, either discharge or death. The oral alterations observed in the patients were grouped into Group 1 (pre-existing conditions and opportunistic oral lesions) and Group 2 (oral mucosal changes related to hospitalization). Results Oral lesions found in the patients of Group 1 are not suggestive of SARS-CoV-2 infection as they are mainly caused by opportunistic infections. On the other hand, oral alterations found in the patients of Group 2 were statistically (P < 0.001) related to intubation and longer period of hospitalisation. Conclusion It is unlikely that ulcerative lesions in the oral cavity are a direct manifestation of SARS-CoV-2 or a marker of COVID-19 progression.
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Affiliation(s)
- Gabriela Schwab
- Laboratory of Virology (Lim-52-hc-fmusp), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Michelle Palmieri
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Rodrigo M. Zerbinati
- Laboratory of Virology (Lim-52-hc-fmusp), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Dmitry J. S. Sarmento
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
- School of Dentistry, State University of Paraíba, Araruna, Brazil
| | - Thais Reis
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Karem L. Ortega
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Italo T. Kano
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Rafael A. V. Caixeta
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Bengt Hasséus
- Department of Oral Medicine and Pathology, Institute of Odontology, University of Gothenburg, Gothenburg, Sweden
| | - Dipak Sapkota
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Roger Junges
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - André L. F. Costa
- Postgraduate Program in Dentistry, Cruzeiro Do Sul University, São Paulo, Brazil
| | - Sumatra M. C. P. Jales
- Division of Dentistry, Hospital Das Clínicas da Faculdade de Medicina da Universidade de São Paulo – Hcfmusp, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - José A. L. Lindoso
- Institute of Infectious Diseases Emilio Ribas, São Paulo, Brazil
- Laboratory of Protozoology (Lim-49-hc-fmusp), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
- Department of Infectious Diseases, School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Camila Barros Gallo
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
| | - Paulo H. Braz-Silva
- Laboratory of Virology (Lim-52-hc-fmusp), Institute of Tropical Medicine of São Paulo, School of Medicine, University of São Paulo, São Paulo, Brazil
- Department of Stomatology, School of Dentistry, University of São Paulo, São Paulo, Brazil
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115
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Schult D, Reitmeier S, Koyumdzhieva P, Lahmer T, Middelhof M, Erber J, Schneider J, Kager J, Frolova M, Horstmann J, Fricke L, Steiger K, Jesinghaus M, Janssen KP, Protzer U, Neuhaus K, Schmid RM, Haller D, Quante M. Gut bacterial dysbiosis and instability is associated with the onset of complications and mortality in COVID-19. Gut Microbes 2022; 14:2031840. [PMID: 35174781 PMCID: PMC8855857 DOI: 10.1080/19490976.2022.2031840] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
There is a growing debate about the involvement of the gut microbiome in COVID-19, although it is not conclusively understood whether the microbiome has an impact on COVID-19, or vice versa, especially as analysis of amplicon data in hospitalized patients requires sophisticated cohort recruitment and integration of clinical parameters. Here, we analyzed fecal and saliva samples from SARS-CoV-2 infected and post COVID-19 patients and controls considering multiple influencing factors during hospitalization. 16S rRNA gene sequencing was performed on fecal and saliva samples from 108 COVID-19 and 22 post COVID-19 patients, 20 pneumonia controls and 26 asymptomatic controls. Patients were recruited over the first and second corona wave in Germany and detailed clinical parameters were considered. Serial samples per individual allowed intra-individual analysis. We found the gut and oral microbiota to be altered depending on number and type of COVID-19-associated complications and disease severity. The occurrence of individual complications was correlated with low-risk (e.g., Faecalibacterium prausznitzii) and high-risk bacteria (e.g., Parabacteroides ssp.). We demonstrated that a stable gut bacterial composition was associated with a favorable disease progression. Based on gut microbial profiles, we identified a model to estimate mortality in COVID-19. Gut microbiota are associated with the occurrence of complications in COVID-19 and may thereby influencing disease severity. A stable gut microbial composition may contribute to a favorable disease progression and using bacterial signatures to estimate mortality could contribute to diagnostic approaches. Importantly, we highlight challenges in the analysis of microbial data in the context of hospitalization.
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Affiliation(s)
- David Schult
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Sandra Reitmeier
- Ziel - Institute for Food & Health, Technische Universität München, Freising, Germany,Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Plamena Koyumdzhieva
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Tobias Lahmer
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Moritz Middelhof
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Johanna Erber
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Jochen Schneider
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Juliane Kager
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Marina Frolova
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Julia Horstmann
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Lisa Fricke
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Katja Steiger
- Institute of Pathology, Technische Universität München, Munich, Germany
| | - Moritz Jesinghaus
- Institute of Pathology, Technische Universität München, Munich, Germany,Institute of Pathology, University Hospital Marburg, Marburg, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Ulrike Protzer
- Institute of Virology, Technische Universität/Helmholtz Zentrum München, Munich, Germany
| | - Klaus Neuhaus
- Ziel - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - Roland M. Schmid
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Dirk Haller
- Ziel - Institute for Food & Health, Technische Universität München, Freising, Germany,Chair of Nutrition and Immunology, Technische Universität München, Freising, Germany
| | - Michael Quante
- Department of Internal Medicine II, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany,Department of Internal Medicine II, Universitätsklinikum Freiburg, Universität Freiburg, Freiburg, Germany,CONTACT Michael Quante Klinik für Innere Medizin II, Hugstetter Str. 55, Freiburg79106, Germany
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116
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Najmi N, Megantara I, Andriani L, Goenawan H, Lesmana R. Importance of gut microbiome regulation for the prevention and recovery process after SARS‑CoV‑2 respiratory viral infection (Review). Biomed Rep 2022; 16:25. [PMID: 35251612 PMCID: PMC8889546 DOI: 10.3892/br.2022.1508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/09/2021] [Indexed: 01/08/2023] Open
Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been reported to affect organs other than the lungs, including the liver, brain, kidneys and intestine, and gastrointestinal symptoms, such as nausea, vomiting, diarrhea and abdominal discomfort, have also been reported. Thus, SARS-CoV-2 could potentially directly or indirectly regulate the gut microbiome profile and its homeostasis. The abundance of Coprobacillus, Clostridium ramosum and Clostridium are associated with the severity of COVID-19, and Firmicutes, Bacteriodetes, Proteobacteria and Actinobacteria are also related to COVID-19 infection. The four phyla are correlated with the severity of COVID-19 infection in patients. The modulation of factors that control the physiological growth of the gut microbiome will determine the proportionate ratio of microbiome types (profile). Taken together, gut microbiome profile alterations in COVID-19 patients may have a cross effect with the modulation of cytokine levels in COVID-19 infection. With these findings, several factors that regulate gut microbiome homeostasis may support the degree of the clinical symptoms and hasten the recovery process after COVID-19 infection.
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Affiliation(s)
- Nuroh Najmi
- Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran, Bandung, West Java 45363, Indonesia
| | - Imam Megantara
- Division of Biological Activty Central Laboratory, Universitas Padjadjaran, Bandung, West Java 45363, Indonesia
| | - Lovita Andriani
- Faculty of Animal Husbandry, Universitas Padjadjaran, Bandung, West Java 45363, Indonesia
| | - Hanna Goenawan
- Division of Biological Activty Central Laboratory, Universitas Padjadjaran, Bandung, West Java 45363, Indonesia
| | - Ronny Lesmana
- Division of Biological Activty Central Laboratory, Universitas Padjadjaran, Bandung, West Java 45363, Indonesia
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117
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Zhou A, Yuan Y, Yang M, Huang Y, Li X, Li S, Yang S, Tang B. Crosstalk Between the Gut Microbiota and Epithelial Cells Under Physiological and Infectious Conditions. Front Cell Infect Microbiol 2022; 12:832672. [PMID: 35155283 PMCID: PMC8829037 DOI: 10.3389/fcimb.2022.832672] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
The gastrointestinal tract (GIT) is considered the largest immunological organ, with a diverse gut microbiota, that contributes to combatting pathogens and maintaining human health. Under physiological conditions, the crosstalk between gut microbiota and intestinal epithelial cells (IECs) plays a crucial role in GIT homeostasis. Gut microbiota and derived metabolites can compromise gut barrier integrity by activating some signaling pathways in IECs. Conversely, IECs can separate the gut microbiota from the host immune cells to avoid an excessive immune response and regulate the composition of the gut microbiota by providing an alternative energy source and releasing some molecules, such as hormones and mucus. Infections by various pathogens, such as bacteria, viruses, and parasites, can disturb the diversity of the gut microbiota and influence the structure and metabolism of IECs. However, the interaction between gut microbiota and IECs during infection is still not clear. In this review, we will focus on the existing evidence to elucidate the crosstalk between gut microbiota and IECs during infection and discuss some potential therapeutic methods, including probiotics, fecal microbiota transplantation (FMT), and dietary fiber. Understanding the role of crosstalk during infection may help us to establish novel strategies for prevention and treatment in patients with infectious diseases, such as C. difficile infection, HIV, and COVID-19.
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Affiliation(s)
- An Zhou
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Yi Yuan
- Institution of Basic Medicine, Third Military Medical University, Chongqing, China
| | - Min Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Yujiao Huang
- The First Clinical College, ChongQing Medical University, Chongqing, China
| | - Xin Li
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Shengpeng Li
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Shiming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
- *Correspondence: Shiming Yang, ; Bo Tang,
| | - Bo Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing, China
- *Correspondence: Shiming Yang, ; Bo Tang,
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118
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Sun Z, Song ZG, Liu C, Tan S, Lin S, Zhu J, Dai FH, Gao J, She JL, Mei Z, Lou T, Zheng JJ, Liu Y, He J, Zheng Y, Ding C, Qian F, Zheng Y, Chen YM. Gut microbiome alterations and gut barrier dysfunction are associated with host immune homeostasis in COVID-19 patients. BMC Med 2022; 20:24. [PMID: 35045853 PMCID: PMC8769945 DOI: 10.1186/s12916-021-02212-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND COVID-19 is an infectious disease characterized by multiple respiratory and extrapulmonary manifestations, including gastrointestinal symptoms. Although recent studies have linked gut microbiota to infectious diseases such as influenza, little is known about the role of the gut microbiota in COVID-19 pathophysiology. METHODS To better understand the host-gut microbiota interactions in COVID-19, we characterized the gut microbial community and gut barrier function using metagenomic and metaproteomic approaches in 63 COVID-19 patients and 8 non-infected controls. Both immunohematological parameters and transcriptional profiles were measured to reflect the immune response in COVID-19 patients. RESULTS Altered gut microbial composition was observed in COVID-19 patients, which was characterized by decreased commensal species and increased opportunistic pathogenic species. Severe illness was associated with higher abundance of four microbial species (i.e., Burkholderia contaminans, Bacteroides nordii, Bifidobacterium longum, and Blautia sp. CAG 257), six microbial pathways (e.g., glycolysis and fermentation), and 10 virulence genes. These severity-related microbial features were further associated with host immune response. For example, the abundance of Bu. contaminans was associated with higher levels of inflammation biomarkers and lower levels of immune cells. Furthermore, human-origin proteins identified from both blood and fecal samples suggested gut barrier dysfunction in COVID-19 patients. The circulating levels of lipopolysaccharide-binding protein increased in patients with severe illness and were associated with circulating inflammation biomarkers and immune cells. Besides, proteins of disease-related bacteria (e.g., B. longum) were detectable in blood samples from patients. CONCLUSIONS Our results suggest that the dysbiosis of the gut microbiome and the dysfunction of the gut barrier might play a role in the pathophysiology of COVID-19 by affecting host immune homeostasis.
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Affiliation(s)
- Zhonghan Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China.,Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China
| | - Zhi-Gang Song
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Chenglin Liu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Shishang Tan
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Shuchun Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Jiajun Zhu
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Fa-Hui Dai
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Jian Gao
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Jia-Lei She
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Zhendong Mei
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Tao Lou
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Jiao-Jiao Zheng
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Yi Liu
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Jiang He
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Yuanting Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Feng Qian
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China
| | - Yan Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China. .,Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China.
| | - Yan-Mei Chen
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai, China.
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119
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Woodall CA, McGeoch LJ, Hay AD, Hammond A. Respiratory tract infections and gut microbiome modifications: A systematic review. PLoS One 2022; 17:e0262057. [PMID: 35025938 PMCID: PMC8757905 DOI: 10.1371/journal.pone.0262057] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/15/2021] [Indexed: 12/15/2022] Open
Abstract
Respiratory tract infections (RTIs) are extremely common and can cause gastrointestinal tract symptoms and changes to the gut microbiota, yet these effects are poorly understood. We conducted a systematic review to evaluate the reported evidence of gut microbiome alterations in patients with a RTI compared to healthy controls (PROSPERO: CRD42019138853). We systematically searched Medline, Embase, Web of Science, Cochrane and the Clinical Trial Database for studies published between January 2015 and June 2021. Studies were eligible for inclusion if they were human cohorts describing the gut microbiome in patients with an RTI compared to healthy controls and the infection was caused by a viral or bacterial pathogen. Dual data screening and extraction with narrative synthesis was performed. We identified 1,593 articles and assessed 11 full texts for inclusion. Included studies (some nested) reported gut microbiome changes in the context of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) (n = 5), influenza (H1N1 and H7N9) (n = 2), Tuberculosis (TB) (n = 4), Community-Acquired Pneumonia CAP (n = 2) and recurrent RTIs (rRTI) (n = 1) infections. We found studies of patients with an RTI compared to controls reported a decrease in gut microbiome diversity (Shannon) of 1.45 units (95% CI, 0.15-2.50 [p, <0.0001]) and a lower abundance of taxa (p, 0.0086). Meta-analysis of the Shannon value showed considerable heterogeneity between studies (I2, 94.42). Unbiased analysis displayed as a funnel plot revealed a depletion of Lachnospiraceae, Ruminococcaceae and Ruminococcus and enrichment of Enterococcus. There was an important absence in the lack of cohort studies reporting gut microbiome changes and high heterogeneity between studies may be explained by variations in microbiome methods and confounder effects. Further human cohort studies are needed to understand RTI-induced gut microbiome changes to better understand interplay between microbes and respiratory health.
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Affiliation(s)
- Claire A. Woodall
- Centre for Academic Primary Care, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Luke J. McGeoch
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Alastair D. Hay
- Centre for Academic Primary Care, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Ashley Hammond
- Centre for Academic Primary Care, Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, United Kingdom
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120
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Wang H, Wang H, Sun Y, Ren Z, Zhu W, Li A, Cui G. Potential Associations Between Microbiome and COVID-19. Front Med (Lausanne) 2022; 8:785496. [PMID: 35004750 PMCID: PMC8727742 DOI: 10.3389/fmed.2021.785496] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has plunged the world into a major crisis. The disease is characterized by strong infectivity, high morbidity, and high mortality. It is still spreading in some countries. Microbiota and their metabolites affect human physiological health and diseases by participating in host digestion and nutrition, promoting metabolic function, and regulating the immune system. Studies have shown that human microecology is associated with many diseases, including COVID-19. In this research, we first reviewed the microbial characteristics of COVID-19 from the aspects of gut microbiome, lung microbime, and oral microbiome. We found that significant changes take place in both the gut microbiome and airway microbiome in patients with COVID-19 and are characterized by an increase in conditional pathogenic bacteria and a decrease in beneficial bacteria. Then, we summarized the possible microecological mechanisms involved in the progression of COVID-19. Intestinal microecological disorders in individuals may be involved in the occurrence and development of COVID-19 in the host through interaction with ACE2, mitochondria, and the lung-gut axis. In addition, fecal bacteria transplantation (FMT), prebiotics, and probiotics may play a positive role in the treatment of COVID-19 and reduce the fatal consequences of the disease.
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Affiliation(s)
- Huifen Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haiyu Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Sun
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhigang Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Weiwei Zhu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guangying Cui
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Zhengzhou, China.,Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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121
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Lau HCH, Ng SC, Yu J. Targeting the Gut Microbiota in Coronavirus Disease 2019: Hype or Hope? Gastroenterology 2022; 162:9-16. [PMID: 34508775 PMCID: PMC8425294 DOI: 10.1053/j.gastro.2021.09.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/29/2021] [Accepted: 09/01/2021] [Indexed: 12/14/2022]
Affiliation(s)
| | - Siew C Ng
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Microbiota I-Center (MagIC), Hong Kong SAR, China
| | - Jun Yu
- Institute of Digestive Disease, Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
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122
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Strati F, Lattanzi G, Amoroso C, Facciotti F. Microbiota-targeted therapies in inflammation resolution. Semin Immunol 2022; 59:101599. [PMID: 35304068 DOI: 10.1016/j.smim.2022.101599] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/24/2022] [Accepted: 02/15/2022] [Indexed: 02/07/2023]
Abstract
Gut microbiota has been shown to systemically shape the immunological landscape, modulate homeostasis and play a role in both health and disease. Dysbiosis of gut microbiota promotes inflammation and contributes to the pathogenesis of several major disorders in gastrointestinal tract, metabolic, neurological and respiratory diseases. Much effort is now focused on understanding host-microbes interactions and new microbiota-targeted therapies are deeply investigated as a means to restore health or prevent disease. This review details the immunoregulatory role of the gut microbiota in health and disease and discusses the most recent strategies in manipulating individual patient's microbiota for the management and prevention of inflammatory conditions.
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Affiliation(s)
- Francesco Strati
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Georgia Lattanzi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Chiara Amoroso
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Federica Facciotti
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy; Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
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123
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Dauby N, Flamand V. From maternal breath to infant's cells: Impact of maternal respiratory infections on infants 'immune responses. Front Pediatr 2022; 10:1046100. [PMID: 36419921 PMCID: PMC9676445 DOI: 10.3389/fped.2022.1046100] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022] Open
Abstract
In utero exposure to maternally-derived antigens following chronic infection is associated with modulation of infants 'immune response, differential susceptibility to post-natal infections and immune response toward vaccines. The maternal environment, both internal (microbiota) and external (exposure to environmental microbes) also modulates infant's immune response but also the clinical phenotype after birth. Vertical transmission of ubiquitous respiratory pathogens such as influenza and COVID-19 is uncommon. Evidence suggest that in utero exposure to maternal influenza and SARS-CoV-2 infections may have a significant impact on the developing immune system with activation of both innate and adaptive responses, possibly related to placental inflammation. Here in, we review how maternal respiratory infections, associated with airway, systemic and placental inflammation but also changes in maternal microbiota might impact infant's immune responses after birth. The clinical impact of immune modifications observed following maternal respiratory infections remains unexplored. Given the high frequencies of respiratory infections during pregnancy (COVID-19, influenza but also RSV and HMPV), the impact on global child health could be important.
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Affiliation(s)
- Nicolas Dauby
- Institute for Medical Immunology, ULB Center for Research in Immunology, Université Libre de Bruxelles (ULB), Brussels, Belgium.,Department of Infectious Diseases, CHU Saint-Pierre, Brussels, Belgium.,School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Véronique Flamand
- Institute for Medical Immunology, ULB Center for Research in Immunology, Université Libre de Bruxelles (ULB), Brussels, Belgium
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124
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Biliński J, Winter K, Jasiński M, Szczęś A, Bilinska N, Mullish BH, Małecka-Panas E, Basak GW. Rapid resolution of COVID-19 after faecal microbiota transplantation. Gut 2022; 71:230-232. [PMID: 34230217 DOI: 10.1136/gutjnl-2021-325010] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/07/2021] [Indexed: 12/29/2022]
Affiliation(s)
- Jarosław Biliński
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, Warszawa, Poland .,Human Biome Institute, Gdańsk, Poland
| | - Katarzyna Winter
- Department of Digestive Tract Diseases, Medical University of Lodz, Lodz, Poland
| | - Marcin Jasiński
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, Warszawa, Poland
| | - Anna Szczęś
- Department of Internal Medicine, Poviat Specialist Hospital in Stalowa Wola, Stalowa Wola, Poland
| | - Natalia Bilinska
- Department of Pediatric Gatroenterology and Pediatrics, Medical University of Warsaw, Warszawa, Poland
| | - Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Ewa Małecka-Panas
- Department of Digestive Tract Diseases, Medical University of Lodz, Lodz, Poland
| | - Grzegorz W Basak
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, Warszawa, Poland.,Human Biome Institute, Gdańsk, Poland
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125
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Rao B, Ren T, Wang X, Wang H, Zou Y, Sun Y, Liu S, Ren Z, Yu Z. Dysbiosis in the Human Microbiome of Cholangiocarcinoma. Front Physiol 2021; 12:715536. [PMID: 34867436 PMCID: PMC8633309 DOI: 10.3389/fphys.2021.715536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
Cholangiocarcinoma (CCA) is the most common malignant tumor of the biliary system with a very poor prognosis. The human microbiome, which is the sum of the genetic information of human microorganisms, plays an important role in regulating the digestion, absorption, immune response, and metabolism of the host. Increasing evidence indicates a close relationship between CCA and the human microbiome. Specific alterations occur in the human microbiome of patients with CCA. Therefore, in this review, we aimed to summarize the recent evidence on dysbiosis in the human microbiome of CCA. Then, we generalized the effect of Helicobacter pylori on CCA. Additionally, the potential mechanism of human microbial dysbiosis promoted the progress of CCA, and its precancerous disease was also explored. Furthermore, the possibility of the human microbiome as a diagnostic and therapeutic target of CCA was discussed.
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Affiliation(s)
- Benchen Rao
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tong Ren
- Department of Breast Surgery, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Xuemei Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haiyu Wang
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yawen Zou
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Sun
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shanshuo Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhigang Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zujiang Yu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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126
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Demirci M. Could Neisseria in oral microbiota modulate the inflammatory response of COVID-19? Oral Dis 2021; 28 Suppl 2:2603-2604. [PMID: 34806814 PMCID: PMC9011821 DOI: 10.1111/odi.14082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/24/2022]
Affiliation(s)
- Mehmet Demirci
- Department of Medical Microbiology, School of Medicine, Kirklareli University, Kirklareli, Turkey
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127
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Assessing saliva microbiome collection and processing methods. NPJ Biofilms Microbiomes 2021; 7:81. [PMID: 34795298 PMCID: PMC8602330 DOI: 10.1038/s41522-021-00254-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/21/2021] [Indexed: 12/29/2022] Open
Abstract
The oral microbiome has been connected with lung health and may be of significance in the progression of SARS-CoV-2 infection. Saliva-based SARS-CoV-2 tests provide the opportunity to leverage stored samples for assessing the oral microbiome. However, these collection kits have not been tested for their accuracy in measuring the oral microbiome. Saliva is highly enriched with human DNA and reducing it prior to shotgun sequencing may increase the depth of bacterial reads. We examined both the effect of saliva collection method and sequence processing on measurement of microbiome depth and diversity by 16S rRNA gene amplicon and shotgun metagenomics. We collected 56 samples from 22 subjects. Each subject provided saliva samples with and without preservative, and a subset provided a second set of samples the following day. 16S rRNA gene (V4) sequencing was performed on all samples, and shotgun metagenomics was performed on a subset of samples collected with preservative with and without human DNA depletion before sequencing. We observed that the beta diversity distances within subjects over time was smaller than between unrelated subjects, and distances within subjects were smaller in samples collected with preservative. Samples collected with preservative had higher alpha diversity measuring both richness and evenness. Human DNA depletion before extraction and shotgun sequencing yielded higher total and relative reads mapping to bacterial sequences. We conclude that collecting saliva with preservative may provide more consistent measures of the oral microbiome and depleting human DNA increases yield of bacterial sequences.
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128
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Miller EH, Annavajhala MK, Chong AM, Park H, Nobel YR, Soroush A, Blackett JW, Krigel A, Phipps MM, Freedberg DE, Zucker J, Sano ED, Uhlemann AC, Abrams JA. Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19. Microbiol Spectr 2021; 9:e0005521. [PMID: 34643448 PMCID: PMC8515944 DOI: 10.1128/spectrum.00055-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/07/2021] [Indexed: 12/15/2022] Open
Abstract
Bacterial-viral interactions in saliva have been associated with morbidity and mortality for respiratory viruses such as influenza and SARS-CoV. However, such transkingdom relationships during SARS-CoV-2 infection are currently unknown. Here, we aimed to elucidate the relationship between saliva microbiota and SARS-CoV-2 in a cohort of newly hospitalized COVID-19 patients and controls. We used 16S rRNA sequencing to compare microbiome diversity and taxonomic composition between COVID-19 patients (n = 53) and controls (n = 59) and based on saliva SARS-CoV-2 viral load as measured using reverse transcription PCR (RT-PCR). The saliva microbiome did not differ markedly between COVID-19 patients and controls. However, we identified significant differential abundance of numerous taxa based on saliva SARS-CoV-2 viral load, including multiple species within Streptococcus and Prevotella. IMPORTANCE Alterations to the saliva microbiome based on SARS-CoV-2 viral load indicate potential biologically relevant bacterial-viral relationships which may affect clinical outcomes in COVID-19 disease.
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Affiliation(s)
- Emily Happy Miller
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Medini K. Annavajhala
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Alexander M. Chong
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
- Microbiome and Pathogen Genomics Collaborative Center, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Heekuk Park
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
- Microbiome and Pathogen Genomics Collaborative Center, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Yael R. Nobel
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Ali Soroush
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - John W. Blackett
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Anna Krigel
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Meaghan M. Phipps
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Daniel E. Freedberg
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Jason Zucker
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Ellen D. Sano
- Department of Emergency Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Anne-Catrin Uhlemann
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
- Microbiome and Pathogen Genomics Collaborative Center, Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
| | - Julian A. Abrams
- Department of Medicine, Columbia University Irving Medical Center, New York, New York, USA
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129
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de Castilhos J, Zamir E, Hippchen T, Rohrbach R, Schmidt S, Hengler S, Schumacher H, Neubauer M, Kunz S, Müller-Esch T, Hiergeist A, Gessner A, Khalid D, Gaiser R, Cullin N, Papagiannarou SM, Beuthien-Baumann B, Krämer A, Bartenschlager R, Jäger D, Müller M, Herth F, Duerschmied D, Schneider J, Schmid RM, Eberhardt JF, Khodamoradi Y, Vehreschild MJGT, Teufel A, Ebert MP, Hau P, Salzberger B, Schnitzler P, Poeck H, Elinav E, Merle U, Stein-Thoeringer CK. Severe Dysbiosis and Specific Haemophilus and Neisseria Signatures as Hallmarks of the Oropharyngeal Microbiome in Critically Ill Coronavirus Disease 2019 (COVID-19) Patients. Clin Infect Dis 2021; 75:e1063-e1071. [PMID: 34694375 PMCID: PMC8586732 DOI: 10.1093/cid/ciab902] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND At the entry site of respiratory virus infections, the oropharyngeal microbiome has been proposed as a major hub integrating viral and host immune signals. Early studies suggested that infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are associated with changes of the upper and lower airway microbiome, and that specific microbial signatures may predict coronavirus disease 2019 (COVID-19) illness. However, the results are not conclusive, as critical illness can drastically alter a patient's microbiome through multiple confounders. METHODS To study oropharyngeal microbiome profiles in SARS-CoV-2 infection, clinical confounders, and prediction models in COVID-19, we performed a multicenter, cross-sectional clinical study analyzing oropharyngeal microbial metagenomes in healthy adults, patients with non-SARS-CoV-2 infections, or with mild, moderate, and severe COVID-19 (n = 322 participants). RESULTS In contrast to mild infections, patients admitted to a hospital with moderate or severe COVID-19 showed dysbiotic microbial configurations, which were significantly pronounced in patients treated with broad-spectrum antibiotics, receiving invasive mechanical ventilation, or when sampling was performed during prolonged hospitalization. In contrast, specimens collected early after admission allowed us to segregate microbiome features predictive of hospital COVID-19 mortality utilizing machine learning models. Taxonomic signatures were found to perform better than models utilizing clinical variables with Neisseria and Haemophilus species abundances as most important features. CONCLUSIONS In addition to the infection per se, several factors shape the oropharyngeal microbiome of severely affected COVID-19 patients and deserve consideration in the interpretation of the role of the microbiome in severe COVID-19. Nevertheless, we were able to extract microbial features that can help to predict clinical outcomes.
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Affiliation(s)
- Juliana de Castilhos
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany,Vale do Rio dos Sinos University (UNISINOS), Sao Leopoldo, Brazil
| | - Eli Zamir
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Theresa Hippchen
- Department of Gastroenterology and Infectious Diseases, University Clinic Heidelberg, Heidelberg, Germany
| | - Roman Rohrbach
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Sabine Schmidt
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Silvana Hengler
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Hanna Schumacher
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Melanie Neubauer
- Department of Medicine II, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Sabrina Kunz
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany
| | - Tonia Müller-Esch
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany
| | - Andreas Hiergeist
- Institute of Clinical Microbiology and Hygiene, University Clinic Regensburg, Regensburg, Germany
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, University Clinic Regensburg, Regensburg, Germany
| | - Dina Khalid
- Department of Virology, University Clinic Heidelberg, Heidelberg, Germany
| | - Rogier Gaiser
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Nyssa Cullin
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | - Stamatia M Papagiannarou
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany
| | | | - Alwin Krämer
- German Cancer Research Center (DKFZ), Research Division Molecular Hematology/Oncology, Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, Heidelberg, Germany,German Cancer Research Center (DKFZ), Research Division Virus-associated Carcinogenesis, Heidelberg
| | - Dirk Jäger
- National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany
| | - Michael Müller
- Thoraxklinik and Translational Lung Research Center, Heidelberg University, Heidelberg, Germany
| | - Felix Herth
- Thoraxklinik and Translational Lung Research Center, Heidelberg University, Heidelberg, Germany
| | - Daniel Duerschmied
- Department of Internal Medicine III, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jochen Schneider
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Roland M Schmid
- Department of Internal Medicine II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Johann F Eberhardt
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany
| | - Yascha Khodamoradi
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany
| | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Frankfurt, Germany,German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Andreas Teufel
- Department of Medicine II, Section of Hepatology, University Medical Center Mannheim, University of Heidelberg, Mannheim, and Center for Preventive Medicine and Digital Health Baden-Württemberg, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Matthias P Ebert
- Department of Medicine II, Section of Hepatology, University Medical Center Mannheim, University of Heidelberg, Mannheim, and Center for Preventive Medicine and Digital Health Baden-Württemberg, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Peter Hau
- Wilhelm Sander-NeuroOncology Unit and Department of Neurology, University Clinic Regensburg, Regensburg, Germany
| | - Bernd Salzberger
- Department of Infectious Disease, University Clinic Regensburg, Regensburg, Germany
| | - Paul Schnitzler
- Department of Virology, University Clinic Heidelberg, Heidelberg, Germany
| | - Hendrik Poeck
- Department of Internal Medicine III, University Clinic Regensburg, Regensburg, Germany,National Center for Tumor Diseases (NCT) WERA
| | - Eran Elinav
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany,Weizmann Institute of Science, Rehovot, Israel
| | - Uta Merle
- Department of Gastroenterology and Infectious Diseases, University Clinic Heidelberg, Heidelberg, Germany
| | - Christoph K Stein-Thoeringer
- German Cancer Research Center (DKFZ), Research Division Microbiome and Cancer, Heidelberg, Germany,National Center for Tumor Diseases (NCT) Heidelberg, Heidelberg, Germany,Corresponding author: Christoph K. Stein-Thoeringer, MD, Microbiome and Cancer Research Division, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 242, 69120 Heidelberg, Germany,
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130
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Haran JP, Bradley E, Zeamer AL, Cincotta L, Salive MC, Dutta P, Mutaawe S, Anya O, Meza-Segura M, Moormann AM, Ward DV, McCormick BA, Bucci V. Inflammation-type dysbiosis of the oral microbiome associates with the duration of COVID-19 symptoms and long COVID. JCI Insight 2021; 6:e152346. [PMID: 34403368 PMCID: PMC8564890 DOI: 10.1172/jci.insight.152346] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/12/2021] [Indexed: 12/19/2022] Open
Abstract
In the COVID-19 pandemic, caused by SARS-CoV-2, many individuals experience prolonged symptoms, termed long-lasting COVID-19 symptoms (long COVID). Long COVID is thought to be linked to immune dysregulation due to harmful inflammation, with the exact causes being unknown. Given the role of the microbiome in mediating inflammation, we aimed to examine the relationship between the oral microbiome and the duration of long COVID symptoms. Tongue swabs were collected from patients presenting with COVID-19 symptoms. Confirmed infections were followed until resolution of all symptoms. Bacterial composition was determined by metagenomic sequencing. We used random forest modeling to identify microbiota and clinical covariates that are associated with long COVID symptoms. Of the patients followed, 63% developed ongoing symptomatic COVID-19 and 37% went on to long COVID. Patients with prolonged symptoms had significantly higher abundances of microbiota that induced inflammation, such as members of the genera Prevotella and Veillonella, which, of note, are species that produce LPS. The oral microbiome of patients with long COVID was similar to that of patients with chronic fatigue syndrome. Altogether, our findings suggest an association with the oral microbiome and long COVID, revealing the possibility that dysfunction of the oral microbiome may have contributed to this draining disease.
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Affiliation(s)
- John P Haran
- Department of Emergency Medicine.,Department of Microbiology and Physiological Systems.,Program in Microbiome Dynamics, and
| | - Evan Bradley
- Department of Emergency Medicine.,Program in Microbiome Dynamics, and
| | - Abigail L Zeamer
- Department of Microbiology and Physiological Systems.,Program in Microbiome Dynamics, and
| | | | | | | | | | | | | | - Ann M Moormann
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Doyle V Ward
- Department of Microbiology and Physiological Systems.,Program in Microbiome Dynamics, and
| | - Beth A McCormick
- Department of Microbiology and Physiological Systems.,Program in Microbiome Dynamics, and
| | - Vanni Bucci
- Department of Microbiology and Physiological Systems.,Program in Microbiome Dynamics, and
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131
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Bao L, Zhang C, Lyu J, Yan C, Cao R, Pan M, Li Y. Beware of pharyngeal Fusobacterium nucleatum in COVID-19. BMC Microbiol 2021; 21:277. [PMID: 34635053 PMCID: PMC8504566 DOI: 10.1186/s12866-021-02336-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/01/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Fusobacterium nucleatum (F. n) is an important opportunistic pathogen causing oral and gastrointestinal disease. Faecalibacterium prausnitzii (F. p) is a next-generation probiotic and could serve as a biomarker of gut eubiosis/dysbiosis to some extent. Alterations in the human oral and gut microbiomes are associated with viral respiratory infection. The aim of this study was to characterise the oral and fecal bacterial biomarker (i.e., F. n and F. p) in COVID-19 patients by qPCR and investigate the pharyngeal microbiome of COVID-19 patients through metagenomic next-generation sequencing (mNGS). RESULTS Pharyngeal F. n was significantly increased in COVID-19 patients, and it was higher in male than female patients. Increased abundance of pharyngeal F. n was associated with a higher risk of a positive SARS-CoV-2 test (adjusted OR = 1.32, 95% CI = 1.06 ~ 1.65, P < 0.05). A classifier to distinguish COVID-19 patients from the healthy controls based on the pharyngeal F. n was constructed and achieved an area under the curve (AUC) of 0.843 (95% CI = 0.688 ~ 0.940, P < 0.001). However, the level of fecal F. n and fecal F. p remained unaltered between groups. Besides, mNGS showed that the pharyngeal swabs of COVID-19 patients were dominated by opportunistic pathogens. CONCLUSIONS Pharyngeal but not fecal F. n was significantly increased in COVID-19 patients, clinicians should pay careful attention to potential coinfection. Pharyngeal F. n may serve as a promising candidate indicator for COVID-19.
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Affiliation(s)
- Lirong Bao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Cheng Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Jinglu Lyu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Caixia Yan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Ranran Cao
- Sichuan Center for Disease Control and Prevention, Chengdu, 610041, China.
| | - Ming Pan
- Sichuan Center for Disease Control and Prevention, Chengdu, 610041, China.
| | - Yan Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
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132
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Gao M, Wang H, Luo H, Sun Y, Wang L, Ding S, Ren H, Gang J, Rao B, Liu S, Wang X, Gao X, Li M, Zou Y, Liu C, Yuan C, Sun J, Cui G, Ren Z. Characterization of the Human Oropharyngeal Microbiomes in SARS-CoV-2 Infection and Recovery Patients. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2102785. [PMID: 34423593 PMCID: PMC8529429 DOI: 10.1002/advs.202102785] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/28/2021] [Indexed: 05/25/2023]
Abstract
Respiratory tract microbiome is closely related to respiratory tract infections, while characterization of oropharyngeal microbiome in recovered coronavirus disease 2019 (COVID-19) patients is not studied. Herein, oropharyngeal swabs are collected from confirmed cases (CCs) with COVID-19 (73 subjects), suspected cases (SCs) (36), confirmed cases who recovered (21), suspected cases who recovered (36), and healthy controls (Hs) (140) and then completed MiSeq sequencing. Oropharyngeal microbial α-diversity is markedly reduced in CCs versus Hs. Opportunistic pathogens are increased, while butyrate-producing genera are decreased in CCs versus Hs. The classifier based on eight optimal microbial markers is constructed through a random forest model and reached great diagnostic efficacy in both discovery and validation cohorts. Notably, the classifier successfully diagnosed SCs with positive IgG antibody as CCs and is demonstrated from the perspective of the microbiome. Importantly, several genera with significant differences gradually increase and decrease along with recovery from COVID-19. Forty-four oropharyngeal operational taxonomy units (OTUs) are closely correlated with 11 clinical indicators of SARS-CoV-2 infection and Hs based on Spearman correlation analysis. Together, this research is the first to characterize oropharyngeal microbiota in recovered COVID-19 cases and suspected cases, to successfully construct and validate the diagnostic model for COVID-19 and to depict the correlations between microbial OTUs and clinical indicators.
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Affiliation(s)
- Ming Gao
- Department of OncologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
- Gene Hospital of Henan Province; Precision Medicine CenterThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
| | - Haiyu Wang
- Gene Hospital of Henan Province; Precision Medicine CenterThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
- Department of Infectious DiseasesThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
| | - Hong Luo
- Guangshan County People's HospitalGuangshan CountyXinyang465450China
| | - Ying Sun
- Gene Hospital of Henan Province; Precision Medicine CenterThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
- Department of Infectious DiseasesThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
| | - Ling Wang
- Department of Clinical LaboratoryHenan Provincial Chest HospitalZhengzhou450008China
| | - Suying Ding
- Health Management CenterThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
| | - Hongyan Ren
- Shanghai Mobio Biomedical Technology Co., Ltd.Shanghai201111China
| | - Jiaqi Gang
- Xiuwu County People's HospitalXiuwu CountyJiaozuo454350China
| | - Benchen Rao
- Gene Hospital of Henan Province; Precision Medicine CenterThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
- Department of Infectious DiseasesThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
| | - Shanshuo Liu
- Gene Hospital of Henan Province; Precision Medicine CenterThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
- Department of Infectious DiseasesThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
| | - Xuemei Wang
- Gene Hospital of Henan Province; Precision Medicine CenterThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
- Department of Infectious DiseasesThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
| | - Xinxin Gao
- Health Management CenterThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
| | - Mengyi Li
- Department of OncologyZhengzhou First People's HospitalZhengzhou450004China
| | - Yawen Zou
- Gene Hospital of Henan Province; Precision Medicine CenterThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
- Department of Infectious DiseasesThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
| | - Chao Liu
- Shanghai Mobio Biomedical Technology Co., Ltd.Shanghai201111China
| | - Chengyu Yuan
- Guangshan County People's HospitalGuangshan CountyXinyang465450China
| | - Jiarui Sun
- Shanghai Mobio Biomedical Technology Co., Ltd.Shanghai201111China
| | - Guangying Cui
- Gene Hospital of Henan Province; Precision Medicine CenterThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
- Department of Infectious DiseasesThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
| | - Zhigang Ren
- Gene Hospital of Henan Province; Precision Medicine CenterThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
- Department of Infectious DiseasesThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou450052China
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133
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Wang X, Xu G, Liu X, Liu Y, Zhang S, Zhang Z. Multiomics: unraveling the panoramic landscapes of SARS-CoV-2 infection. Cell Mol Immunol 2021; 18:2313-2324. [PMID: 34471261 PMCID: PMC8408367 DOI: 10.1038/s41423-021-00754-0] [Citation(s) in RCA: 24] [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: 04/28/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
In response to emerging infectious diseases, such as the recent pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it is critical to quickly identify and understand responsible pathogens, risk factors, host immune responses, and pathogenic mechanisms at both the molecular and cellular levels. The recent development of multiomic technologies, including genomics, proteomics, metabolomics, and single-cell transcriptomics, has enabled a fast and panoramic grasp of the pathogen and the disease. Here, we systematically reviewed the major advances in the virology, immunology, and pathogenic mechanisms of SARS-CoV-2 infection that have been achieved via multiomic technologies. Based on well-established cohorts, omics-based methods can greatly enhance the mechanistic understanding of diseases, contributing to the development of new diagnostics, drugs, and vaccines for emerging infectious diseases, such as COVID-19.
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Affiliation(s)
- Xin Wang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Gang Xu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Xiaoju Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Yang Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.
- Shenzhen Research Center for Communicable Disease Diagnosis and Treatment of Chinese Academy of Medical Science, Shenzhen, Guangdong Province, China.
- Guangdong Key Laboratory for Anti-infection Drug Quality Evaluation, Shenzhen, Guangdong Province, China.
- Shenzhen Bay Laboratory, Shenzhen, Guangdong Province, China.
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134
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Abstract
High expression of the transmembrane protein angiotensin I converting enzyme 2 (ACE2), more than 100-times higher as in the lung, and transmembrane serine protease 2 (TMPRSS2) in the gastrointestinal tract leads to infection with SARS-CoV-2. According to meta-analysis data, 9.8–20% of COVID-19 patients experience gastrointestinal symptoms, where diarrhoea is the most frequent, and about 50% shed viruses with high titre through their faeces, where a first faecal transmission was reported. Furthermore, gut inflammation, intestinal damage, and weakening of the gut mucosal integrity that leads to increased permeability has been shown in different studies for COVID-19 patients. This can lead to increased inflammation and bacteraemia. Low mucosal integrity combined with low intestinal damage is a good predictor for disease progression and submission to the intensive care unit (ICU). Several pilot studies have shown that the gut microbiome of COVID-19 patients is changed, microbial richness and diversity were lower, and opportunistic pathogens that can cause bacteraemia were enriched compared to a healthy control group. In a large proportion of these patients, dysbiosis was not resolved at discharge from the hospital and one study showed dysbiosis is still present after 3 months post COVID-19. Consequently, there might be a link between dysbiosis of the gut microbiome in COVID-19 patients and chronic COVID-19 syndrome (CCS). Various clinical trials are investigating the benefit of probiotics for acute COVID-19 patients, the majority of which have not reported results yet. However, two clinical trials have shown that a certain combination of probiotics is beneficial and safe for acute COVID-19 patients. Mortality was 11% for the probiotic treatment group, and 22% for the control group. Furthermore, for the probiotic group, symptoms cleared faster, and an 8-fold decreased risk of developing a respiratory failure was calculated. In conclusion, evidence is arising that inflammation, increased permeability, and microbiome dysbiosis in the gut occur in COVID-19 patients and thus provide new targets for adjuvant treatments of acute and chronic COVID-19. More research in this area is needed.
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135
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Zuo T, Wu X, Wen W, Lan P. Gut Microbiome Alterations in COVID-19. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:679-688. [PMID: 34560321 PMCID: PMC8478109 DOI: 10.1016/j.gpb.2021.09.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/09/2021] [Accepted: 09/14/2021] [Indexed: 12/20/2022]
Abstract
Since the outset of the coronavirus disease 2019 (COVID-19) pandemic, the gut microbiome in COVID-19 has garnered substantial interest, given its significant roles in human health and pathophysiology. Accumulating evidence is unveiling that the gut microbiome is broadly altered in COVID-19, including the bacterial microbiome, mycobiome, and virome. Overall, the gut microbial ecological network is significantly weakened and becomes sparse in patients with COVID-19, together with a decrease in gut microbiome diversity. Beyond the existence of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), the gut microbiome of patients with COVID-19 is also characterized by enrichment of opportunistic bacteria, fungi, and eukaryotic viruses, which are also associated with disease severity and presentation. Meanwhile, a multitude of symbiotic bacteria and bacteriophages are decreased in abundance in patients with COVID-19. Such gut microbiome features persist in a significant subset of patients with COVID-19 even after disease resolution, coinciding with ‘long COVID’ (also known as post-acute sequelae of COVID-19). The broadly-altered gut microbiome is largely a consequence of SARS-CoV-2infection and its downstream detrimental effects on the systemic host immunity and the gut milieu. The impaired host immunity and distorted gut microbial ecology, particularly loss of low-abundance beneficial bacteria and blooms of opportunistic fungi including Candida, may hinder the reassembly of the gut microbiome post COVID-19. Future investigation is necessary to fully understand the role of the gut microbiome in host immunity against SARS-CoV-2 infection, as well as the long-term effect of COVID-19 on the gut microbiome in relation to the host health after the pandemic.
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Affiliation(s)
- Tao Zuo
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510655, China; Center for Fecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510655, China.
| | - Xiaojian Wu
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510655, China; Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510655, China.
| | - Weiping Wen
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510080, China; Guangzhou Key Laboratory of Otorhinolaryngology, Guangzhou 510080, China; Department of Otorhinolaryngology, Head and Neck Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510655, China.
| | - Ping Lan
- Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510655, China; Center for Fecal Microbiota Transplantation Research, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510655, China; Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University, Guangzhou 510655, China.
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136
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Overview on the Prevalence of Fungal Infections, Immune Response, and Microbiome Role in COVID-19 Patients. J Fungi (Basel) 2021; 7:jof7090720. [PMID: 34575758 PMCID: PMC8466761 DOI: 10.3390/jof7090720] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 01/08/2023] Open
Abstract
Patients with severe COVID-19, such as individuals in intensive care units (ICU), are exceptionally susceptible to bacterial and fungal infections. The most prevalent fungal infections are aspergillosis and candidemia. Nonetheless, other fungal species (for instance, Histoplasma spp., Rhizopus spp., Mucor spp., Cryptococcus spp.) have recently been increasingly linked to opportunistic fungal diseases in COVID-19 patients. These fungal co-infections are described with rising incidence, severe illness, and death that is associated with host immune response. Awareness of the high risks of the occurrence of fungal co-infections is crucial to downgrade any arrear in diagnosis and treatment to support the prevention of severe illness and death directly related to these infections. This review analyses the fungal infections, treatments, outcome, and immune response, considering the possible role of the microbiome in these patients. The search was performed in Medline (PubMed), using the words "fungal infections COVID-19", between 2020-2021.
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137
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Meng Z, Guo S, Zhou Y, Li M, Wang M, Ying B. Applications of laboratory findings in the prevention, diagnosis, treatment, and monitoring of COVID-19. Signal Transduct Target Ther 2021; 6:316. [PMID: 34433805 PMCID: PMC8386162 DOI: 10.1038/s41392-021-00731-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 07/21/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
The worldwide pandemic of coronavirus disease 2019 (COVID-19) presents us with a serious public health crisis. To combat the virus and slow its spread, wider testing is essential. There is a need for more sensitive, specific, and convenient detection methods of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Advanced detection can greatly improve the ability and accuracy of the clinical diagnosis of COVID-19, which is conducive to the early suitable treatment and supports precise prophylaxis. In this article, we combine and present the latest laboratory diagnostic technologies and methods for SARS-CoV-2 to identify the technical characteristics, considerations, biosafety requirements, common problems with testing and interpretation of results, and coping strategies of commonly used testing methods. We highlight the gaps in current diagnostic capacity and propose potential solutions to provide cutting-edge technical support to achieve a more precise diagnosis, treatment, and prevention of COVID-19 and to overcome the difficulties with the normalization of epidemic prevention and control.
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Affiliation(s)
- Zirui Meng
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Shuo Guo
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yanbing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Mengjiao Li
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
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138
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Effects of hyperventilation with face mask on brain network in patients with epilepsy. Epilepsy Res 2021; 176:106741. [PMID: 34418857 DOI: 10.1016/j.eplepsyres.2021.106741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/20/2021] [Accepted: 08/12/2021] [Indexed: 12/28/2022]
Abstract
OBJECTIVES During the ongoing pandemic of COVID-19, wearing face masks was recommended, including patients with epilepsy doing the hyperventilation (HV) test during electroencephalogram (EEG) examination somewhere. However, evidence was still limited about the effect of HV with face mask on cortical excitability of patients with epilepsy. The motivation of this work is to make use of the graph theory of EEG to characterize the cortical excitability of patients with epilepsy when they did HV under the condition wearing a surgical face mask. METHODS We recruited 19 patients with epilepsy and 17 normal controls. All of participants completed two HV experiments, including HV with face mask (HV+) and HV without a mask (HV). The interval was 30 min and the sequence was random. Each experiment consisted of three segments: resting EEG, EEG of HV, and EEG of post-HV. EEG were recorded successively during each experiment. Participants were asked to evaluate the discomfort degree using a questionnaire when every HV is completed. RESULTS All of the participants felt more uncomfortable after HV + . Moreover, not only HV decreased small-worldness index in patients with epilepsy, but also HV + significantly increased the clustering coefficient in patients with epilepsy. Importantly, the three-way of Mask*HV*Epilepsy showed interaction in the clustering coefficient in the delta band, as well as in the path length and the small-worldness index in the theta band. CONCLUSIONS The results of this study indicated that patients with epilepsy showed the increased excitability of brain network during HV + . We should pay more attention to the adverse effect on brain network excitability caused by HV + in patients with epilepsy. In the clinical practice under the COVID-19 pandemic, it is important that the wearing face mask remain cautious for the individuals with epilepsy when they carried out HV behavior such as exercise (e.g., running, etc.).
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139
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Abstract
Gut microbiota has emerged as a major metabolically active organ with critical functions in both health and disease. The trillions of microorganisms hosted by the gastrointestinal tract are involved in numerous physiological and metabolic processes including modulation of appetite and regulation of energy in the host spanning from periphery to the brain. Indeed, bacteria and their metabolic byproducts are working in concert with the host chemosensory signaling pathways to affect both short- and long-term ingestive behavior. Sensing of nutrients and taste by specialized G protein-coupled receptor cells is important in transmitting food-related signals, optimizing nutrition as well as in prevention and treatment of several diseases, notably obesity, diabetes and associated metabolic disorders. Further, bacteria metabolites interact with specialized receptors cells expressed by gut epithelium leading to taste and appetite response changes to nutrients. This review describes recent advances on the role of gut bacteria in taste perception and functions. It further discusses how intestinal dysbiosis characteristic of several pathological conditions may alter and modulate taste preference and food consumption via changes in taste receptor expression.
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140
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Gray N, Lawler NG, Zeng AX, Ryan M, Bong SH, Boughton BA, Bizkarguenaga M, Bruzzone C, Embade N, Wist J, Holmes E, Millet O, Nicholson JK, Whiley L. Diagnostic Potential of the Plasma Lipidome in Infectious Disease: Application to Acute SARS-CoV-2 Infection. Metabolites 2021; 11:467. [PMID: 34357361 PMCID: PMC8306636 DOI: 10.3390/metabo11070467] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023] Open
Abstract
Improved methods are required for investigating the systemic metabolic effects of SARS-CoV-2 infection and patient stratification for precision treatment. We aimed to develop an effective method using lipid profiles for discriminating between SARS-CoV-2 infection, healthy controls, and non-SARS-CoV-2 respiratory infections. Targeted liquid chromatography-mass spectrometry lipid profiling was performed on discovery (20 SARS-CoV-2-positive; 37 healthy controls; 22 COVID-19 symptoms but SARS-CoV-2negative) and validation (312 SARS-CoV-2-positive; 100 healthy controls) cohorts. Orthogonal projection to latent structure-discriminant analysis (OPLS-DA) and Kruskal-Wallis tests were applied to establish discriminant lipids, significance, and effect size, followed by logistic regression to evaluate classification performance. OPLS-DA reported separation of SARS-CoV-2 infection from healthy controls in the discovery cohort, with an area under the curve (AUC) of 1.000. A refined panel of discriminant features consisted of six lipids from different subclasses (PE, PC, LPC, HCER, CER, and DCER). Logistic regression in the discovery cohort returned a training ROC AUC of 1.000 (sensitivity = 1.000, specificity = 1.000) and a test ROC AUC of 1.000. The validation cohort produced a training ROC AUC of 0.977 (sensitivity = 0.855, specificity = 0.948) and a test ROC AUC of 0.978 (sensitivity = 0.948, specificity = 0.922). The lipid panel was also able to differentiate SARS-CoV-2-positive individuals from SARS-CoV-2-negative individuals with COVID-19-like symptoms (specificity = 0.818). Lipid profiling and multivariate modelling revealed a signature offering mechanistic insights into SARS-CoV-2, with strong predictive power, and the potential to facilitate effective diagnosis and clinical management.
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Affiliation(s)
- Nicola Gray
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
- Centre for Computational and Systems Medicine, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
| | - Nathan G. Lawler
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
- Centre for Computational and Systems Medicine, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
| | - Annie Xu Zeng
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
| | - Monique Ryan
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
| | - Sze How Bong
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
| | - Berin A. Boughton
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
- Centre for Computational and Systems Medicine, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
| | - Maider Bizkarguenaga
- Centro de Investigación Cooperativa en Biociencias—CIC bioGUNE, Precision Medicine and Metabolism Laboratory, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain; (M.B.); (C.B.); (N.E.)
| | - Chiara Bruzzone
- Centro de Investigación Cooperativa en Biociencias—CIC bioGUNE, Precision Medicine and Metabolism Laboratory, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain; (M.B.); (C.B.); (N.E.)
| | - Nieves Embade
- Centro de Investigación Cooperativa en Biociencias—CIC bioGUNE, Precision Medicine and Metabolism Laboratory, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain; (M.B.); (C.B.); (N.E.)
| | - Julien Wist
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
- Chemistry Department, Universidad del Valle, Cali 76001, Colombia
| | - Elaine Holmes
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
- Centre for Computational and Systems Medicine, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, UK
| | - Oscar Millet
- Centro de Investigación Cooperativa en Biociencias—CIC bioGUNE, Precision Medicine and Metabolism Laboratory, Basque Research and Technology Alliance, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain; (M.B.); (C.B.); (N.E.)
| | - Jeremy K. Nicholson
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
- Centre for Computational and Systems Medicine, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
- Institute of Global Health Innovation, Faculty Building South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| | - Luke Whiley
- Australian National Phenome Centre, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia; (N.G.); (N.G.L.); (A.X.Z.); (M.R.); (S.H.B.); (B.A.B.); (J.W.); (E.H.)
- Centre for Computational and Systems Medicine, Health Futures Institute, Harry Perkins Institute, Murdoch University, 5 Robin Warren Drive, Perth, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
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Association between the nasopharyngeal microbiome and metabolome in patients with COVID-19. Synth Syst Biotechnol 2021; 6:135-143. [PMID: 34151035 PMCID: PMC8200311 DOI: 10.1016/j.synbio.2021.06.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
SARS-CoV-2, the causative agent for COVID-19, infect human mainly via respiratory tract, which is heavily inhabited by local microbiota. However, the interaction between SARS-CoV-2 and nasopharyngeal microbiota, and the association with metabolome has not been well characterized. Here, metabolomic analysis of blood, urine, and nasopharyngeal swabs from a group of COVID-19 and non-COVID-19 patients, and metagenomic analysis of pharyngeal samples were used to identify the key features of COVID-19. Results showed lactic acid, l-proline, and chlorogenic acid methyl ester (CME) were significantly reduced in the sera of COVID-19 patients compared with non-COVID-19 ones. Nasopharyngeal commensal bacteria including Gemella morbillorum, Gemella haemolysans and Leptotrichia hofstadii were notably depleted in the pharynges of COVID-19 patients, while Prevotella histicola, Streptococcus sanguinis, and Veillonella dispar were relatively increased. The abundance of G. haemolysans and L. hofstadii were significantly positively associated with serum CME, which might be an anti-SARS-CoV-2 bacterial metabolite. This study provides important information to explore the linkage between nasopharyngeal microbiota and disease susceptibility. The findings were based on a very limited number of patients enrolled in this study; a larger size of cohort will be appreciated for further investigation.
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