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Wahl A, Yao W, Liao B, Chateau M, Richardson C, Ling L, Franks A, Senthil K, Doyon G, Li F, Frost J, Whitehurst CB, Pagano JS, Fletcher CA, Azcarate-Peril MA, Hudgens MG, Rogala AR, Tucker JD, McGowan I, Sartor RB, Garcia JV. A germ-free humanized mouse model shows the contribution of resident microbiota to human-specific pathogen infection. Nat Biotechnol 2024; 42:905-915. [PMID: 37563299 PMCID: PMC11073568 DOI: 10.1038/s41587-023-01906-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 07/10/2023] [Indexed: 08/12/2023]
Abstract
Germ-free (GF) mice, which are depleted of their resident microbiota, are the gold standard for exploring the role of the microbiome in health and disease; however, they are of limited value in the study of human-specific pathogens because they do not support their replication. Here, we develop GF mice systemically reconstituted with human immune cells and use them to evaluate the role of the resident microbiome in the acquisition, replication and pathogenesis of two human-specific pathogens, Epstein-Barr virus (EBV) and human immunodeficiency virus (HIV). Comparison with conventional (CV) humanized mice showed that resident microbiota enhance the establishment of EBV infection and EBV-induced tumorigenesis and increase mucosal HIV acquisition and replication. HIV RNA levels were higher in plasma and tissues of CV humanized mice compared with GF humanized mice. The frequency of CCR5+ CD4+ T cells throughout the intestine was also higher in CV humanized mice, indicating that resident microbiota govern levels of HIV target cells. Thus, resident microbiota promote the acquisition and pathogenesis of two clinically relevant human-specific pathogens.
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Affiliation(s)
- Angela Wahl
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Wenbo Yao
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Baolin Liao
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Morgan Chateau
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cara Richardson
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lijun Ling
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Adrienne Franks
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Krithika Senthil
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Genevieve Doyon
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Fengling Li
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Josh Frost
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Comparative Medicine, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christopher B Whitehurst
- Department of Pathology, Microbiology, and Immunology, New York Medical College, Valhalla, NY, USA
| | - Joseph S Pagano
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Craig A Fletcher
- Division of Comparative Medicine, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - M Andrea Azcarate-Peril
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- UNC Microbiome Core, University of North Carolina, Chapel Hill, NC, USA
| | - Michael G Hudgens
- Department of Biostatistics, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Allison R Rogala
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Comparative Medicine, Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joseph D Tucker
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Ian McGowan
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
- Orion Biotechnology, Ottawa, Ontario, Canada
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Gastroenterology and Hepatology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J Victor Garcia
- International Center for the Advancement of Translational Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for AIDS Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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Germ-free humanized mice reveal a crucial role for the gut microbiota in HIV and EBV pathogenesis. Nat Biotechnol 2024; 42:854-855. [PMID: 37568032 DOI: 10.1038/s41587-023-01908-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
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3
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Yuan F, Yang L, Hsiao SH, Herndon NL, Gaulke CA, Fang Y. A neonatal piglet model reveals interactions between nasal microbiota and influenza A virus pathogenesis. Virology 2024; 592:109996. [PMID: 38301448 DOI: 10.1016/j.virol.2024.109996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/17/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024]
Abstract
While vaccination and therapeutics for prevention/treatment of influenza are available, new strategies are needed to combat influenza disease in susceptible populations, particularly young children and newborns. Host associated microbiota play an important role in modulating the virulence of numerous pathogens, including the influenza A virus. In this study, we examined microbiome-influenza interactions in a neonatal piglet model system. The nasal microbiome of newborn piglets was longitudinally sampled before and after intranasal infection with recombinant viruses expressing hemagglutinins (HAs) derived from distinct zoonotic H1 subtypes. We found that viruses expressing different parental HAs manifested unique patterns of pathogenicity, and varied impacts on microbial community diversity. Despite these virus specific differences, a consistent microbial signature of viral infection was detected. Our results indicate that influenza A virus infection associates with the restructuring of nasal microbiome and such shifts in microbial diversity may contribute to outcomes of viral infection in neonatal piglets.
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Affiliation(s)
- Fangfeng Yuan
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA
| | - Lufan Yang
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA
| | - Shih-Hsuan Hsiao
- Veterinary Diagnostic Laboratory, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Nicole L Herndon
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Christopher A Gaulke
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA; Personalized Nutrition Initiative, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA; Cancer Center at Illinois, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA.
| | - Ying Fang
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA.
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Tchoupou Saha OLF, Dubourg G, Yacouba A, Tola R, Raoult D, Lagier JC. Description of nasopharyngeal bacterial pathogens associated with different SARS-CoV-2 variants. Microb Pathog 2024; 188:106561. [PMID: 38307371 DOI: 10.1016/j.micpath.2024.106561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024]
Abstract
The emergence of the coronavirus pandemic facilitated the acquisition of mutations in the SARS-CoV-2 genome, resulting in the appearance of new variants over the past three years. We previously identified several taxa associated with the clinical outcome of COVID-19 disease in a retrospective study involving 120 patients (infected patients and negative subjects). However, little is known about whether the different variants could influence variations in the composition of the nasopharyngeal microbiota. In this study, we used multiplex pathogen-specific PCR to analyse the presence of nasopharyngeal bacterial pathogens from 400 SARS-CoV-2 positive patients (equally distributed in the four SARS-CoV-2 variants studied: B.1.1.7 (Alpha), B.1 0.617.2 (Delta), B.1.160 (Marseille-4), and B.1.1.529 (omicron)). We then compared them to 400 patients who tested negative for all respiratory viruses tested in this study, including SARS-CoV-2. We first observed an enrichment of Staphylococcus aureus (P ≤ .05) and Corynebacterium propinquum (P ≤ .05) in COVID-19-positive patients, regardless of the variant, compared to negative subjects. We specifically highlighted a significantly higher frequency of S. aureus (P ≤ .0001), C. propinquum (P ≤ .0001), and Klebsiella pneumoniae (P ≤ .0001), in patients infected with the omicron variant, whereas that of Haemophilus influenzae was higher in patients infected with Marseille-4 (P ≤ .001) and Alpha (P ≤ .01) variants. Our results suggest that the nasopharyngeal bacterial pathogens have their own specificity according to the SARS-CoV-2 variant and independently of the season. Additional studies are needed to determine the role of these pathogens in the evolution of the clinical outcome of patients.
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Affiliation(s)
- Ornella La Fortune Tchoupou Saha
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Grégory Dubourg
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France.
| | - Abdourahamane Yacouba
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | | | - Didier Raoult
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Jean-Christophe Lagier
- Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), AP-HM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France.
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5
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Wang X, Sun L, Li P, Zhang S. Changes in the gut microbiome can predict and decrease Epstein-Barr virus infection risk in children after liver transplantation. Transpl Infect Dis 2023; 25:e14114. [PMID: 37639316 DOI: 10.1111/tid.14114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/02/2023] [Accepted: 07/27/2023] [Indexed: 08/29/2023]
Abstract
OBJECTIVE Primary Epstein-Barr virus (EBV) infection is observed in 60% of children during the first year after liver transplantation as usage of imm-unosuppressant. Finding predictive indicators of EBV infection is important to reduce the morbidity and mortality of EBV infection-related diseases by suggesting a dose reduction of immunosuppressant. METHODS We compared and analysed the gut microbiome of EBV-infected children with an asymptomatic virus-carrying status and EBV-uninfected children after liver transplantation using high-throughput sequencing. RESULTS Significant differences in gut microbiome composition in two groups were detected. In detail, Firmicutes and Lactobacillus were increased in EBV-infected group, while Clostridium was increased in EBV-uninfected group. Furthermore, CD4 percentage in T cells of blood showed a significant positive correlation with the content of Clostridium sp. CAG: 127 in EBV-uninfected group. CONCLUSION Changes in the gut microbiome could predict and decrease the EBV infection risk of children after liver transplantation.
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Affiliation(s)
- Xu Wang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, P. R. China
| | - Liying Sun
- Department of Liver Transplantation, Beijing Friendship Hospital, Capital Medical University, Beijing, P. R. China
| | - Peng Li
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, P. R. China
| | - Shutian Zhang
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, P. R. China
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6
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Husso A, Pessa-Morikawa T, Koistinen VM, Kärkkäinen O, Kwon HN, Lahti L, Iivanainen A, Hanhineva K, Niku M. Impacts of maternal microbiota and microbial metabolites on fetal intestine, brain, and placenta. BMC Biol 2023; 21:207. [PMID: 37794486 PMCID: PMC10552303 DOI: 10.1186/s12915-023-01709-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 09/21/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND The maternal microbiota modulates fetal development, but the mechanisms of these earliest host-microbe interactions are unclear. To investigate the developmental impacts of maternal microbial metabolites, we compared full-term fetuses from germ-free and specific pathogen-free mouse dams by gene expression profiling and non-targeted metabolomics. RESULTS In the fetal intestine, critical genes mediating host-microbe interactions, innate immunity, and epithelial barrier were differentially expressed. Interferon and inflammatory signaling genes were downregulated in the intestines and brains of the fetuses from germ-free dams. The expression of genes related to neural system development and function, translation and RNA metabolism, and regulation of energy metabolism were significantly affected. The gene coding for the insulin-degrading enzyme (Ide) was most significantly downregulated in all tissues. In the placenta, genes coding for prolactin and other essential regulators of pregnancy were downregulated in germ-free dams. These impacts on gene expression were strongly associated with microbially modulated metabolite concentrations in the fetal tissues. Aryl sulfates and other aryl hydrocarbon receptor ligands, the trimethylated compounds TMAO and 5-AVAB, Glu-Trp and other dipeptides, fatty acid derivatives, and the tRNA nucleobase queuine were among the compounds strongly associated with gene expression differences. A sex difference was observed in the fetal responses to maternal microbial status: more genes were differentially regulated in male fetuses than in females. CONCLUSIONS The maternal microbiota has a major impact on the developing fetus, with male fetuses potentially more susceptible to microbial modulation. The expression of genes important for the immune system, neurophysiology, translation, and energy metabolism are strongly affected by the maternal microbial status already before birth. These impacts are associated with microbially modulated metabolites. We identified several microbial metabolites which have not been previously observed in this context. Many of the potentially important metabolites remain to be identified.
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Affiliation(s)
- Aleksi Husso
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Tiina Pessa-Morikawa
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Ville Mikael Koistinen
- Food Sciences Unit, Department of Life Technologies, University of Turku, Turku, Finland
- Institute of Public Health and Clinical Nutrition, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Afekta Technologies Ltd., Kuopio, Finland
| | - Olli Kärkkäinen
- Afekta Technologies Ltd., Kuopio, Finland
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Hyuk Nam Kwon
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- School of Biological Sciences and Basic-Clinical Convergence Research Institute, University of Ulsan, Ulsan, 44610, South Korea
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Antti Iivanainen
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Kati Hanhineva
- Food Sciences Unit, Department of Life Technologies, University of Turku, Turku, Finland
- Institute of Public Health and Clinical Nutrition, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Afekta Technologies Ltd., Kuopio, Finland
| | - Mikael Niku
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
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Zeng Q, Zeng R, Ye J. Alteration of the oral and gut microbiota in patients with Kawasaki disease. PeerJ 2023; 11:e15662. [PMID: 37456866 PMCID: PMC10340105 DOI: 10.7717/peerj.15662] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/07/2023] [Indexed: 07/18/2023] Open
Abstract
Background Kawasaki disease (KD) is a multi-systemic vasculitis that primarily affects children and has an unknown cause. Although an increasing number of studies linking the gut microbiota with KD, the unchallengeable etiology of KD is not available. Methods Here, we obtained fecal and oral samples from KD patients and healthy controls, and then we use high-throughput sequencing to examine the diversity and composition of microbiota. Results Results showed that both in the gut and oral microbiota, the diversity of KD patients was significantly lower than that of the healthy controls. In the gut microbiota, a higher abundance of Enterococcus (40.12% vs less than 0.1%), Bifidobacterium (20.71% vs 3.06%), Escherichia-Shigella (17.56% vs 0.61%), Streptococcus (5.97% vs 0.11%) and Blautia (4.69% vs 0.1%) was observed in the KD patients, and enrichment of Enterococcus in the patients was observed. In terms of oral microbiota, the prevalence of Streptococcus (21.99% vs 0.1%), Rothia (3.02% vs 0.1%), and Escherichia-Shigella (0.68% vs 0.0%) were significantly higher in the KD patients, with the enrichment of Streptococcus and Escherichia-Shigella. Additionally, significant differences in microbial community function between KD patients and healthy controls in the fecal samples were also observed, which will affect the colonization and reproduction of gut microbiota. Conclusions These results suggested that the dysbiosis of gut and oral microbiota are both related to KD pathogenesis, of which, the prevalence of Enterococcus in the gut and higher abundance of Streptococcus and Escherichia-Shigella in the oral cavity will be a potential biomarker of the KD. Overall, this study not only confirms that the disturbance of gut microbiota is a causative trigger of KD but also provides new insight into the oral microbiota involved in KD pathogenesis.
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Affiliation(s)
- Qinghuang Zeng
- School of Clinical Medicine, Fujian Medical University, Fuzhou, China
- Affiliated Hospital of Putian University, Putian, Fujian, China
| | - Renhe Zeng
- School of Clinical Medicine, Fujian Medical University, Fuzhou, China
- Affiliated Hospital of Putian University, Putian, Fujian, China
| | - Jianbin Ye
- School of Basic Medicine Science, Putian University, Putian, China
- School of Pharmarcy, Fujian Medical University, Fuzhou, China
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Durairajan SSK, Singh AK, Saravanan UB, Namachivayam M, Radhakrishnan M, Huang JD, Dhodapkar R, Zhang H. Gastrointestinal Manifestations of SARS-CoV-2: Transmission, Pathogenesis, Immunomodulation, Microflora Dysbiosis, and Clinical Implications. Viruses 2023; 15:1231. [PMID: 37376531 DOI: 10.3390/v15061231] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 06/29/2023] Open
Abstract
The clinical manifestation of COVID-19, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in the respiratory system of humans is widely recognized. There is increasing evidence suggesting that SARS-CoV-2 possesses the capability to invade the gastrointestinal (GI) system, leading to the manifestation of symptoms such as vomiting, diarrhea, abdominal pain, and GI lesions. These symptoms subsequently contribute to the development of gastroenteritis and inflammatory bowel disease (IBD). Nevertheless, the pathophysiological mechanisms linking these GI symptoms to SARS-CoV-2 infection remain unelucidated. During infection, SARS-CoV-2 binds to angiotensin-converting enzyme 2 and other host proteases in the GI tract during the infection, possibly causing GI symptoms by damaging the intestinal barrier and stimulating inflammatory factor production, respectively. The symptoms of COVID-19-induced GI infection and IBD include intestinal inflammation, mucosal hyperpermeability, bacterial overgrowth, dysbiosis, and changes in blood and fecal metabolomics. Deciphering the pathogenesis of COVID-19 and understanding its exacerbation may provide insights into disease prognosis and pave the way for the discovery of potential novel targets for disease prevention or treatment. Besides the usual transmission routes, SARS-CoV-2 can also be transmitted via the feces of an infected person. Hence, it is crucial to implement preventive and control measures in order to mitigate the fecal-to-oral transmission of SARS-CoV-2. Within this context, the identification and diagnosis of GI tract symptoms during these infections assume significance as they facilitate early detection of the disease and the development of targeted therapeutics. The present review discusses the receptors, pathogenesis, and transmission of SARS-CoV-2, with a particular focus on the induction of gut immune responses, the influence of gut microbes, and potential therapeutic targets against COVID-19-induced GI infection and IBD.
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Affiliation(s)
| | - Abhay Kumar Singh
- Department of Microbiology, School of Life Sciences, Central University of Tamil Nadu, Tiruvarur 610005, India
| | - Udhaya Bharathy Saravanan
- Department of Microbiology, School of Life Sciences, Central University of Tamil Nadu, Tiruvarur 610005, India
| | - Mayurikaa Namachivayam
- Department of Microbiology, School of Life Sciences, Central University of Tamil Nadu, Tiruvarur 610005, India
| | - Moorthi Radhakrishnan
- Department of Microbiology, School of Life Sciences, Central University of Tamil Nadu, Tiruvarur 610005, India
| | - Jian-Dong Huang
- Department of Biochemistry, School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong 999077, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Rahul Dhodapkar
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Government of India, Puducherry 605006, India
| | - Hongjie Zhang
- School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China
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9
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Zuckerman NS, Shulman LM. Next-Generation Sequencing in the Study of Infectious Diseases. Infect Dis (Lond) 2023. [DOI: 10.1007/978-1-0716-2463-0_1090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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10
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Yadav A, Pandey R. Viral infectious diseases severity: co-presence of transcriptionally active microbes (TAMs) can play an integral role for disease severity. Front Immunol 2022; 13:1056036. [PMID: 36532032 PMCID: PMC9755851 DOI: 10.3389/fimmu.2022.1056036] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/21/2022] [Indexed: 12/04/2022] Open
Abstract
Humans have been challenged by infectious diseases for all of their recorded history, and are continually being affected even today. Next-generation sequencing (NGS) has enabled identification of, i) culture independent microbes, ii) emerging disease-causing pathogens, and iii) understanding of the genome architecture. This, in turn, has highlighted that pathogen/s are not a monolith, and thereby allowing for the differentiation of the wide-ranging disease symptoms, albeit infected by a primary pathogen. The conventional 'one disease - one pathogen' paradigm has been positively revisited by considering limited yet important evidence of the co-presence of multiple transcriptionally active microbes (TAMs), potential pathogens, in various infectious diseases, including the COVID-19 pandemic. The ubiquitous microbiota presence inside humans gives reason to hypothesize that the microbiome, especially TAMs, contributes to disease etiology. Herein, we discuss current evidence and inferences on the co-infecting microbes particularly in the diseases caused by the RNA viruses - Influenza, Dengue, and the SARS-CoV-2. We have highlighted that the specific alterations in the microbial taxonomic abundances (dysbiosis) is functionally connected to the exposure of primary infecting pathogen/s. The microbial presence is intertwined with the differential host immune response modulating differential disease trajectories. The microbiota-host interactions have been shown to modulate the host immune responses to Influenza and SARS-CoV-2 infection, wherein the active commensal microbes are involved in the generation of virus-specific CD4 and CD8 T-cells following the influenza virus infection. Furthermore, COVID-19 dysbiosis causes an increase in inflammatory cytokines such as IL-6, TNF-α, and IL-1β, which might be one of the important predisposing factors for severe infection. Through this article, we aim to provide a comprehensive view of functional microbiomes that can have a significant regulatory impact on predicting disease severity (mild, moderate and severe), as well as clinical outcome (survival and mortality). This can offer fresh perspectives on the novel microbial biomarkers for stratifying patients for severe disease symptoms, disease prevention and augmenting treatment regimens.
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Affiliation(s)
- Aanchal Yadav
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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11
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Long COVID and the Neuroendocrinology of Microbial Translocation Outside the GI Tract: Some Treatment Strategies. ENDOCRINES 2022. [DOI: 10.3390/endocrines3040058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Similar to previous pandemics, COVID-19 has been succeeded by well-documented post-infectious sequelae, including chronic fatigue, cough, shortness of breath, myalgia, and concentration difficulties, which may last 5 to 12 weeks or longer after the acute phase of illness. Both the psychological stress of SARS-CoV-2 infection and being diagnosed with COVID-19 can upregulate cortisol, a stress hormone that disrupts the efferocytosis effectors, macrophages, and natural killer cells, leading to the excessive accumulation of senescent cells and disruption of biological barriers. This has been well-established in cancer patients who often experience unrelenting fatigue as well as gut and blood–brain barrier dysfunction upon treatment with senescence-inducing radiation or chemotherapy. In our previous research from 2020 and 2021, we linked COVID-19 to myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) via angiotensin II upregulation, premature endothelial senescence, intestinal barrier dysfunction, and microbial translocation from the gastrointestinal tract into the systemic circulation. In 2021 and 2022, these hypotheses were validated and SARS-CoV-2-induced cellular senescence as well as microbial translocation were documented in both acute SARS-CoV-2 infection, long COVID, and ME/CFS, connecting intestinal barrier dysfunction to disabling fatigue and specific infectious events. The purpose of this narrative review is to summarize what is currently known about host immune responses to translocated gut microbes and how these responses relate to fatiguing illnesses, including long COVID. To accomplish this goal, we examine the role of intestinal and blood–brain barriers in long COVID and other illnesses typified by chronic fatigue, with a special emphasis on commensal microbes functioning as viral reservoirs. Furthermore, we discuss the role of SARS-CoV-2/Mycoplasma coinfection in dysfunctional efferocytosis, emphasizing some potential novel treatment strategies, including the use of senotherapeutic drugs, HMGB1 inhibitors, Toll-like receptor 4 (TLR4) blockers, and membrane lipid replacement.
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12
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Wang Z, Guo K, Liu Y, Huang C, Wu M. Dynamic impact of virome on colitis and colorectal cancer: Immunity, inflammation, prevention and treatment. Semin Cancer Biol 2022; 86:943-954. [PMID: 34656791 PMCID: PMC9008076 DOI: 10.1016/j.semcancer.2021.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/20/2021] [Accepted: 10/08/2021] [Indexed: 02/05/2023]
Abstract
The gut microbiome includes a series of microorganism genomes, such as bacteriome, virome, mycobiome, etc. The gut microbiota is critically involved in intestine immunity and diseases, including inflammatory bowel disease (IBD) and colorectal cancer (CRC); however, the underlying mechanism remains incompletely understood. Clarifying the relationship between microbiota and inflammation may profoundly improve our understanding of etiology, disease progression, patient management, and the development of prevention and treatment. In this review, we discuss the latest studies of the influence of enteric viruses (i.e., commensal viruses, pathogenic viruses, and bacteriophages) in the initiation, progression, and complication of colitis and colorectal cancer, and their potential for novel preventative approaches and therapeutic application. We explore the interplay between gut viruses and host immune systems for its effects on the severity of inflammatory diseases and cancer, including both direct and indirect interactions between enteric viruses with other microbes and microbial products. Furthermore, the underlying mechanisms of the virome's roles in gut inflammatory response have been explained to infer potential therapeutic targets with examples in specific clinical trials. Given that very limited literature has thus far discussed these various topics with the gut virome, we believe these extensive analyses may provide insight into the understanding of the molecular pathogenesis of IBD and CRC, which could help add the design of improved therapies for these important human diseases.
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Affiliation(s)
- Zhihan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58202, USA
| | - Kai Guo
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yingying Liu
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58202, USA
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
| | - Min Wu
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58202, USA.
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13
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Clinton NA, Hameed SA, Agyei EK, Jacob JC, Oyebanji VO, Jabea CE. Crosstalk between the Intestinal Virome and Other Components of the Microbiota, and Its Effect on Intestinal Mucosal Response and Diseases. J Immunol Res 2022; 2022:7883945. [PMID: 36203793 PMCID: PMC9532165 DOI: 10.1155/2022/7883945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
In recent years, there has been ample evidence illustrating the effect of microbiota on gut immunity, homeostasis, and disease. Most of these studies have engaged more efforts in understanding the role of the bacteriome in gut mucosal immunity and disease. However, studies on the virome and its influence on gut mucosal immunity and pathology are still at infancy owing to limited metagenomic tools. Nonetheless, the existing studies on the virome have largely been focused on the bacteriophages as these represent the main component of the virome with little information on endogenous retroviruses (ERVs) and eukaryotic viruses. In this review, we describe the gut virome, and its role in gut mucosal response and disease progression. We also explore the crosstalk between the virome and other microorganisms in the gut mucosa and elaborate on how these interactions shape the gut mucosal immunity going from bacteriophages through ERVs to eukaryotic viruses. Finally, we elucidate the potential contribution of this crosstalk in the pathogenesis of inflammatory bowel diseases and colon cancer.
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Affiliation(s)
- Njinju Asaba Clinton
- Health and Empowerment Foundation, Cameroon
- Mbonge District Hospital, Cameroon
- University of Buea, Cameroon
| | | | - Eugene Kusi Agyei
- Faculty of Pharmacy and Pharmaceutical Sciences, Kwame Nkrumah University of Science and Technology, Ghana
| | | | | | - Cyril Ekabe Jabea
- Health and Empowerment Foundation, Cameroon
- Mbonge District Hospital, Cameroon
- University of Buea, Cameroon
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14
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Malik J, Ahmed S, Yaseen Z, Alanazi M, Alharby TN, Alshammari HA, Anwar S. Association of SARS-CoV-2 and Polypharmacy with Gut-Lung Axis: From Pathogenesis to Treatment. ACS OMEGA 2022; 7:33651-33665. [PMID: 36164411 PMCID: PMC9491241 DOI: 10.1021/acsomega.2c02524] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 08/29/2022] [Indexed: 06/12/2023]
Abstract
SARS-CoV-2 is a novel infectious contagion leading to COVID-19 disease. The virus has affected the lives of millions of people across the globe with a high mortality rate. It predominantly affects the lung (respiratory system), but it also affects other organs, including the cardiovascular, psychological, and gastrointestinal (GIT) systems. Moreover, elderly and comorbid patients with compromised organ functioning and pre-existing polypharmacy have worsened COVID-19-associated complications. Microbiota (MB) of the lung plays an important role in developing COVID-19. The extent of damage mainly depends on the predominance of opportunistic pathogens and, inversely, with the predominance of advantageous commensals. Changes in the gut MB are associated with a bidirectional shift in the interaction among the gut with a number of vital human organs, which leads to severe disease symptoms. This review focuses on dysbiosis in the gut-lung axis, COVID-19-induced worsening of comorbidities, and the influence of polypharmacy on MB.
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Affiliation(s)
- Jonaid
Ahmad Malik
- Department
of Pharmacology and Toxicology, National
Institute of Pharmaceutical Education and Research, Guwahati, Assam 781101, India
- Department
of Biomedical Engineering, Indian Institute
of Technology Rupnagar 140001, India
| | - Sakeel Ahmed
- Department
of Pharmacology and Toxicology, National
Institute of Pharmaceutical Education and Research, Ahmedabad, Gujarat 382355, India
| | - Zahid Yaseen
- Department
of Pharmaceutical Biotechnology, Delhi Pharmaceutical
Sciences and Research University, New Delhi, Delhi 110017, India
| | - Muteb Alanazi
- Department
of Clinical Pharmacy, College of Pharmacy, University of Hail, Hail 81422, Saudi Arabia
| | - Tareq Nafea Alharby
- Department
of Clinical Pharmacy, College of Pharmacy, University of Hail, Hail 81422, Saudi Arabia
| | | | - Sirajudheen Anwar
- Department
of Pharmacology and Toxicology, College of Pharmacy, University of Hail, Hail 81422, Saudi Arabia
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15
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Positive Effects of α-Lactalbumin in the Management of Symptoms of Polycystic Ovary Syndrome. Nutrients 2022; 14:nu14153220. [PMID: 35956395 PMCID: PMC9370664 DOI: 10.3390/nu14153220] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/18/2022] Open
Abstract
To date, the involvement of α-Lactalbumin (α-LA) in the management of polycystic ovary syndrome (PCOS) refers to its ability to improve intestinal absorption of natural molecules like inositols, overcoming the inositol resistance. However, due to its own aminoacidic building blocks, α-LA is involved in various biological processes that can open new additional applications. A great portion of women with PCOS exhibit gastrointestinal dysbiosis, which is in turn one of the triggering mechanisms of the syndrome. Due to its prebiotic effect, α-LA can recover dysbiosis, also improving the insulin resistance, obesity and intestinal inflammation frequently associated with PCOS. Further observations suggest that altered gut microbiota negatively influence mental wellbeing. Depressive mood and low serotonin levels are indeed common features of women with PCOS. Thanks to its content of tryptophan, which is the precursor of serotonin, and considering the strict link between gut and brain, using α-LA contributes to preserving mental well-being by maintaining high levels of serotonin. In addition, considering women with PCOS seeking pregnancy, both altered microbiota and serotonin levels can induce later consequences in the offspring. Therefore, a deeper knowledge of potential applications of α-LA is required to transition to preclinical and clinical studies extending its therapeutic advantages in PCOS.
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16
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Onisiforou A, Spyrou GM. Immunomodulatory effects of microbiota-derived metabolites at the crossroad of neurodegenerative diseases and viral infection: network-based bioinformatics insights. Front Immunol 2022; 13:843128. [PMID: 35928817 PMCID: PMC9344014 DOI: 10.3389/fimmu.2022.843128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Bidirectional cross-talk between commensal microbiota and the immune system is essential for the regulation of immune responses and the formation of immunological memory. Perturbations of microbiome-immune system interactions can lead to dysregulated immune responses against invading pathogens and/or to the loss of self-tolerance, leading to systemic inflammation and genesis of several immune-mediated pathologies, including neurodegeneration. In this paper, we first investigated the contribution of the immunomodulatory effects of microbiota (bacteria and fungi) in shaping immune responses and influencing the formation of immunological memory cells using a network-based bioinformatics approach. In addition, we investigated the possible role of microbiota-host-immune system interactions and of microbiota-virus interactions in a group of neurodegenerative diseases (NDs): Amyotrophic Lateral Sclerosis (ALS), Multiple Sclerosis (MS), Parkinson’s disease (PD) and Alzheimer’s disease (AD). Our analysis highlighted various aspects of the innate and adaptive immune response systems that can be modulated by microbiota, including the activation and maturation of microglia which are implicated in the development of NDs. It also led to the identification of specific microbiota components which might be able to influence immune system processes (ISPs) involved in the pathogenesis of NDs. In addition, it indicated that the impact of microbiota-derived metabolites in influencing disease-associated ISPs, is higher in MS disease, than in AD, PD and ALS suggesting a more important role of microbiota mediated-immune effects in MS.
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17
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Privitera GF, Alaimo S, Ferro A, Pulvirenti A. Virus finding tools: current solutions and limitations. Brief Bioinform 2022; 23:6618234. [PMID: 35753694 DOI: 10.1093/bib/bbac235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/02/2022] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The study of the Human Virome remains challenging nowadays. Viral metagenomics, through high-throughput sequencing data, is the best choice for virus discovery. The metagenomics approach is culture-independent and sequence-independent, helping search for either known or novel viruses. Though it is estimated that more than 40% of the viruses found in metagenomics analysis are not recognizable, we decided to analyze several tools to identify and discover viruses in RNA-seq samples. RESULTS We have analyzed eight Virus Tools for the identification of viruses in RNA-seq data. These tools were compared using a synthetic dataset of 30 viruses and a real one. Our analysis shows that no tool succeeds in recognizing all the viruses in the datasets. So we can conclude that each of these tools has pros and cons, and their choice depends on the application domain. AVAILABILITY Synthetic data used through the review and raw results of their analysis can be found at https://zenodo.org/record/6426147. FASTQ files of real data can be found in GEO (https://www.ncbi.nlm.nih.gov/gds) or ENA (https://www.ebi.ac.uk/ena/browser/home). Raw results of their analysis can be downloaded from https://zenodo.org/record/6425917.
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Affiliation(s)
- Grete Francesca Privitera
- Department of Physics and Astronomy, University of Catania, Viale A. Doria, 6, 95125, Catania, Italy
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dept. of Math. and Comp. Science Viale A. Doria, 6, 95125, Catania, Italy
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dept. of Math. and Comp. Science Viale A. Doria, 6, 95125, Catania, Italy
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dept. of Math. and Comp. Science Viale A. Doria, 6, 95125, Catania, Italy
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18
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Tiamani K, Luo S, Schulz S, Xue J, Costa R, Khan Mirzaei M, Deng L. The role of virome in the gastrointestinal tract and beyond. FEMS Microbiol Rev 2022; 46:6608358. [PMID: 35700129 PMCID: PMC9629487 DOI: 10.1093/femsre/fuac027] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 01/11/2023] Open
Abstract
The human gut virome is comprised of diverse commensal and pathogenic viruses. The colonization by these viruses begins right after birth through vaginal delivery, then continues through breastfeeding, and broader environmental exposure. Their constant interaction with their bacterial hosts in the body shapes not only our microbiomes but us. In addition, these viruses interact with the immune cells, trigger a broad range of immune responses, and influence different metabolic pathways. Besides its key role in regulating the human gut homeostasis, the intestinal virome contributes to disease development in distant organs, both directly and indirectly. In this review, we will describe the changes in the gut virome through life, health, and disease, followed by discussing the interactions between the virome, the microbiome, and the human host as well as providing an overview of their contribution to gut disease and disease of distant organs.
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Affiliation(s)
| | | | - Sarah Schulz
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Jinling Xue
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Rita Costa
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Mohammadali Khan Mirzaei
- Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany,Chair of Microbial Disease Prevention, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Li Deng
- Corresponding author: Institute of Virology, Helmholtz Centre Munich — German Research Centre for Environmental Health, 85764 Neuherberg, Germany; Chair of Prevention of Microbial Diseases, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany. E-mail:
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19
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The relationship among avian influenza, gut microbiota and chicken immunity: An updated overview. Poult Sci 2022; 101:102021. [PMID: 35939896 PMCID: PMC9386105 DOI: 10.1016/j.psj.2022.102021] [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: 01/01/2022] [Revised: 06/16/2022] [Accepted: 06/16/2022] [Indexed: 02/08/2023] Open
Abstract
The alimentary tract in chickens plays a crucial role in immune cell formation and immune challenges, which regulate intestinal flora and sustain extra-intestinal immunity. The interaction between pathogenic microorganisms and the host commensal microbiota as well as the variety and integrity of gut microbiota play a vital role in health and disease conditions. Thus, several studies have highlighted the importance of gut microbiota in developing immunity against viral infections in chickens. The gut microbiota (such as different species of Lactobacillus, Blautia Bifidobacterium, Faecalibacterium, Clostridium XlVa, and members of firmicutes) encounters different pathogens through different mechanisms. The digestive tract is a highly reactive environment, and infectious microorganisms can disturb its homeostasis, resulting in dysbiosis and mucosal infections. Avian influenza viruses (AIV) are highly infectious zoonotic viruses that lead to severe economic losses and pose a threat to the poultry industry worldwide. AIV is a challenging virus that affects gut integrity, disrupts microbial homeostasis and induces inflammatory damage in the intestinal mucosa. H9N2 AIV infection elevates the expression of proinflammatory cytokines, such as interferon (IFN-γ and IFNα) and interleukins (IL-17A and IL-22), and increases the proliferation of members of proteobacteria, particularly Escherichia coli. On the contrary, it decreases the proliferation of certain beneficial bacteria, such as Enterococcus, Lactobacillus and other probiotic microorganisms. In addition, H9N2 AIV decreases the expression of primary gel-forming mucin, endogenous trefoil factor family peptides and tight junction proteins (ZO-1, claudin 3, and occludin), resulting in severe intestinal damage. This review highlights the relationship among AIV, gut microbiota and immunity in chicken.
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20
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Effect of Killed PRRSV Vaccine on Gut Microbiota Diversity in Pigs. Viruses 2022; 14:v14051081. [PMID: 35632822 PMCID: PMC9145812 DOI: 10.3390/v14051081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/05/2022] [Accepted: 05/15/2022] [Indexed: 02/05/2023] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is one of the most economically important pathogens affecting the global swine industry. Vaccination is still a main strategy for PRRSV control; however, host factors associated with vaccine efficacy remain poorly understood. Growing evidence suggests that mucosa-associated microbiomes may play a role in the responses to vaccination. In this study, we investigated the effects of a killed virus vaccine on the gut microbiome diversity in pigs. Fecal microbial communities were longitudinally assessed in three groups of pigs (vaccinated/challenged with PRRSV, unvaccinated/challenged with PRRSV, and unvaccinated/unchallenged) before and after vaccination and after viral challenge. We observed significant interaction effects between viral challenge and vaccination on both taxonomic richness and community diversity of the gut microbiota. While some specific taxonomic alterations appear to be enhanced in vaccinated/challenged pigs, others appeared to be more consistent with the levels in control animals (unvaccinated/unchallenged), indicating that vaccination incompletely protects against viral impacts on the microbiome. The abundances of several microbial taxa were further determined to be correlated with the level of viral load and the amount of PRRSV reactive CD4+ and CD8+ T-cells. This study highlights the potential roles of gut microbiota in the response of pigs to vaccination, which may pave the road for the development of novel strategies to enhance vaccine efficacy.
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21
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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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22
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Tati S, Alisaraie L. Recruitment of dynein and kinesin to viral particles. FASEB J 2022; 36:e22311. [DOI: 10.1096/fj.202101900rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/14/2022] [Accepted: 03/29/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Sayi’Mone Tati
- School of Pharmacy Memorial University of Newfoundland St. John’s Newfoundland Canada
| | - Laleh Alisaraie
- School of Pharmacy Memorial University of Newfoundland St. John’s Newfoundland Canada
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23
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Blanco-Fuertes M, Correa-Fiz F, López-Serrano S, Sibila M, Aragon V. Sow vaccination against virulent Glaesserella parasuis shapes the nasal microbiota of their offspring. Sci Rep 2022; 12:3357. [PMID: 35233006 PMCID: PMC8888576 DOI: 10.1038/s41598-022-07382-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/14/2022] [Indexed: 01/08/2023] Open
Abstract
Glaesserella parasuis is the etiological agent of Glässer's disease, a common pathology in the pork industry with higher prevalence in the postweaning period. Vaccination is one of the strategies to control this disease. Here, we investigated the effect that sow vaccination against virulent strains of G. parasuis had in the nasal microbiota of their offspring. Nasal swabs from fifteen days-old piglets from vaccinated (vs-P, n = 11) and unvaccinated sows (cs-P, n = 11) were obtained and DNA was extracted for 16S amplicon sequencing. Microbiota composition was different, with lower diversity in vs-P, and a strong clustering of the groups in beta diversity analysis. Among the 1509 sequences associated to either study group, all the sequences classified as G. parasuis (10 ASVs) had lower relative abundance in the vs-P group. A list of 32 inferred metabolic pathways were statistically different between groups. A distinctive structure of the two microbial networks was detected, with modules in the cs-P not conserved in the vs-P network. In conclusion, vaccination of the sows had a large effect in the microbiota composition of their offspring that went beyond the effect on the targeted pathogen. The mechanisms underneath these changes may include alteration of the microbiota network due to the elimination of the targeted pathogen and/or immunological changes.
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Affiliation(s)
- Miguel Blanco-Fuertes
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Barcelona, Spain
| | - Florencia Correa-Fiz
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Barcelona, Spain.
| | - Sergi López-Serrano
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Barcelona, Spain
| | - Marina Sibila
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Barcelona, Spain
| | - Virginia Aragon
- IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, Barcelona, Spain.
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24
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Wen Y, Xu H, Han J, Jin R, Chen H. How Does Epstein–Barr Virus Interact With Other Microbiomes in EBV-Driven Cancers? Front Cell Infect Microbiol 2022; 12:852066. [PMID: 35281433 PMCID: PMC8904896 DOI: 10.3389/fcimb.2022.852066] [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: 01/10/2022] [Accepted: 01/28/2022] [Indexed: 12/12/2022] Open
Abstract
The commensal microbiome refers to a large spectrum of microorganisms which mainly consists of viruses and bacteria, as well as some other components such as protozoa and fungi. Epstein–Barr virus (EBV) is considered as a common component of the human commensal microbiome due to its spread worldwide in about 95% of the adult population. As the first oncogenic virus recognized in human, numerous studies have reported the involvement of other components of the commensal microbiome in the increasing incidence of EBV-driven cancers. Additionally, recent advances have also defined the involvement of host–microbiota interactions in the regulation of the host immune system in EBV-driven cancers as well as other circumstances. The regulation of the host immune system by the commensal microbiome coinfects with EBV could be the implications for how we understand the persistence and reactivation of EBV, as well as the progression of EBV-associated cancers, since majority of the EBV persist as asymptomatic carrier. In this review, we attempt to summarize the possible mechanisms for EBV latency, reactivation, and EBV-driven tumorigenesis, as well as casting light on the role of other components of the microbiome in EBV infection and reactivation. Besides, whether novel microbiome targeting strategies could be applied for curing of EBV-driven cancer is discussed as well.
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Affiliation(s)
| | | | | | - Runming Jin
- *Correspondence: Hongbo Chen, ; Runming Jin,
| | - Hongbo Chen
- *Correspondence: Hongbo Chen, ; Runming Jin,
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Perturbation of alphavirus and flavivirus infectivity by components of the bacterial cell wall. J Virol 2022; 96:e0006022. [PMID: 35107376 DOI: 10.1128/jvi.00060-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The impact of the host microbiota on arbovirus infections is currently not well understood. Arboviruses are viruses transmitted through the bites of infected arthropods, predominantly mosquitoes or ticks. The first site of arbovirus inoculation is the biting site in the host skin, which is colonized by a complex microbial community that could possibly influence arbovirus infection. We demonstrated that pre-incubation of arboviruses with certain components of the bacterial cell wall, including lipopolysaccharides (LPS) of some Gram-negative bacteria and lipoteichoic acids or peptidoglycan of certain Gram-positive bacteria, significantly reduced arbovirus infectivity in vitro. This inhibitory effect was observed for arboviruses of different virus families, including chikungunya virus of the Alphavirus genus and Zika virus of the Flavivirus genus, showing that this is a broad phenomenon. A modest inhibitory effect was observed following incubation with a panel of heat-inactivated bacteria, including bacteria residing on the skin. No viral inhibition was observed after pre-incubation of cells with LPS. Furthermore, a virucidal effect of LPS on viral particles was noticed by electron microscopy. Therefore, the main inhibitory mechanism seems to be due to a direct effect on the virus particles. Together, these results suggest that bacteria are able to decrease the infectivity of alphaviruses and flaviviruses. Importance During the past decades the world has experienced a vast increase in epidemics of alphavirus and flavivirus infections. These viruses can cause severe diseases such as hemorrhagic fever, encephalitis and arthritis. Several alpha- and flaviviruses, such as chikungunya virus, Zika virus and dengue virus, are significant global health threats because of their high disease burden, their widespread (re-)emergence and the lack of (good) anti-arboviral strategies. Despite the clear health burden, alphavirus and flavivirus infection and disease are not fully understood. A knowledge gap in the interplay between the host and the arbovirus is the potential interaction with host skin bacteria. Therefore, we studied the effect of (skin) bacteria and bacterial cell wall components on alphavirus and flavivirus infectivity in cell culture. Our results show that certain bacterial cell wall components markedly reduced viral infectivity by directly interacting with the virus particle.
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Padilha de Lima A, Macedo Rogero M, Araujo Viel T, Garay-Malpartida HM, Aprahamian I, Lima Ribeiro SM. Interplay between Inflammaging, Frailty and Nutrition in Covid-19: Preventive and Adjuvant Treatment Perspectives. J Nutr Health Aging 2022; 26:67-76. [PMID: 35067706 PMCID: PMC8713542 DOI: 10.1007/s12603-021-1720-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/06/2021] [Indexed: 02/06/2023]
Abstract
As humans age, their immune system undergoes modifications, including a low-grade inflammatory status called inflammaging. These changes are associated with a loss of physical and immune resilience, amplifying the risk of being malnourished and frail. Under the COVID-19 scenario, inflammaging increases the susceptibility to poor prognostics. We aimed to bring the current concepts of inflammaging and its relationship with frailty and COVID-19 prognostic; highlight the importance of evaluating the nutritional risk together with frailty aiming to monitor older adults in COVID-19 scenario; explore some compounds with potential to modulate inflammaging in perspective to manage the COVID-19 infection. Substances such as probiotics and senolytics can help reduce the high inflammatory status. Also, the periodic evaluation of nutrition risk and frailty will allow interventions, assuring the appropriate care.
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Affiliation(s)
- A Padilha de Lima
- Sandra Maria Lima Ribeiro, University of São Paulo- Public Health School, Av Dr. Arnaldo 715, Sao Paulo- SP- Brazil, e-mail:
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Elias G, Meysman P, Bartholomeus E, De Neuter N, Keersmaekers N, Suls A, Jansens H, Souquette A, De Reu H, Emonds MP, Smits E, Lion E, Thomas PG, Mortier G, Van Damme P, Beutels P, Laukens K, Van Tendeloo V, Ogunjimi B. Preexisting memory CD4 T cells in naïve individuals confer robust immunity upon hepatitis B vaccination. eLife 2022; 11:68388. [PMID: 35074048 PMCID: PMC8824481 DOI: 10.7554/elife.68388] [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: 03/14/2021] [Accepted: 01/07/2022] [Indexed: 11/22/2022] Open
Abstract
Antigen recognition through the T cell receptor (TCR) αβ heterodimer is one of the primary determinants of the adaptive immune response. Vaccines activate naïve T cells with high specificity to expand and differentiate into memory T cells. However, antigen-specific memory CD4 T cells exist in unexposed antigen-naïve hosts. In this study, we use high-throughput sequencing of memory CD4 TCRβ repertoire and machine learning to show that individuals with preexisting vaccine-reactive memory CD4 T cell clonotypes elicited earlier and higher antibody titers and mounted a more robust CD4 T cell response to hepatitis B vaccine. In addition, integration of TCRβ sequence patterns into a hepatitis B epitope-specific annotation model can predict which individuals will have an early and more vigorous vaccine-elicited immunity. Thus, the presence of preexisting memory T cell clonotypes has a significant impact on immunity and can be used to predict immune responses to vaccination. Immune cells called CD4 T cells help the body build immunity to infections caused by bacteria and viruses, or after vaccination. Receptor proteins on the outside of the cells recognize pathogens, foreign molecules called antigens, or vaccine antigens. Vaccine antigens are usually inactivated bacteria or viruses, or fragments of these pathogens. After recognizing an antigen, CD4 T cells develop into memory CD4 T cells ready to defend against future infections with the pathogen. People who have never been exposed to a pathogen, or have never been vaccinated against it, may nevertheless have preexisting memory cells ready to defend against it. This happens because CD4 T cells can recognize multiple targets, which enables the immune system to be ready to defend against both new and familiar pathogens. Elias, Meysman, Bartholomeus et al. wanted to find out whether having preexisting memory CD4 T cells confers an advantage for vaccine-induced immunity. Thirty-four people who were never exposed to hepatitis B or vaccinated against it participated in the study. These individuals provided blood samples before vaccination, with 2 doses of the hepatitis B vaccine, and at 3 time points afterward. Using next generation immune sequencing and machine learning techniques, Elias et al. analyzed the individuals’ memory CD4 T cells before and after vaccination. The experiments showed that preexisting memory CD4 T cells may determine vaccination outcomes, and people with more preexisting memory cells develop quicker and stronger immunity after vaccination against hepatitis B. This information may help scientists to better understand how people develop immunity to pathogens. It may guide them develop better vaccines or predict who will develop immunity after vaccination.
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Affiliation(s)
- George Elias
- Laboratory of Experimental Hematology (LEH), University of Antwerp
| | - Pieter Meysman
- Biomedical Informatics Research Network Antwerp, Department of Mathematics and Informatics, University of Antwerp
| | | | - Nicolas De Neuter
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Nina Keersmaekers
- Centre for Health Economics Research & Modeling Infectious Diseases, University of Antwerp
| | - Arvid Suls
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Hilde Jansens
- Department of Clinical Microbiology, Antwerp University Hospital
| | - Aisha Souquette
- Department of Immunology, St. Jude Children's Research Hospital
| | - Hans De Reu
- Laboratory of Experimental Hematology, University of Antwerp
| | | | - Evelien Smits
- Laboratory of Experimental Hematology, University of Antwerp
| | - Eva Lion
- Laboratory of Experimental Hematology, University of Antwerp
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital
| | - Geert Mortier
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Pierre Van Damme
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Philippe Beutels
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Kris Laukens
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
| | - Viggo Van Tendeloo
- Janssen Research and Development, Immunosciences WWDA, Johnson and Johnson
| | - Benson Ogunjimi
- Antwerp Unit for Data Analysis and Computation in Immunology and Sequencing, University of Antwerp
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Aan FJ, Glibetic N, Montoya-Uribe V, Matter ML. COVID-19 and the Microbiome: The Gut-Lung Connection. COMPREHENSIVE GUT MICROBIOTA 2022. [PMCID: PMC8131000 DOI: 10.1016/b978-0-12-819265-8.00048-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Abstract
Viruses are essentially, obligate intracellular parasites. They require a host to replicate their genetic material, spread to other cells, and eventually to other hosts. For humans, most viral infections are not considered lethal, regardless if at the cellular level, the virus can obliterate individual cells. Constant genomic mutations, (which can alter the antigenic content of viruses such as influenza or coronaviruses), zoonosis or immunosuppression/immunocompromisation, is when viruses achieve higher host mortality. Frequent examples of the severe consequenses of viral infection can be seen in children and the elderly. In most instances, the immune system will take a multifaceted approach in defending the host against viruses. Depending on the virus, the individual, and the point of entry, the immune system will initiate a robust response which involves multiple components. In this chapter, we expand on the total immune system, breaking it down to the two principal types: Innate and Adaptive Immunity, their different roles in viral recognition and clearance. Finally, how different viruses activate and evade different arms of the immune system.
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Abstract
The COVID-19 pandemic has highlighted the need to identify additional antiviral small molecules to complement existing therapies. Although increasing evidence suggests that metabolites produced by the human microbiome have diverse biological activities, their antiviral properties remain poorly explored. Using a cell-based SARS-CoV-2 infection assay, we screened culture broth extracts from a collection of phylogenetically diverse human-associated bacteria for the production of small molecules with antiviral activity. Bioassay-guided fractionation uncovered three bacterial metabolites capable of inhibiting SARS-CoV-2 infection. This included the nucleoside analogue N6-(Δ2-isopentenyl)adenosine, the 5-hydroxytryptamine receptor agonist tryptamine, and the pyrazine 2,5-bis(3-indolylmethyl)pyrazine. The most potent of these, N6-(Δ2-isopentenyl)adenosine, had a 50% inhibitory concentration (IC50) of 2 μM. These natural antiviral compounds exhibit structural and functional similarities to synthetic drugs that have been clinically examined for use against COVID-19. Our discovery of structurally diverse metabolites with anti-SARS-CoV-2 activity from screening a small fraction of the bacteria reported to be associated with the human microbiome suggests that continued exploration of phylogenetically diverse human-associated bacteria is likely to uncover additional small molecules that inhibit SARS-CoV-2 as well as other viral infections. IMPORTANCE The continued prevalence of COVID-19 and the emergence of new variants has once again put the spotlight on the need for the identification of SARS-CoV-2 antivirals. The human microbiome produces an array of small molecules with bioactivities (e.g., host receptor ligands), but its ability to produce antiviral small molecules is relatively underexplored. Here, using a cell-based screening platform, we describe the isolation of three microbiome-derived metabolites that are able to prevent SARS-CoV-2 infection in vitro. These molecules display structural similarities to synthetic drugs that have been explored for the treatment of COVID-19, and these results suggest that the microbiome may be a fruitful source of the discovery of small molecules with antiviral activities.
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Qi L, Huang X, He C, Ji D, Li F. Steroid-resistant intestinal aGVHD and refractory CMV and EBV infections complicated by haplo-HSCT were successfully rescued by FMT and CTL infusion. J Int Med Res 2021; 49:3000605211063292. [PMID: 34918995 PMCID: PMC8728789 DOI: 10.1177/03000605211063292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Haploidentical hematopoietic stem cell transplantation (haplo-HSCT) produces similar survival outcomes as HLA-matched sibling donor allogeneic HCST in younger patients with acquired severe aplastic anemia (SAA). This study reported a 29-years-old man with SAA and intracranial hemorrhage who underwent haplo-HSCT with a modified BU/CY + ATG conditioning regimen. Neutrophil and platelet engraftment were both achieved on day 14 after HSCT. The patient developed grade IV acute graft-versus-host disease (aGVHD) on day 20 and acquired cytomegalovirus (CMV) and Epstein-Barr virus (EBV) infections on day 47. After the failure of methylprednisolone, basiliximab, ruxolitinib, and antiviral treatment, the patient was diagnosed with steroid-resistant grade IV aGVHD and refractory CMV and EBV infections. We performed fecal microbiota transplantation and infused CMV- and EBV-specific cytotoxic T lymphocytes. After that the stool volume and frequency gradually decreased, and viral DNA was undetectable on day 80. This report provides helpful clinical experience for treating steroid-resistant aGVHD and refractory viral infections.
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Affiliation(s)
- Ling Qi
- Department of Hematology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xianbao Huang
- Department of Hematology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Cong He
- Institute of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Dexiang Ji
- Department of Hematology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Fei Li
- Department of Hematology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Institute of Hematology, Jiangxi Academy of Clinical Medical Sciences, Nanchang, China
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Liu TFD, Philippou E, Kolokotroni O, Siakallis G, Rahima K, Constantinou C. Gut and airway microbiota and their role in COVID-19 infection and pathogenesis: a scoping review. Infection 2021; 50:815-847. [PMID: 34671922 PMCID: PMC8528184 DOI: 10.1007/s15010-021-01715-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/09/2021] [Indexed: 12/24/2022]
Abstract
Background The SARS-CoV-2 virus is responsible for the COVID-19 pandemic. Researchers have been studying the pathogenesis of the virus with the aim to improve our current diagnosis and management strategies. The microbiota have been proposed to play a key role in the pathogenesis of the disease. Purpose To investigate and report on the current available evidence on any associations between the gut and/or airway microbiota and the pathogenesis of COVID-19. Methods Using a predefined protocol in compliance with the PRISMA guidelines, a search was conducted on MEDLINE, Science Direct, DOAJ and Cochrane databases on primary research studies assessing the association between COVID-19 infection and the gut and/or airway microbiota. Results Twenty-two studies were included in the current review; nineteen studies concluded an association between the gut and/or airway dysbiosis and SARS-CoV-2, while 3 studies failed to observe a significant association between the airway microbiome and SARS-CoV-2 infection. Specifically, most studies reported a decrease in microbial diversity and therefore development of intestinal dysbiosis in COVID-19-positive patients compared to healthy controls as well as a possible association between increased intestinal dysbiosis and disease severity. Conclusion During infection with SARS-CoV-2, there are significant changes in the composition of the gut and airway microbiota. Furthermore, the gut microbiota may have a more important role than the airway microbiota in COVID-19 infection. In the future, studies should be more carefully designed to derive more conclusive evidence on the role of the gut and airway microbiota following infection with SARS-CoV-2 which will lead to the formulation of better management strategies in combating COVID-19. Supplementary Information The online version contains supplementary material available at 10.1007/s15010-021-01715-5.
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Affiliation(s)
- Tik Fung Dave Liu
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, 21 Ilia Papakyriakou, 2414 Engomi, P.O. Box 24005, 1700, Nicosia, Cyprus
| | - Elena Philippou
- Department of Life and Health Sciences, School of Sciences and Engineering, University of Nicosia, Nicosia, Cyprus
- Department of Nutrition and Dietetics, King's College London, London, UK
| | - Ourania Kolokotroni
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, 21 Ilia Papakyriakou, 2414 Engomi, P.O. Box 24005, 1700, Nicosia, Cyprus
| | - Georgios Siakallis
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, 21 Ilia Papakyriakou, 2414 Engomi, P.O. Box 24005, 1700, Nicosia, Cyprus
| | - Kenan Rahima
- Queen Elizabeth The Queen Mother Hospital, Margate, UK
| | - Constantina Constantinou
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, 21 Ilia Papakyriakou, 2414 Engomi, P.O. Box 24005, 1700, Nicosia, Cyprus.
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Seibert B, Cáceres CJ, Cardenas-Garcia S, Carnaccini S, Geiger G, Rajao DS, Ottesen E, Perez DR. Mild and Severe SARS-CoV-2 Infection Induces Respiratory and Intestinal Microbiome Changes in the K18-hACE2 Transgenic Mouse Model. Microbiol Spectr 2021; 9:e0053621. [PMID: 34378965 PMCID: PMC8455067 DOI: 10.1128/spectrum.00536-21] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/15/2021] [Indexed: 01/27/2023] Open
Abstract
Transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in millions of deaths and declining economies around the world. K18-hACE2 mice develop disease resembling severe SARS-CoV-2 infection in a virus dose-dependent manner. The relationship between SARS-CoV-2 and the intestinal or respiratory microbiome is not fully understood. In this context, we characterized the cecal and lung microbiomes of SARS-CoV-2-challenged K18-hACE2 transgenic mice in the presence or absence of treatment with the Mpro inhibitor GC-376. Cecum microbiome showed decreased Shannon and inverse (Inv) Simpson diversity indexes correlating with SARS-CoV-2 infection dosage and a difference of Bray-Curtis dissimilarity distances among control and infected mice. Bacterial phyla such as Firmicutes, particularly, Lachnospiraceae and Oscillospiraceae, were significantly less abundant, while Verrucomicrobia, particularly, the family Akkermansiaceae, were increasingly more prevalent during peak infection in mice challenged with a high virus dose. In contrast to the cecal microbiome, the lung microbiome showed similar microbial diversity among the control, low-, and high-dose challenge virus groups, independent of antiviral treatment. Bacterial phyla in the lungs such as Bacteroidetes decreased, while Firmicutes and Proteobacteria were significantly enriched in mice challenged with a high dose of SARS-CoV-2. In summary, we identified changes in the cecal and lung microbiomes of K18-hACE2 mice with severe clinical signs of SARS-CoV-2 infection. IMPORTANCE The COVID-19 pandemic has resulted in millions of deaths. The host's respiratory and intestinal microbiome can affect directly or indirectly the immune system during viral infections. We characterized the cecal and lung microbiomes in a relevant mouse model challenged with a low or high dose of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the presence or absence of an antiviral Mpro inhibitor, GC-376. Decreased microbial diversity and taxonomic abundances of the phyla Firmicutes, particularly, Lachnospiraceae, correlating with infection dosage were observed in the cecum. In addition, microbes within the family Akkermansiaceae were increasingly more prevalent during peak infection, which is observed in other viral infections. The lung microbiome showed similar microbial diversity to that of the control, independent of antiviral treatment. Decreased Bacteroidetes and increased Firmicutes and Proteobacteria were observed in the lungs in a virus dose-dependent manner. These studies add to a better understanding of the complexities associated with the intestinal microbiome during respiratory infections.
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Affiliation(s)
- Brittany Seibert
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - C. Joaquín Cáceres
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Stivalis Cardenas-Garcia
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Silvia Carnaccini
- Tifton Diagnostic Laboratory, College of Veterinary Medicine, University of Georgia, Tifton, Georgia, USA
| | - Ginger Geiger
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Daniela S. Rajao
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
| | - Elizabeth Ottesen
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Daniel R. Perez
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, USA
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Schnepf D, Hernandez P, Mahlakõiv T, Crotta S, Sullender ME, Peterson ST, Ohnemus A, Michiels C, Gentle I, Dumoutier L, Reis CA, Diefenbach A, Wack A, Baldridge MT, Staeheli P. Rotavirus susceptibility of antibiotic-treated mice ascribed to diminished expression of interleukin-22. PLoS One 2021; 16:e0247738. [PMID: 34383769 PMCID: PMC8360596 DOI: 10.1371/journal.pone.0247738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/13/2021] [Indexed: 12/28/2022] Open
Abstract
The commensal microbiota regulates susceptibility to enteric pathogens by fine-tuning mucosal innate immune responses, but how susceptibility to enteric viruses is shaped by the microbiota remains incompletely understood. Past reports have indicated that commensal bacteria may either promote or repress rotavirus replication in the small intestine of mice. We now report that rotavirus replicated more efficiently in the intestines of germ-free and antibiotic-treated mice compared to animals with an unmodified microbiota. Antibiotic treatment also facilitated rotavirus replication in type I and type III interferon (IFN) receptor-deficient mice, revealing IFN-independent proviral effects. Expression of interleukin-22 (IL-22) was strongly diminished in the intestine of antibiotic-treated mice. Treatment with exogenous IL-22 blocked rotavirus replication in microbiota-depleted wild-type and Stat1-/- mice, demonstrating that the antiviral effect of IL-22 in animals with altered microbiome is not dependent on IFN signaling. In antibiotic-treated animals, IL-22-induced a specific set of genes including Fut2, encoding fucosyl-transferase 2 that participates in the biosynthesis of fucosylated glycans which can mediate rotavirus binding. Interestingly, IL-22 also blocked rotavirus replication in antibiotic-treated Fut2-/- mice. Furthermore, IL-22 inhibited rotavirus replication in antibiotic-treated mice lacking key molecules of the necroptosis or pyroptosis pathways of programmed cell death. Taken together, our results demonstrate that IL-22 determines rotavirus susceptibility of antibiotic-treated mice, yet the IL-22-induced effector molecules conferring rotavirus resistance remain elusive.
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Affiliation(s)
- Daniel Schnepf
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
| | - Pedro Hernandez
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR3215, Development and Homeostasis of Mucosal Tissues Group, Paris, France
| | - Tanel Mahlakõiv
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
| | - Stefania Crotta
- Immunoregulation Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Meagan E. Sullender
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Stefan T. Peterson
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Annette Ohnemus
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
| | - Camille Michiels
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Ian Gentle
- Institute of Medical Microbiology and Hygiene, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Laure Dumoutier
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Celso A. Reis
- Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal
- Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
| | - Andreas Diefenbach
- Institute of Microbiology, Infectious Diseases and Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Mucosal and Developmental Immunology, Deutsches Rheuma-Forschungszentrum, an Institute of the Leibniz Gemeinschaft, Berlin, Germany
| | - Andreas Wack
- Immunoregulation Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Megan T. Baldridge
- Department of Medicine, Division of Infectious Diseases, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Peter Staeheli
- Institute of Virology, Medical Center University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
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Blostein F, Foote S, Salzman E, McNeil DW, Marazita ML, Martin ET, Foxman B. Associations Between Salivary Bacteriome Diversity and Salivary Human Herpesvirus Detection in Early Childhood: A Prospective Cohort Study. J Pediatric Infect Dis Soc 2021; 10:856-863. [PMID: 34173666 PMCID: PMC8459089 DOI: 10.1093/jpids/piab044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/26/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND The bacteriome is associated with susceptibility to some eukaryotic viruses, but no study has examined associations between the salivary bacteriome and human herpesviruses (HHVs). We provide new prevalence and incidence estimates for salivary herpesviruses detection and estimate associations with bacteriome diversity in young children. METHODS Salivary samples collected at ages ~2, 8, 12, and 24 months from 153 children participating in the Center for Oral Health Research in Appalachia cohort 2 (COHRA2) were screened for HHVs using the Fast-Track Neuro9 multiplex PCR assay, and for the bacteriome using 16S rRNA amplicon sequencing. We used Cox proportional hazard models to test for associations between the salivary bacteriome and hazards of cytomegalovirus (CMV) and human herpesvirus-6 (HHV6). RESULTS CMV, HHV6, and Epstein-Barr virus (EBV) were detected at all visits. Human herpesvirus-7 (HHV7) was first detected at the 8-month visit and herpes simplex virus 1 (HSV1) was only detected at the 12-month visit. Varicella-zoster virus, herpes simplex virus 2, and human herpesvirus-8 were never detected. HHV6 (24-month cumulative incidence: 73.8%) and CMV (24-month cumulative incidence: 32.3%) were detected most frequently. Increasing salivary bacteriome diversity was associated with longer survival to first detection of CMV (hazard ratio [95% CI]: 0.24 [0.12, 0.49]) and HHV6 (hazard ratio [95% CI]: 0.24 [0.13, 0.44]). CONCLUSION CMV, HHV6, EBV, HHV7, and HSV1 were detected in the saliva during the first 2 years of life. Time to first detection of CMV and HHV6 was associated with salivary bacteriome diversity, suggesting a possible interaction between HHVs and the salivary bacteriome.
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Affiliation(s)
- Freida Blostein
- Department of Epidemiology, Center for Molecular and Clinical Epidemiology of Infectious Diseases, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Sydney Foote
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Elizabeth Salzman
- Department of Epidemiology, Center for Molecular and Clinical Epidemiology of Infectious Diseases, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Daniel W McNeil
- Department of Clinical Psychology, West Virginia University, Morgantown, West Virginia, USA
| | - Mary L Marazita
- Department of Oral and Craniofacial Sciences, Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA,Clinical and Translational Sciences Institute, and Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Emily T Martin
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Betsy Foxman
- Department of Epidemiology, Center for Molecular and Clinical Epidemiology of Infectious Diseases, University of Michigan School of Public Health, Ann Arbor, Michigan, USA,Corresponding Author: Betsy Foxman, PhD, Department of Epidemiology, University of Michigan School of Public Health, M5108 SPH II, 1415 Washington Heights, Ann Arbor, MI 48109-2029. E-mail:
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Roach SN, Langlois RA. Intra- and Cross-Species Transmission of Astroviruses. Viruses 2021; 13:v13061127. [PMID: 34208242 PMCID: PMC8230745 DOI: 10.3390/v13061127] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/30/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Astroviruses are non-enveloped, single-stranded RNA viruses that infect mammalian and avian species. In humans, astrovirus infections are one of the most common causes of gastroenteritis in children. Infection has also been linked to serious neurological complications, especially in immunocompromised individuals. More extensive disease has also been characterized in non-human mammalian and avian species. To date, astroviruses have been detected in over 80 different avian and mammalian hosts. As the number of hosts continues to rise, the need to understand how astroviruses transmit within a given species as well as to new host species becomes increasingly important. Here, we review the current understanding of astrovirus transmission, the factors that influence viral spread, and the potential for cross-species transmission. Additionally, we highlight the current gaps in knowledge and areas of future research that will be key to understanding astrovirus transmission and zoonotic potential.
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Affiliation(s)
- Shanley N. Roach
- Biochemistry, Molecular Biology, and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Ryan A. Langlois
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
- Correspondence:
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Abstract
Vaccines are the most effective means available for preventing infectious diseases. However, vaccine-induced immune responses are highly variable between individuals and between populations in different regions of the world. Understanding the basis of this variation is, thus, of fundamental importance to human health. Although the factors that are associated with intra- and inter-population variation in vaccine responses are manifold, emerging evidence points to a key role for the gut microbiome in controlling immune responses to vaccination. Much of this evidence comes from studies in mice, and causal evidence for the impact of the microbiome on human immunity is sparse. However, recent studies on vaccination in subjects treated with broad-spectrum antibiotics have provided causal evidence and mechanistic insights into how the microbiota controls immune responses in humans.
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Pereira TN, Carvalho FD, Rugani JN, de Carvalho VR, Jarusevicius J, Souza-Neto JA, Moreira LA. Mayaro Virus: The Potential Role of Microbiota and Wolbachia. Pathogens 2021; 10:pathogens10050525. [PMID: 33925275 PMCID: PMC8145793 DOI: 10.3390/pathogens10050525] [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: 02/18/2021] [Revised: 04/08/2021] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
The Mayaro virus (MAYV) is an arbovirus that circulates mainly in tropical forests or rural areas in Latin America and is transmitted mainly by Haemagogus mosquitoes. The objective of this study was to evaluate the vector competence, microbiome, and the presence of Wolbachia in three Aedes albopictus populations infected with MAYV. The vector competence was assessed based on viral infection and transmission by RT-qPCR. In addition, the microbiome was evaluated by amplification of the 16S rRNA V4 region and PCR to detect the presence of Wolbachia (strain wAlbA/wAlbB). Our results show that all three populations were susceptible to MAYV infection. The potential transmission of the MAYV was consistent in all populations of naïve mosquitoes injected (more than 50%). The microbiome analysis revealed 118 OTUs (operational taxonomic unit) from the three populations, 8 phyla, 15 classes, 26 orders, 35 families, 65 genera, and 53 species. All populations had Pseudomonas and Wolbachia as predominant genera. There was no difference between the variables for MAYV and Wolbachia (wAlbA or wAlbB) in the abdomen. However, in the head + thorax samples at 14 dpi, there was a difference between the two populations, indicating a possible correlation between the presence of Wolbachia (wAlbB) and infection. Overall, we show evidence that Ae. albopictus displays significant infection and transmission competence for the MAYV in the laboratory, and its bacterial microbiota play an important role in the host, mainly the strains of Wolbachia. The influence of the intestinal microbiota of Ae. albopictus is poorly known, and a better understanding of these interactions would open new perspectives for disease control through the manipulation of microbial communities. The exact contribution of this mosquito species to the transmission of the MAYV in the field remains to be confirmed.
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Affiliation(s)
- Thiago Nunes Pereira
- Grupo Mosquitos Vetores: Endossimbiontes e Interação Patógeno-Vetor, Instituto René Rachou-Fiocruz, Belo Horizonte 30190-002, Brazil; (T.N.P.); (F.D.C.)
| | - Fabiano Duarte Carvalho
- Grupo Mosquitos Vetores: Endossimbiontes e Interação Patógeno-Vetor, Instituto René Rachou-Fiocruz, Belo Horizonte 30190-002, Brazil; (T.N.P.); (F.D.C.)
| | - Jerônimo Nunes Rugani
- Grupo Taxonomia de Flebotomíneos e Epidemiologia das Leishmanioses, Instituto René Rachou-Fiocruz, Belo Horizonte 30190-002, Brazil;
| | - Vanessa Rafaela de Carvalho
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (V.R.d.C.); (J.A.S.-N.)
- School of Agricultural Sciences, Central Multiuser Laboratory, São Paulo State University (UNESP), Botucatu 18610-034, Brazil
| | - Jaqueline Jarusevicius
- Institute of Biotechnology, São Paulo State University (UNESP), Botucatu 18607-440, Brazil;
| | - Jayme A. Souza-Neto
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu 18610-034, Brazil; (V.R.d.C.); (J.A.S.-N.)
- School of Agricultural Sciences, Central Multiuser Laboratory, São Paulo State University (UNESP), Botucatu 18610-034, Brazil
| | - Luciano Andrade Moreira
- Grupo Mosquitos Vetores: Endossimbiontes e Interação Patógeno-Vetor, Instituto René Rachou-Fiocruz, Belo Horizonte 30190-002, Brazil; (T.N.P.); (F.D.C.)
- Correspondence:
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Abstract
Scientists have invested considerable resources in the study of the microbiota of the human body. These microorganisms play pivotal roles in immunity and disease. Of which, probiotics are live beneficial microorganisms that keep your intestinal or lung microbiota healthy, and occupy a special role in combating the infections. Thus, it is critical to understand their contributions to these processes. Technology can facilitate advanced studies of the microbiota, including how it develops and its positive and negatives effects on the immune system. This paper investigates how several factors (e.g. birth delivery mode, metabolic activities, types of microorganisms, and immune system interactions) affect the microbiota, particularly in early life. The paper also discusses how gastrointestinal microbes in particular may be associated with certain disease processes, such as those related to schizophrenia, autism, and diabetes. Clinical studies show that certain probiotic strains, like Lactobacillus rhamnosus GG and Bifidobacterium animalis ssp. lactis help to prevent infection of pathogenic organisms (both bacterial and viral). This research may yield crucial contributions to disease prevention and public health. The dysbiosis may result in changes in the acquired immunity later on. The probiotic strains can prevent viral replication during SARS-CoV-2 or COVID-19 infection by reducing proinflammatory cytokines. There has been much interest into the intestinal flora as proposed by the diversity, volume, and proposed role in disease. Future research in the field of microbiome should be done in order to uncover their association to gut virome by noting both their influence on each other and relevant health and disease.
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Jain T, Sharma P, Are AC, Vickers SM, Dudeja V. New Insights Into the Cancer-Microbiome-Immune Axis: Decrypting a Decade of Discoveries. Front Immunol 2021; 12:622064. [PMID: 33708214 PMCID: PMC7940198 DOI: 10.3389/fimmu.2021.622064] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022] Open
Abstract
The past decade has witnessed groundbreaking advances in the field of microbiome research. An area where immense implications of the microbiome have been demonstrated is tumor biology. The microbiome affects tumor initiation and progression through direct effects on the tumor cells and indirectly through manipulation of the immune system. It can also determine response to cancer therapies and predict disease progression and survival. Modulation of the microbiome can be harnessed to potentiate the efficacy of immunotherapies and decrease their toxicity. In this review, we comprehensively dissect recent evidence regarding the interaction of the microbiome and anti-tumor immune machinery and outline the critical questions which need to be addressed as we further explore this dynamic colloquy.
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Affiliation(s)
| | | | | | - Selwyn M. Vickers
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Vikas Dudeja
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL, United States
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Effects of ploidy and salmonid alphavirus infection on the skin and gill microbiome of Atlantic salmon (Salmo salar). PLoS One 2021; 16:e0243684. [PMID: 33606747 PMCID: PMC7894865 DOI: 10.1371/journal.pone.0243684] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/01/2021] [Indexed: 01/04/2023] Open
Abstract
The microbial communities that live in symbiosis with the mucosal surfaces of animals provide the host with defense strategies against pathogens. These microbial communities are largely shaped by the environment and the host genetics. Triploid Atlantic salmon (Salmo salar) are being considered for aquaculture as they are reproductively sterile and thus cannot contaminate the natural gene pool. It has not been previously investigated how the microbiome of triploid salmon compares to that of their diploid counterparts. In this study, we compare the steady-state skin and gill microbiome of both diploid and triploid salmon, and determine the effects of salmonid alphavirus 3 experimental infection on their microbial composition. Our results show limited differences in the skin-associated microbiome between triploid and diploid salmon, irrespective of infection. In the gills, we observed a high incidence of the bacterial pathogen Candidatus Branchiomonas, with higher abundance in diploid compared to triploid control fish. Diploid salmon infected with SAV3 showed greater histopathological signs of epitheliocystis compared to controls, a phenomenon not observed in triploid fish. Our results indicate that ploidy can affect the alpha diversity of the gills but not the skin-associated microbial community. Importantly, during a natural outbreak of Branchiomonas sp. the gill microbiome of diploid Atlantic salmon became significantly more dominated by this pathogen than in triploid animals. Thus, our results suggest that ploidy may play a role on Atlantic salmon gill health and provide insights into co-infection with SAV3 and C. Branchiomonas in Atlantic salmon.
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Mazzarelli A, Giancola ML, Farina A, Marchioni L, Rueca M, Gruber CEM, Bartolini B, Ascoli Bartoli T, Maffongelli G, Capobianchi MR, Ippolito G, Di Caro A, Nicastri E, Pazienza V. 16S rRNA gene sequencing of rectal swab in patients affected by COVID-19. PLoS One 2021; 16:e0247041. [PMID: 33596245 PMCID: PMC7888592 DOI: 10.1371/journal.pone.0247041] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/31/2021] [Indexed: 12/23/2022] Open
Abstract
COronaVIrus Disease-2019 (COVID-19) is a pandemic respiratory infection caused by a new betacoronavirus, the Severe Acute Respiratory Syndrome-CoronaVirus-2 (SARS-CoV-2). Few data are reported on the gut microbiota in COVID-19 patients. 16S rRNA gene sequencing was performed to reveal an altered composition of the gut microbiota in patients with COVID-19 pneumonia admitted in intensive care unit (ICU) (i-COVID19), or in infectious disease wards (w-COVID19) as compared to controls (CTRL). i-COVID19 patients showed a decrease of Chao1 index as compared to CTRL and w-COVID19 patients indicating that patients in ICU displayed a lower microbial richness while no change was observed as for Shannon Index. At the phylum level, an increase of Proteobacteria was detected in w-COVID19 patients as compared to CTRL. A decrease of Fusobacteria and Spirochetes has been found, with the latter decreased in i-COVID19 patients as compared to CTRL. Significant changes in gut microbial communities in patients with COVID-19 pneumonia with different disease severity compared to CTRL have been identified. Our preliminary data may provide valuable information and promising biomarkers for the diagnosis of the disease and, when validated in larger cohort, it could facilitate the stratification of patients based on the microbial signature.
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Affiliation(s)
- Antonio Mazzarelli
- National Institute for Infectious Diseases, INMI “Lazzaro Spallanzani”, IRCCS, Rome, Italy
| | - Maria Letizia Giancola
- National Institute for Infectious Diseases, INMI “Lazzaro Spallanzani”, IRCCS, Rome, Italy
| | - Anna Farina
- National Institute for Infectious Diseases, INMI “Lazzaro Spallanzani”, IRCCS, Rome, Italy
| | - Luisa Marchioni
- National Institute for Infectious Diseases, INMI “Lazzaro Spallanzani”, IRCCS, Rome, Italy
| | - Martina Rueca
- National Institute for Infectious Diseases, INMI “Lazzaro Spallanzani”, IRCCS, Rome, Italy
| | | | - Barbara Bartolini
- National Institute for Infectious Diseases, INMI “Lazzaro Spallanzani”, IRCCS, Rome, Italy
| | - Tommaso Ascoli Bartoli
- National Institute for Infectious Diseases, INMI “Lazzaro Spallanzani”, IRCCS, Rome, Italy
| | - Gaetano Maffongelli
- National Institute for Infectious Diseases, INMI “Lazzaro Spallanzani”, IRCCS, Rome, Italy
| | | | - Giuseppe Ippolito
- National Institute for Infectious Diseases, INMI “Lazzaro Spallanzani”, IRCCS, Rome, Italy
| | - Antonino Di Caro
- National Institute for Infectious Diseases, INMI “Lazzaro Spallanzani”, IRCCS, Rome, Italy
- * E-mail:
| | - Emanuele Nicastri
- National Institute for Infectious Diseases, INMI “Lazzaro Spallanzani”, IRCCS, Rome, Italy
| | - Valerio Pazienza
- Division of Gastroenterology, Fondazione-IRCCS “Casa Sollievo della Sofferenza” Hospital, S. Giovanni Rotondo (FG), Italy
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Bavananthasivam J, Astill J, Matsuyama-Kato A, Taha-Abdelaziz K, Shojadoost B, Sharif S. Gut microbiota is associated with protection against Marek's disease virus infection in chickens. Virology 2021; 553:122-130. [PMID: 33271490 DOI: 10.1016/j.virol.2020.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/02/2020] [Accepted: 10/28/2020] [Indexed: 12/25/2022]
Abstract
Marek's Disease Virus (MDV) infects chickens via respiratory route and causes lymphomas in internal organs including gastrointestinal tract. MDV infection causes a shift in the gut microbiota composition. However, interactions between the gut microbiota and immune responses against MDV infection are not well understood. Therefore, the current study was performed to understand the effect of the gut microbiota on Marek's disease (MD) pathogenesis. The findings showed that depletion of gut microbiota increased the severity of MD in infected chickens. In addition, an increase in the transcription of interferon (IFN)-α, IFN-β and IFN-γ in the bursa of Fabricius at 4 days post-infection (dpi) was observed in the gut microbiota depleted chickens. The observations in this study shed more light on the association between the gut microbiota and MDV infection in chickens. More research is needed to explore the mechanisms of involvement of the gut microbiota in immunity against MD in chickens.
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Affiliation(s)
- Jegarubee Bavananthasivam
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2W1, Canada; Department of Pathology and Molecular Medicine & McMaster Immunology Research Centre, M.G DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Jake Astill
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Ayumi Matsuyama-Kato
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Khaled Taha-Abdelaziz
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2W1, Canada; Pathology Department, Faculty of Veterinary Medicine, Beni-Suef University, Al Shamlah, 62511, Beni-Suef, Egypt
| | - Bahram Shojadoost
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Shayan Sharif
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
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Büttiker P, Weissenberger S, Stefano GB, Kream RM, Ptacek R. SARS-CoV-2, Trait Anxiety, and the Microbiome. Front Psychiatry 2021; 12:720082. [PMID: 34566721 PMCID: PMC8455943 DOI: 10.3389/fpsyt.2021.720082] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/16/2021] [Indexed: 12/21/2022] Open
Abstract
During the COVID-19 pandemic, research on the relationships between the virus and its human host has become fundamental to understand this pathology and its effects. Attaining this profound understanding is critical for the effective containment and treatment of infections caused by the virus. In this review, we present some possible mechanisms by which psychopathological symptoms emerge following viral infections of the central nervous system (CNS). These proposed mechanisms are based on microbial communication and the induced priming of microglial antibody activation within the CNS through Toll-like receptor signaling. In this process, chronic microglial activation causes increased glutamate release in virally-altered, high-density neuronal structures, thereby modulating cognitive networks and information integration processes. This modulation, in turn, we suggest, affects the accuracy of sensory integration and connectivity of major control networks, such as the default mode network. The chronic activation of immunological responses and neurochemical shifts toward an elevated glutamate/gamma-aminobutyric acid ratio lead to negative reinforcement learning and suboptimal organismic functioning, for example, maintaining the body in an anxious state, which can later become internalized as trait anxiety. Therefore, we hypothesize that the homeostatic relationship between host, microbiome, and virome, would be decisive in determining the efficiency of subsequent immunological responses, disease susceptibility, and long-term psychopathological effects of diseases that impact the CNS, such as the COVID-19.
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Affiliation(s)
- Pascal Büttiker
- First Faculty of Medicine, Center for Cognitive and Molecular Neuroscience, Charles University in Prague, Prague, Czechia
| | - Simon Weissenberger
- First Faculty of Medicine, Center for Cognitive and Molecular Neuroscience, Charles University in Prague, Prague, Czechia.,Department of Psychology, University of New York in Prague, Prague, Czechia
| | - George B Stefano
- First Faculty of Medicine, Center for Cognitive and Molecular Neuroscience, Charles University in Prague, Prague, Czechia
| | - Richard M Kream
- First Faculty of Medicine, Center for Cognitive and Molecular Neuroscience, Charles University in Prague, Prague, Czechia
| | - Radek Ptacek
- First Faculty of Medicine, Center for Cognitive and Molecular Neuroscience, Charles University in Prague, Prague, Czechia
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Donati Zeppa S, Agostini D, Piccoli G, Stocchi V, Sestili P. Gut Microbiota Status in COVID-19: An Unrecognized Player? Front Cell Infect Microbiol 2020; 10:576551. [PMID: 33324572 PMCID: PMC7725702 DOI: 10.3389/fcimb.2020.576551] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 10/30/2020] [Indexed: 01/07/2023] Open
Abstract
Infection with the SARS-CoV-2 virus causes cardiopulmonary and vascular complications, ranging in severity. Understanding the pathogenic mechanisms of the novel SARS-CoV2 infection and progression can provide potential novel targets for its prevention and/or treatment. Virus microbiota reciprocal interactions have been studied in a variety of viral infections. For example, the integrity of Coronavirus particles can be disrupted by surfactin, a bacterial surface molecule that targets other viruses, including that of influenza A. In this light, intestinal microbiota likely influences COVID-19 virulence, while from its side SARS-CoV-2 may affect the intestinal microbiome promoting dysbiosis and other deleterious consequences. Hence, the microbiota pre-existing health status and its alterations in the course of SARS-CoV-2 infection, are likely to play an important, still underscored role in determining individual susceptibility and resilience to COVID-19. Indeed, the vast majority of COVID-19 worst clinical conditions and fatalities develop in subjects with specific risk factors such as aging and the presence of one or more comorbidities, which are intriguingly characterized also by unhealthy microbiome status. Moreover, these comorbidities require complex pharmacological regimens known as "polypharmacy" that may further affect microbiota integrity and worsen the resilience to viral infections. This complex situation may represent a further and underestimated risk with regard to COVID-19 clinical burden for the elderly and comorbid people. Here, we discuss the possible biological, physiopathological, and clinical implications of gut microbiota in COVID-19 and the strategies to improve/maintain its healthy status as a simple and adjunctive strategy to reduce COVID-19 virulence and socio-sanitary burden.
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Affiliation(s)
- Sabrina Donati Zeppa
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
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46
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Baghbani T, Nikzad H, Azadbakht J, Izadpanah F, Haddad Kashani H. Dual and mutual interaction between microbiota and viral infections: a possible treat for COVID-19. Microb Cell Fact 2020; 19:217. [PMID: 33243230 PMCID: PMC7689646 DOI: 10.1186/s12934-020-01483-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/20/2020] [Indexed: 02/07/2023] Open
Abstract
All of humans and other mammalian species are colonized by some types of microorganisms such as bacteria, archaea, unicellular eukaryotes like fungi and protozoa, multicellular eukaryotes like helminths, and viruses, which in whole are called microbiota. These microorganisms have multiple different types of interaction with each other. A plethora of evidence suggests that they can regulate immune and digestive systems and also play roles in various diseases, such as mental, cardiovascular, metabolic and some skin diseases. In addition, they take-part in some current health problems like diabetes mellitus, obesity, cancers and infections. Viral infection is one of the most common and problematic health care issues, particularly in recent years that pandemics like SARS and COVID-19 caused a lot of financial and physical damage to the world. There are plenty of articles investigating the interaction between microbiota and infectious diseases. We focused on stimulatory to suppressive effects of microbiota on viral infections, hoping to find a solution to overcome this current pandemic. Then we reviewed mechanistically the effects of both microbiota and probiotics on most of the viruses. But unlike previous studies which concentrated on intestinal microbiota and infection, our focus is on respiratory system's microbiota and respiratory viral infection, bearing in mind that respiratory system is a proper entry site and residence for viruses, and whereby infection, can lead to asymptomatic, mild, self-limiting, severe or even fatal infection. Finally, we overgeneralize the effects of microbiota on COVID-19 infection. In addition, we reviewed the articles about effects of the microbiota on coronaviruses and suggest some new therapeutic measures.
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Affiliation(s)
- Taha Baghbani
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Hossein Nikzad
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Javid Azadbakht
- Department of Radiology, Faculty of Medicin, Kashan University of Medical Sciences, Kashan, Iran
| | - Fatemeh Izadpanah
- Food and Drug Laboratory Research Center and Food and Drug Reference Control Laboratories Center, Food & Drug Administration of Iran, MOH & ME, Tehran, Iran
| | - Hamed Haddad Kashani
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran.
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Giuffrè M, Moretti R, Campisciano G, da Silveira ABM, Monda VM, Comar M, Di Bella S, Antonello RM, Luzzati R, Crocè LS. You Talking to Me? Says the Enteric Nervous System (ENS) to the Microbe. How Intestinal Microbes Interact with the ENS. J Clin Med 2020; 9:E3705. [PMID: 33218203 PMCID: PMC7699249 DOI: 10.3390/jcm9113705] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022] Open
Abstract
Mammalian organisms form intimate interfaces with commensal and pathogenic gut microorganisms. Increasing evidence suggests a close interaction between gut microorganisms and the enteric nervous system (ENS), as the first interface to the central nervous system. Each microorganism can exert a different effect on the ENS, including phenotypical neuronal changes or the induction of chemical transmitters that interact with ENS neurons. Some pathogenic bacteria take advantage of the ENS to create a more suitable environment for their growth or to promote the effects of their toxins. In addition, some commensal bacteria can affect the central nervous system (CNS) by locally interacting with the ENS. From the current knowledge emerges an interesting field that may shape future concepts on the pathogen-host synergic interaction. The aim of this narrative review is to report the current findings regarding the inter-relationships between bacteria, viruses, and parasites and the ENS.
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Affiliation(s)
- Mauro Giuffrè
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.G.); (R.M); (R.M.A.); (R.L.); (L.S.C.)
- Italian Liver Foundation, 34129 Trieste, Italy
| | - Rita Moretti
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.G.); (R.M); (R.M.A.); (R.L.); (L.S.C.)
| | - Giuseppina Campisciano
- Department of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health-IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (G.C.); (M.C.)
| | | | | | - Manola Comar
- Department of Advanced Microbiology Diagnosis and Translational Research, Institute for Maternal and Child Health-IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (G.C.); (M.C.)
| | - Stefano Di Bella
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.G.); (R.M); (R.M.A.); (R.L.); (L.S.C.)
| | - Roberta Maria Antonello
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.G.); (R.M); (R.M.A.); (R.L.); (L.S.C.)
| | - Roberto Luzzati
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.G.); (R.M); (R.M.A.); (R.L.); (L.S.C.)
| | - Lory Saveria Crocè
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34149 Trieste, Italy; (M.G.); (R.M); (R.M.A.); (R.L.); (L.S.C.)
- Italian Liver Foundation, 34129 Trieste, Italy
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48
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Lajqi T, Stojiljkovic M, Williams DL, Hudalla H, Bauer M, Witte OW, Wetzker R, Bauer R, Schmeer C. Memory-Like Responses of Brain Microglia Are Controlled by Developmental State and Pathogen Dose. Front Immunol 2020; 11:546415. [PMID: 33101271 PMCID: PMC7546897 DOI: 10.3389/fimmu.2020.546415] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 08/14/2020] [Indexed: 01/01/2023] Open
Abstract
Microglia, the innate immune cells of the central nervous system, feature adaptive immune memory with implications for brain homeostasis and pathologies. However, factors involved in the emergence and regulation of these opposing responses in microglia have not been fully addressed. Recently, we showed that microglia from the newborn brain display features of trained immunity and immune tolerance after repeated contact with pathogens in a dose-dependent manner. Here, we evaluate the impact of developmental stage on adaptive immune responses of brain microglia after repeated challenge with ultra-low (1 fg/ml) and high (100 ng/ml) doses of the endotoxin LPS in vitro. We find that priming of naïve microglia derived from newborn but not mature and aged murine brain with ultra-low LPS significantly increased levels of pro-inflammatory mediators TNF-α, IL-6, IL-1β, MMP-9, and iNOS as well as neurotrophic factors indicating induction of trained immunity (p < 0.05). In contrast, stimulation with high doses of LPS led to a robust downregulation of pro-inflammatory cytokines and iNOS independent of the developmental state, indicating induced immune tolerance. Furthermore, high-dose priming with LPS upregulated anti-inflammatory mediators IL-10, Arg-1, TGF- β, MSR1, and IL-4 in newborn microglia (p < 0.05). Our data indicate pronounced plasticity of the immune response of neonate microglia compared with microglia derived from mature and aged mouse brain. Induced trained immunity after priming with ultra-low LPS doses may be responsible for enhanced neuro-inflammatory susceptibility of immature brain. In contrast, the immunosuppressed phenotype following high-dose LPS priming might be prone to attenuate excessive damage after recurrent systemic inflammation.
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Affiliation(s)
- Trim Lajqi
- Institute of Molecular Cell Biology, Jena University Hospital, Jena, Germany.,Department of Neonatology, Heidelberg University Children's Hospital, Heidelberg, Germany
| | - Milan Stojiljkovic
- Hans-Berger Department of Neurology, Jena University Hospital, Jena, Germany
| | - David L Williams
- Department of Surgery and Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Hannes Hudalla
- Department of Neonatology, Heidelberg University Children's Hospital, Heidelberg, Germany
| | - Michael Bauer
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
| | - Otto W Witte
- Hans-Berger Department of Neurology, Jena University Hospital, Jena, Germany.,Jena Center for Healthy Aging, Jena University Hospital, Jena, Germany
| | - Reinhard Wetzker
- Department of Anesthesiology and Intensive Care Medicine, Jena University Hospital, Jena, Germany
| | - Reinhard Bauer
- Institute of Molecular Cell Biology, Jena University Hospital, Jena, Germany
| | - Christian Schmeer
- Hans-Berger Department of Neurology, Jena University Hospital, Jena, Germany
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49
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Zheng L, Liang X, Shi R, Li P, Zhao J, Li G, Wang S, Han S, Radosevich M, Zhang Y. Viral Abundance and Diversity of Production Fluids in Oil Reservoirs. Microorganisms 2020; 8:microorganisms8091429. [PMID: 32957569 PMCID: PMC7563284 DOI: 10.3390/microorganisms8091429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 11/16/2022] Open
Abstract
Viruses are widely distributed in various ecosystems and have important impacts on microbial evolution, community structure and function and nutrient cycling in the environment. Viral abundance, diversity and distribution are important for a better understanding of ecosystem functioning and have often been investigated in marine, soil, and other environments. Though microbes have proven useful in oil recovery under extreme conditions, little is known about virus community dynamics in such systems. In this study, injection water and production fluids were sampled in two blocks of the Daqing oilfield limited company where water flooding and microbial flooding were continuously used to improve oil recovery. Virus-like particles (VLPs) and bacteria in these samples were extracted and enumerated with epifluorescence microscopy, and viromes of these samples were also sequenced with Illumina Hiseq PE150. The results showed that a large number of viruses existed in the oil reservoir, and VLPs abundance of production wells was 3.9 ± 0.7 × 108 mL-1 and virus to bacteria ratio (VBR) was 6.6 ± 1.1 during water flooding. Compared with water flooding, the production wells of microbial flooding had relative lower VLPs abundance (3.3 ± 0.3 × 108 mL-1) but higher VBR (7.9 ± 2.2). Assembled viral contigs were mapped to an in-house virus reference data separate from the GenBank non-redundant nucleotide (NT) database, and the sequences annotated as virus accounted for 35.34 and 55.04% of total sequences in samples of water flooding and microbial flooding, respectively. In water flooding, 7 and 6 viral families were identified in the injection and production wells, respectively. In microbial flooding, 6 viral families were identified in the injection and production wells. The total number of identified viral species in the injection well was higher than that in the production wells for both water flooding and microbial flooding. The Shannon diversity index was higher in the production well of water flooding than in the production well of microbial flooding. These results show that viruses are very abundant and diverse in the oil reservoir's ecosystem, and future efforts are needed to reveal the potential function of viral communities in this extreme environment.
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Affiliation(s)
- Liangcan Zheng
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolong Liang
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, TN 37996, USA; (X.L.); (M.R.)
| | - Rongjiu Shi
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
| | - Ping Li
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinyi Zhao
- No. 2 Oil Production Company, Daqing Oilfield Limited Company, Daqing 163414, China; (J.Z.); (G.L.)
| | - Guoqiao Li
- No. 2 Oil Production Company, Daqing Oilfield Limited Company, Daqing 163414, China; (J.Z.); (G.L.)
| | - Shuang Wang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
| | - Siqin Han
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
| | - Mark Radosevich
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, TN 37996, USA; (X.L.); (M.R.)
| | - Ying Zhang
- Key Laboratory of Pollution Ecology and Environmental Engineering, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China; (L.Z.); (R.S.); (P.L.); (S.W.); (S.H.)
- Correspondence:
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50
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Zhang W, Gu Q, Niu J, Wang JJ. The RNA Virome and Its Dynamics in an Invasive Fruit Fly, Bactrocera dorsalis, Imply Interactions Between Host and Viruses. MICROBIAL ECOLOGY 2020; 80:423-434. [PMID: 32300830 DOI: 10.1007/s00248-020-01506-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/17/2020] [Indexed: 06/11/2023]
Abstract
The oriental fruit fly, Bactrocera dorsalis (Hendel), is an important invasive agricultural insect pest with a wide host range, and has spread around the world over the last century. This evolutionary trait may have arisen primarily from interactions between B. dorsalis and other invertebrates that share the same ecological niches. The invasive behavior of B. dorsalis also frequently exposes them to diverse species of viruses. Thereby, RNA viromes may be useful microbial markers to understand the ecological evolution of B. dorsalis as well as to investigate virus-host interactions. Here, we reported eight novel RNA viruses in B. dorsalis of a lab colony, including four positive-strand RNA viruses, two negative-strand RNA viruses, and two double-stranded RNA viruses using high-throughput sequencing technology. Analysis of the virus-derived small RNAs suggested that most of these viruses may be active and trigger the host antiviral RNAi responses. The viruses were also detected in various geographical populations of B. dorsalis, implying that there is a strong association between the viromes and host. In addition, these viruses infected specific fly tissues, predominately the central nervous system and gut. Furthermore, we explored the dynamics of the viruses when hosts were exposed to short- or long-term stressors, which showed that titers of some viruses were responsively altered in the stressed B. dorsalis. The discovery of these viruses may enrich our understanding of the species diversity of RNA viruses and also provide information on viruses in association with host adaptation in insects.
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Affiliation(s)
- Wei Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Qiaoying Gu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China.
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