1
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Jiang D, Goswami R, Dennis M, Heimsath H, Kozlowski PA, Ardeshir A, Van Rompay KKA, De Paris K, Permar SR, Surana NK. Sutterella and its metabolic pathways positively correlate with vaccine-elicited antibody responses in infant rhesus macaques. Front Immunol 2023; 14:1283343. [PMID: 38124733 PMCID: PMC10731017 DOI: 10.3389/fimmu.2023.1283343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction It is becoming clearer that the microbiota helps drive responses to vaccines; however, little is known about the underlying mechanism. In this study, we aimed to identify microbial features that are associated with vaccine immunogenicity in infant rhesus macaques. Methods We analyzed 16S rRNA gene sequencing data of 215 fecal samples collected at multiple timepoints from 64 nursery-reared infant macaques that received various HIV vaccine regimens. PERMANOVA tests were performed to determine factors affecting composition of the gut microbiota throughout the first eight months of life in these monkeys. We used DESeq2 to identify differentially abundant bacterial taxa, PICRUSt2 to impute metagenomic information, and mass spectrophotometry to determine levels of fecal short-chain fatty acids and bile acids. Results Composition of the early-life gut microbial communities in nursery-reared rhesus macaques from the same animal care facility was driven by age, birth year, and vaccination status. We identified a Sutterella and a Rodentibacter species that positively correlated with vaccine-elicited antibody responses, with the Sutterella species exhibiting more robust findings. Analysis of Sutterella-related metagenomic data revealed five metabolic pathways that significantly correlated with improved antibody responses following HIV vaccination. Given these pathways have been associated with short-chain fatty acids and bile acids, we quantified the fecal concentration of these metabolites and found several that correlated with higher levels of HIV immunogen-elicited plasma IgG. Discussion Our findings highlight an intricate bidirectional relationship between the microbiota and vaccines, where multiple aspects of the vaccination regimen modulate the microbiota and specific microbial features facilitate vaccine responses. An improved understanding of this microbiota-vaccine interplay will help develop more effective vaccines, particularly those that are tailored for early life.
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Affiliation(s)
- Danting Jiang
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, United States
- Program in Computational Biology and Bioinformatics, Duke University School of Medicine, Durham, NC, United States
| | - Ria Goswami
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, United States
| | - Maria Dennis
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, United States
| | - Holly Heimsath
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States
| | - Pamela A. Kozlowski
- Department of Microbiology, Immunology and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Amir Ardeshir
- California National Primate Research Center, University of California, Davis, Davis, CA, United States
| | - Koen K. A. Van Rompay
- California National Primate Research Center, University of California, Davis, Davis, CA, United States
| | - Kristina De Paris
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States
| | - Sallie R. Permar
- Department of Pediatrics, Weill Cornell Medicine, New York, NY, United States
| | - Neeraj K. Surana
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, United States
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, NC, United States
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, United States
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2
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Zabel B, Mäkelä SM, Nedveck D, Hibberd AA, Yeung N, Latvala S, Lehtoranta L, Junnila J, Walters KB, Morovic W, Lehtinen MJ. The Effect of Bifidobacterium animalis subsp. lactis Bl-04 on Influenza A Virus Infection in Mice. Microorganisms 2023; 11:2582. [PMID: 37894240 PMCID: PMC10609243 DOI: 10.3390/microorganisms11102582] [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: 09/11/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Influenza A virus infection is a major global disease requiring annual vaccination. Clinical studies indicate that certain probiotics may support immune function against influenza and other respiratory viruses, but direct molecular evidence is scarce. Here, mice were treated with a placebo or Bifidobacterium animalis subsp. lactis Bl-04 (Bl-04) orally via food (cereal) and also by gavage and exposed to Influenza A virus H1N1 (H1N1). The symptoms of the infection were observed, and tissues and digesta were collected for viral load RT-qPCR, transcriptomics, and microbiomics. The treatment decreased the viral load by 48% at day 3 post-infection in lungs and symptoms of infection at day 4 compared to placebo. Tissue transcriptomics showed differences between the Bl-04 and placebo groups in the genes in the Influenza A pathway in the intestine, blood, and lungs prior to and post-infection, but the results were inconclusive. Moreover, 16S rRNA gene profiling and qPCR showed the presence of Bl-04 in the intestine, but without major shifts in the microbiome. In conclusion, Bl-04 treatment may influence the host response against H1N1 in a murine challenge model; however, further studies are required to elucidate the mechanism of action.
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Affiliation(s)
- Bryan Zabel
- Health & Biosciences, International Flavors & Fragrances, 3329 Agriculture Dr., Madison, WI 53716, USA
| | - Sanna M Mäkelä
- Health & Biosciences, International Flavors & Fragrances, Sokeritehtaantie 20, 02460 Kantvik, Finland
| | - Derek Nedveck
- Health & Biosciences, International Flavors & Fragrances, 3329 Agriculture Dr., Madison, WI 53716, USA
| | - Ashley A Hibberd
- Health & Biosciences, International Flavors & Fragrances, 3329 Agriculture Dr., Madison, WI 53716, USA
| | - Nicolas Yeung
- Health & Biosciences, International Flavors & Fragrances, Sokeritehtaantie 20, 02460 Kantvik, Finland
| | - Sinikka Latvala
- Health & Biosciences, International Flavors & Fragrances, Sokeritehtaantie 20, 02460 Kantvik, Finland
| | - Liisa Lehtoranta
- Health & Biosciences, International Flavors & Fragrances, Sokeritehtaantie 20, 02460 Kantvik, Finland
| | | | - Kevin B Walters
- Department of Infectious Disease Research, Southern Research Institute, 431 Aviation Way, Frederick, MD 21701, USA
| | - Wesley Morovic
- Health & Biosciences, International Flavors & Fragrances, 3329 Agriculture Dr., Madison, WI 53716, USA
| | - Markus J Lehtinen
- Health & Biosciences, International Flavors & Fragrances, Sokeritehtaantie 20, 02460 Kantvik, Finland
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3
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Li H, Wu X, Zeng H, Chang B, Cui Y, Zhang J, Wang R, Ding T. Unique microbial landscape in the human oropharynx during different types of acute respiratory tract infections. MICROBIOME 2023; 11:157. [PMID: 37482605 PMCID: PMC10364384 DOI: 10.1186/s40168-023-01597-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 06/12/2023] [Indexed: 07/25/2023]
Abstract
BACKGROUND Secondary bacterial infections and pneumonia are major mortality causes of respiratory viruses, and the disruption of the upper respiratory tract (URT) microbiota is a crucial component of this process. However, whether this URT dysbiosis associates with the viral species (in other words, is viral type-specific) is unclear. RESULTS Here, we recruited 735 outpatients with upper respiratory symptoms, identified the infectious virus types in 349 participants using multiplex RT-PCR, and profiled their upper respiratory microbiome using the 16S ribosomal RNA gene and metagenomic gene sequencing. Microbial and viral data were subsequently used as inputs for multivariate analysis aimed at revealing viral type-specific disruption of the upper respiratory microbiota. We found that the oropharyngeal microbiota shaped by influenza A virus (FluA), influenza B virus (FluB), respiratory syncytial virus (RSV), and human rhinovirus (HRV) infections exhibited three distinct patterns of dysbiosis, and Veillonella was identified as a prominent biomarker for any type of respiratory viral infections. Influenza virus infections are significantly correlated with increased oropharynx microbiota diversity and enrichment of functional metabolic pathways such as L-arginine biosynthesis and tetracycline resistance gene tetW. We used the GRiD algorithm and found the predicted growth rate of common respiratory pathogens was increased upon influenza virus infection, while commensal bacteria, such as Streptococcus infantis and Streptococcus mitis, may act as a colonization resistance to the overgrowth of these pathogens. CONCLUSIONS We found that respiratory viral infections are linked with viral type-specific disruption of the upper respiratory microbiota, particularly, influenza infections uniquely associated with increased microbial diversity and growth rates of specific pathogens in URT. These findings are essential for clarifying the differences and dynamics of respiratory microbiota in healthy participants and acute respiratory viral infections, which contribute to elucidating the pathogenesis of viral-host-bacterial interactions to provide insights into future studies on effective prevention and treatment of respiratory tract infections. Video Abstract.
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Affiliation(s)
- Hui Li
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Xiaorong Wu
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Hong Zeng
- Center for Disease Control and Prevention of Nanhai District, Foshan, 528200, China
| | - Bozhen Chang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Ying Cui
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Jingxiang Zhang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Ruixia Wang
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China
| | - Tao Ding
- Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, China.
- Key Laboratory of Tropical Diseases Control (Sun Yat-Sen University), Ministry of Education, Guangzhou, 510080, China.
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Huang J, Xu Y. Autoimmunity: A New Focus on Nasal Polyps. Int J Mol Sci 2023; 24:ijms24098444. [PMID: 37176151 PMCID: PMC10179643 DOI: 10.3390/ijms24098444] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Chronic rhinosinusitis with nasal polyps (CRSwNP) has long been considered a benign, chronic inflammatory, and hyperplastic disease. Recent studies have shown that autoimmune-related mechanisms are involved in the pathology of nasal polyps. Activated plasma cells, eosinophils, basophils, innate type 2 lymphocytes, mast cells, and proinflammatory cytokine in polyp tissue indicate the mobilization of innate and adaptive immune pathways during polyp formation. The discovery of a series of autoantibodies further supports the autoimmune nature of nasal polyps. Local homeostasis dysregulation, infection, and chronic inflammation may trigger autoimmunity through several mechanisms, including autoantigens overproduction, microbial translocation, molecular mimicry, superantigens, activation or inhibition of receptors, bystander activation, dysregulation of Toll-Like Receptors (TLRs), epitope spreading, autoantigens complementarity. In this paper, we elaborated on the microbiome-mediated mechanism, abnormal host immunity, and genetic changes to update the role of autoimmunity in the pathogenesis of chronic rhinosinusitis with nasal polyps.
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Affiliation(s)
- Jingyu Huang
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Yu Xu
- Department of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
- Research Institute of Otolaryngology-Head and Neck Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, China
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5
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Sarkar S, Routhray S, Ramadass B, Parida PK. A Review on the Nasal Microbiome and Various Disease Conditions for Newer Approaches to Treatments. Indian J Otolaryngol Head Neck Surg 2023; 75:755-763. [PMID: 37206729 PMCID: PMC10188862 DOI: 10.1007/s12070-022-03205-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/23/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction: Commensal bacteria have always played a significant role in the maintenance of health and disease but are being unravelled only recently. Studies suggest that the nasal microbiome has a significant role in the development of various disease conditions. Search engines were used for searching articles having a nasal microbiome and disease correlation. In olfactory dysfunction, dysbiosis of the microbiome may have a significant role to play in the pathogenesis. The nasal microbiome influences the phenotype of CRS and is also capable of modulating the immune response and plays a role in polyp formation. Microbiome dysbiosis has a pivotal role in the development of Allergic Rhinitis; but, yet known how is this role played. The nasal microbiome has a close association with the severity and phenotype of asthma. They contribute significantly to the onset, severity, and development of asthma. The nasal microbiome has a significant impact on the immunity and protection of its host. The nasal microbiome has been a stimulus in the development of Otitis Media and its manifestations. Studies suggest that the resident nasal microbiome is responsible for the initiation of neurodegenerative diseases like Parkinson's Disease.Materials and Methods: Literature search from PubMed, Medline, and Google with the Mesh terms: nasal microbiome AND diseases. Conclusion: With increasing evidence on the role of the nasal microbiome on various diseases, it would be interesting to see how this microbiome can be modulated by pro/pre/post biotics to prevent a disease or the severity of illness.
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Affiliation(s)
- Saurav Sarkar
- Department of Otorhinolaryngology and Head Neck Surgery, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Samapika Routhray
- Department of Dentistry, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Balamurugan Ramadass
- Department of Biochemistry, All India Institute of Medical Sciences, Bhubaneswar, India
| | - Pradipta Kumar Parida
- Department of Otorhinolaryngology and Head Neck Surgery, All India Institute of Medical Sciences, Bhubaneswar, India
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6
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Hernández-Terán A, Vega-Sánchez AE, Mejía-Nepomuceno F, Serna-Muñoz R, Rodríguez-Llamazares S, Salido-Guadarrama I, Romero-Espinoza JA, Guadarrama-Pérez C, Sandoval-Gutierrez JL, Campos F, Mondragón-Rivero EN, Ramírez-Venegas A, Castillejos-López M, Téllez-Navarrete NA, Pérez-Padilla R, Vázquez-Pérez JA. Microbiota composition in the lower respiratory tract is associated with severity in patients with acute respiratory distress by influenza. Virol J 2023; 20:19. [PMID: 36726151 PMCID: PMC9891757 DOI: 10.1186/s12985-023-01979-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/28/2023] [Indexed: 02/03/2023] Open
Abstract
Several factors are associated with the severity of the respiratory disease caused by the influenza virus. Although viral factors are one of the most studied, in recent years the role of the microbiota and co-infections in severe and fatal outcomes has been recognized. However, most of the work has focused on the microbiota of the upper respiratory tract (URT), hindering potential insights from the lower respiratory tract (LRT) that may help to understand the role of the microbiota in Influenza disease. In this work, we characterized the microbiota of the LRT of patients with Influenza A using 16S rRNA sequencing. We tested if patients with different outcomes (deceased/recovered) and use of antibiotics differ in their microbial community composition. We found important differences in the diversity and composition of the microbiota between deceased and recovered patients. In particular, we detected a high abundance of opportunistic pathogens such as Granulicatella, in patients either deceased or with antibiotic treatment. Also, we found antibiotic treatment correlated with lower diversity of microbial communities and with lower probability of survival in Influenza A patients. Altogether, the loss of microbial diversity could generate a disequilibrium in the community, potentially compromising the immune response increasing viral infectivity, promoting the growth of potentially pathogenic bacteria that, together with altered biochemical parameters, can be leading to severe forms of the disease. Overall, the present study gives one of the first characterizations of the diversity and composition of microbial communities in the LRT of Influenza patients and its relationship with clinical variables and disease severity.
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Affiliation(s)
- Alejandra Hernández-Terán
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Angel E. Vega-Sánchez
- grid.419179.30000 0000 8515 3604Servicio de Urgencias Médicas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Fidencio Mejía-Nepomuceno
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Ricardo Serna-Muñoz
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Sebastián Rodríguez-Llamazares
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Iván Salido-Guadarrama
- grid.419218.70000 0004 1773 5302Departamento de Bioinformática y Análisis Estadísticos, Instituto Nacional de Perinatología Isidro Espinosa De los Reyes, INPER, Ciudad de Mexico, Mexico
| | - Jose A. Romero-Espinoza
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Cristobal Guadarrama-Pérez
- grid.419179.30000 0000 8515 3604Servicio de Urgencias Médicas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Jose L. Sandoval-Gutierrez
- grid.419179.30000 0000 8515 3604Servicio Auxiliar de Diagnóstico y Paramédicos, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Fernando Campos
- grid.419179.30000 0000 8515 3604Unidad de Terapia Intensiva, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Erika N. Mondragón-Rivero
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Alejandra Ramírez-Venegas
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Manuel Castillejos-López
- grid.419179.30000 0000 8515 3604Departamento de Unidad de Epidemiología Hospitalaria e Infectología, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Norma A. Téllez-Navarrete
- grid.419179.30000 0000 8515 3604Laboratorio de Inmunología Integrativa, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Rogelio Pérez-Padilla
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
| | - Joel A. Vázquez-Pérez
- grid.419179.30000 0000 8515 3604Departamento de Investigación en Tabaquismo y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, INER, Ciudad de Mexico, Mexico
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Cai L, Xu H, Cui Z. Factors Limiting the Translatability of Rodent Model-Based Intranasal Vaccine Research to Humans. AAPS PharmSciTech 2022; 23:191. [PMID: 35819736 PMCID: PMC9274968 DOI: 10.1208/s12249-022-02330-9] [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: 01/11/2022] [Accepted: 06/09/2022] [Indexed: 12/19/2022] Open
Abstract
The intranasal route of vaccination presents an attractive alternative to parenteral routes and offers numerous advantages, such as the induction of both mucosal and systemic immunity, needle-free delivery, and increased patient compliance. Despite demonstrating promising results in preclinical studies, however, few intranasal vaccine candidates progress beyond early clinical trials. This discrepancy likely stems in part from the limited predictive value of rodent models, which are used frequently in intranasal vaccine research. In this review, we explored the factors that limit the translatability of rodent-based intranasal vaccine research to humans, focusing on the differences in anatomy, immunology, and disease pathology between rodents and humans. We also discussed approaches that minimize these differences and examined alternative animal models that would produce more clinically relevant research.
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Affiliation(s)
- Lucy Cai
- University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas, 75390, USA
| | - Haiyue Xu
- The University of Texas at Austin, College of Pharmacy, Division of Molecular Pharmaceutics and Drug Delivery, 2409 University Ave., A1900, Austin, Texas, 78712, USA
| | - Zhengrong Cui
- The University of Texas at Austin, College of Pharmacy, Division of Molecular Pharmaceutics and Drug Delivery, 2409 University Ave., A1900, Austin, Texas, 78712, USA.
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8
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Ferrari L, Favero C, Solazzo G, Mariani J, Luganini A, Ferraroni M, Montomoli E, Milani GP, Bollati V. Nasopharyngeal Bacterial Microbiota Composition and SARS-CoV-2 IgG Antibody Maintenance in Asymptomatic/Paucisymptomatic Subjects. Front Cell Infect Microbiol 2022; 12:882302. [PMID: 35873175 PMCID: PMC9297915 DOI: 10.3389/fcimb.2022.882302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/28/2022] [Indexed: 12/24/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes the coronavirus disease 2019 (COVID-19), ranging from asymptomatic conditions to severe/fatal lung injury and multi-organ failure. Growing evidence shows that the nasopharyngeal microbiota composition may predict the severity of respiratory infections and may play a role in the protection from viral entry and the regulation of the immune response to the infection. In the present study, we have characterized the nasopharyngeal bacterial microbiota (BNM) composition and have performed factor analysis in a group of 54 asymptomatic/paucisymptomatic subjects who tested positive for nasopharyngeal swab SARS-CoV-2 RNA and/or showed anti-RBD-IgG positive serology at the enrolment. We investigated whether BNM was associated with SARS-CoV-2 RNA positivity and serum anti-RBD-IgG antibody development/maintenance 20–28 weeks after the enrolment. Shannon’s entropy α-diversity index [odds ratio (OR) = 5.75, p = 0.0107] and the BNM Factor1 (OR = 2.64, p = 0.0370) were positively associated with serum anti-RBD-IgG antibody maintenance. The present results suggest that BNM composition may influence the immunological memory against SARS-CoV-2 infections. To the best of our knowledge, this is the first study investigating the link between BNM and specific IgG antibody maintenance. Further studies are needed to unveil the mechanisms through which the BNM influences the adaptive immune response against viral infections.
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Affiliation(s)
- Luca Ferrari
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Mila-no, Milan, Italy
- Department of Preventive Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Chiara Favero
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Mila-no, Milan, Italy
| | - Giulia Solazzo
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Mila-no, Milan, Italy
| | - Jacopo Mariani
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Mila-no, Milan, Italy
| | - Anna Luganini
- Laboratory of Microbiology and Virology, Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Turin, Italy
| | - Monica Ferraroni
- Branch of Medical Statistics, Biometry, and Epidemiology "G. A. Maccacaro", Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Emanuele Montomoli
- Department of Molecular and Developmental Medicine, Università degli Studi di Siena, Siena, Italy
| | - Gregorio Paolo Milani
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Pediatric Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Valentina Bollati
- EPIGET Lab, Department of Clinical Sciences and Community Health, Università degli Studi di Mila-no, Milan, Italy
- Department of Preventive Medicine, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- *Correspondence: Valentina Bollati,
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9
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Tamanai-Shacoori Z, Le Gall-David S, Moussouni F, Sweidan A, Polard E, Bousarghin L, Jolivet-Gougeon A. SARS-CoV-2 and Prevotella spp.: friend or foe? A systematic literature review. J Med Microbiol 2022; 71. [PMID: 35511246 DOI: 10.1099/jmm.0.001520] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
During this global pandemic of the COVID-19 disease, a lot of information has arisen in the media and online without scientific validation, and among these is the possibility that this disease could be aggravated by a secondary bacterial infection such as Prevotella, as well as the interest or not in using azithromycin, a potentially active antimicrobial agent. The aim of this study was to carry out a systematic literature review, to prove or disprove these allegations by scientific arguments. The search included Medline, PubMed, and Pubtator Central databases for English-language articles published 1999-2021. After removing duplicates, a total of final eligible studies (n=149) were selected. There were more articles showing an increase of Prevotella abundance in the presence of viral infection like that related to Human Immunodeficiency Virus (HIV), Papillomavirus (HPV), Herpesviridae and respiratory virus, highlighting differences according to methodologies and patient groups. The arguments for or against the use of azithromycin are stated in light of the results of the literature, showing the role of intercurrent factors, such as age, drug consumption, the presence of cancer or periodontal diseases. However, clinical trials are lacking to prove the direct link between the presence of Prevotella spp. and a worsening of COVID-19, mainly those using azithromycin alone in this indication.
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Affiliation(s)
- Zohreh Tamanai-Shacoori
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Sandrine Le Gall-David
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Fouzia Moussouni
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Alaa Sweidan
- Laboratory of Microbiology, Department of Life and Earth Sciences, Faculty of Sciences, Lebanese University, Hadath Campus, Beirut, Lebanon
| | - Elisabeth Polard
- Teaching Hospital Rennes, Service de Pharmacovigilance, F-35033 Rennes, France
| | - Latifa Bousarghin
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
| | - Anne Jolivet-Gougeon
- Univ Rennes, INSERM, INRAE, CHU Rennes, Institut NUMECAN (Nutrition Metabolisms and Cancer), F-35000 Rennes, France
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10
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Hou K, Wu ZX, Chen XY, Wang JQ, Zhang D, Xiao C, Zhu D, Koya JB, Wei L, Li J, Chen ZS. Microbiota in health and diseases. Signal Transduct Target Ther 2022; 7:135. [PMID: 35461318 PMCID: PMC9034083 DOI: 10.1038/s41392-022-00974-4] [Citation(s) in RCA: 544] [Impact Index Per Article: 272.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 02/07/2023] Open
Abstract
The role of microbiota in health and diseases is being highlighted by numerous studies since its discovery. Depending on the localized regions, microbiota can be classified into gut, oral, respiratory, and skin microbiota. The microbial communities are in symbiosis with the host, contributing to homeostasis and regulating immune function. However, microbiota dysbiosis can lead to dysregulation of bodily functions and diseases including cardiovascular diseases (CVDs), cancers, respiratory diseases, etc. In this review, we discuss the current knowledge of how microbiota links to host health or pathogenesis. We first summarize the research of microbiota in healthy conditions, including the gut-brain axis, colonization resistance and immune modulation. Then, we highlight the pathogenesis of microbiota dysbiosis in disease development and progression, primarily associated with dysregulation of community composition, modulation of host immune response, and induction of chronic inflammation. Finally, we introduce the clinical approaches that utilize microbiota for disease treatment, such as microbiota modulation and fecal microbial transplantation.
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Affiliation(s)
- Kaijian Hou
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, The First Affiliated Hospital of Medical College of Shantou University, Shantou, Guangdong, 515000, China
| | - Zhuo-Xun Wu
- Department of Pharmaceutical Sciences, Institute for Biotechnology, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA
| | - Xuan-Yu Chen
- Department of Pharmaceutical Sciences, Institute for Biotechnology, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA
| | - Jing-Quan Wang
- Department of Pharmaceutical Sciences, Institute for Biotechnology, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA
| | - Dongya Zhang
- Microbiome Research Center, Moon (Guangzhou) Biotech Ltd, Guangzhou, 510535, China
| | - Chuanxing Xiao
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, The First Affiliated Hospital of Medical College of Shantou University, Shantou, Guangdong, 515000, China
| | - Dan Zhu
- Department of Endocrine and Metabolic Diseases, Longhu Hospital, The First Affiliated Hospital of Medical College of Shantou University, Shantou, Guangdong, 515000, China
| | - Jagadish B Koya
- Department of Pharmaceutical Sciences, Institute for Biotechnology, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA
| | - Liuya Wei
- School of Pharmacy, Weifang Medical University, Weifang, Shandong, 261053, China
| | - Jilin Li
- Department of Cardiovascular, The Second Affiliated Hospital of Medical College of Shantou University, Shantou, Guangdong, 515000, China
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, Institute for Biotechnology, College of Pharmacy and Health Sciences, St. John's University, Queens, NY, 11439, USA
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11
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Lynn DJ, Benson SC, Lynn MA, Pulendran B. Modulation of immune responses to vaccination by the microbiota: implications and potential mechanisms. Nat Rev Immunol 2022; 22:33-46. [PMID: 34002068 PMCID: PMC8127454 DOI: 10.1038/s41577-021-00554-7] [Citation(s) in RCA: 111] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/12/2021] [Indexed: 02/05/2023]
Abstract
The need for highly effective vaccines that induce robust and long-lasting immunity has never been more apparent. However, for reasons that are still poorly understood, immune responses to vaccination are highly variable between different individuals and different populations. Furthermore, vaccine immunogenicity is frequently suboptimal in the very populations who are at most risk from infectious disease, including infants, the elderly, and those living in low-income and middle-income countries. Although many factors have the potential to influence vaccine immunogenicity and therefore vaccine effectiveness, increasing evidence from clinical studies and animal models now suggests that the composition and function of the gut microbiota are crucial factors modulating immune responses to vaccination. In this Review, we synthesize this evidence, discuss the immunological mechanisms that potentially mediate these effects and consider the potential of microbiota-targeted interventions to optimize vaccine effectiveness.
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Affiliation(s)
- David J Lynn
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia.
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia.
| | - Saoirse C Benson
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, South Australia, Australia
| | - Miriam A Lynn
- Precision Medicine Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
| | - Bali Pulendran
- Stanford University School of Medicine, Stanford University, Stanford, CA, USA
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12
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Fromentin M, Ricard JD, Roux D. Lung Microbiome in Critically Ill Patients. Life (Basel) 2021; 12:life12010007. [PMID: 35054400 PMCID: PMC8778861 DOI: 10.3390/life12010007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 12/11/2022] Open
Abstract
The historical hypothesis of sterility of the lungs was invalidated over a decade ago when studies demonstrated the existence of sparse but very diverse bacterial populations in the normal lung and the association between pulmonary dysbiosis and chronic respiratory diseases. Under mechanical ventilation, dysbiosis occurs rapidly with a gradual decline in diversity over time and the progressive predominance of a bacterial pathogen (mainly Proteobacteria) when lung infection occurs. During acute respiratory distress syndrome, an enrichment in bacteria of intestinal origin, mainly Enterobacteriaceae, is observed. However, the role of this dysbiosis in the pathogenesis of ventilator-associated pneumonia and acute respiratory distress syndrome is not yet fully understood. The lack of exploration of other microbial populations, viruses (eukaryotes and prokaryotes) and fungi is a key issue. Further analysis of the interaction between these microbial kingdoms and a better understanding of the host−microbiome interaction are necessary to fully elucidate the role of the microbiome in the pathogenicity of acute diseases. The validation of a consensual and robust methodology in order to make the comparison of the different studies relevant is also required. Filling these different gaps should help develop preventive and therapeutic strategies for both acute respiratory distress syndrome and ventilator-associated pneumonia.
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Affiliation(s)
- Mélanie Fromentin
- Anesthesiology and Intensive Care Department, AP-HP, Hôpital Cochin, 75014 Paris, France;
- UMR1137 IAME, Université de Paris, INSERM, 75018 Paris, France;
| | - Jean-Damien Ricard
- UMR1137 IAME, Université de Paris, INSERM, 75018 Paris, France;
- Médecine Intensive Réanimation, AP-HP, Hôpital Louis Mourier, DMU ESPRIT, 92700 Colombes, France
| | - Damien Roux
- Médecine Intensive Réanimation, AP-HP, Hôpital Louis Mourier, DMU ESPRIT, 92700 Colombes, France
- Institut Necker-Enfants Malades, Université de Paris, INSERM U1151, CNRS UMR 8253, 75015 Paris, France
- Correspondence: ; Tel.: +33-1-47-60-63-29
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13
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Haile AF, Woodfint RM, Kim E, Joldrichsen MR, Berhe N, Gebreyes WA, Boyaka PN. Broad-Spectrum and Gram-Negative-Targeting Antibiotics Differentially Regulate Antibody Isotype Responses to Injected Vaccines. Vaccines (Basel) 2021; 9:vaccines9111240. [PMID: 34835171 PMCID: PMC8619726 DOI: 10.3390/vaccines9111240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 11/19/2022] Open
Abstract
Antibiotics are extensively used worldwide for the treatment of common infections by agents such as E. coli and Salmonella. They also represent the most common cause of alteration of the microbiota in people. We addressed whether broad-spectrum and Gram-negative-targeting antibiotics differentially regulate systemic and mucosal immune responses to vaccines. Antibiotics treatment enhances serum IgG1 responses in mice immunized systemically with a model polyvalent vaccine. This increase was not seen for other IgG subclasses and was dependent on the immunogenicity of vaccine antigens. The broad-spectrum antibiotic cocktail also enhanced serum IgA responses. Interestingly, both the broad spectrum and the antibiotic targeting Gram-negative bacteria enhanced the number of IgA antibody secreting cells in the intestinal lamina propria. This effect was unlikely to be due to an increase in cells expressing gut-homing receptors (i.e., CCR9 and α4β7) in peripheral tissues. On the other hand, the microbiome in mice treated with antibiotics was characterized by an overall reduction of the number of firmicutes. Furthermore, Bacteroidetes were increased by either treatment, and Proteobacteria were increased by the broad-spectrum antibiotics cocktail. Thus, immunoglobulin isotype and subclass responses are differentially regulated by oral antibiotics treatment and the gut microbiota shapes mucosal antibody responses after systemic immunization.
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Affiliation(s)
- Aklilu F. Haile
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; (A.F.H.); (R.M.W.); (E.K.); (M.R.J.)
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa 1000, Ethiopia;
| | - Rachel M. Woodfint
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; (A.F.H.); (R.M.W.); (E.K.); (M.R.J.)
| | - Eunsoo Kim
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; (A.F.H.); (R.M.W.); (E.K.); (M.R.J.)
| | - Marisa R. Joldrichsen
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; (A.F.H.); (R.M.W.); (E.K.); (M.R.J.)
| | - Nega Berhe
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa 1000, Ethiopia;
| | - Wondwoossen A. Gebreyes
- Department of Preventive Medicine, The Ohio State University, Columbus, OH 43210, USA;
- Global One Health Initiative, The Ohio State University, Columbus, OH 43210, USA
- Infection Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Prosper N. Boyaka
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH 43210, USA; (A.F.H.); (R.M.W.); (E.K.); (M.R.J.)
- Global One Health Initiative, The Ohio State University, Columbus, OH 43210, USA
- Infection Diseases Institute, The Ohio State University, Columbus, OH 43210, USA
- Department Microbial Immunity and Infection, The Ohio State University, Columbus, OH 43210, USA
- Correspondence:
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14
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Elgamal Z, Singh P, Geraghty P. The Upper Airway Microbiota, Environmental Exposures, Inflammation, and Disease. ACTA ACUST UNITED AC 2021; 57:medicina57080823. [PMID: 34441029 PMCID: PMC8402057 DOI: 10.3390/medicina57080823] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 02/07/2023]
Abstract
Along with playing vital roles in pathogen exclusion and immune system priming, the upper airways (UAs) and their microbiota are essential for myriad physiological functions such as conditioning and transferring inhaled air. Dysbiosis, a microbial imbalance, is linked with various diseases and significantly impedes the quality of one’s life. Daily inhaled exposures and/or underlying conditions contribute to adverse changes to the UA microbiota. Such variations in the microbial community exacerbate UA and pulmonary disorders via modulating inflammatory and immune pathways. Hence, exploring the UA microbiota’s role in maintaining homeostasis is imperative. The microbial composition and subsequent relationship with airborne exposures, inflammation, and disease are crucial for strategizing innovating UA diagnostics and therapeutics. The development of a healthy UA microbiota early in life contributes to normal respiratory development and function in the succeeding years. Although different UA cavities present a unique microbial profile, geriatrics have similar microbes across their UAs. This lost community segregation may contribute to inflammation and disease, as it stimulates disadvantageous microbial–microbial and microbial–host interactions. Varying inflammatory profiles are associated with specific microbial compositions, while the same is true for many disease conditions and environmental exposures. A shift in the microbial composition is also detected upon the administration of numerous therapeutics, highlighting other beneficial and adverse side effects. This review examines the role of the UA microbiota in achieving homeostasis, and the impact on the UAs of environmental airborne pollutants, inflammation, and disease.
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Affiliation(s)
- Ziyad Elgamal
- Department of Biomedical Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Department of Medicine, Division of Pulmonary & Critical Care Medicine, State University of New York Downstate Medical Centre, Brooklyn, NY 11203, USA
| | - Pratyush Singh
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada;
| | - Patrick Geraghty
- Department of Medicine, Division of Pulmonary & Critical Care Medicine, State University of New York Downstate Medical Centre, Brooklyn, NY 11203, USA
- Correspondence: ; Tel.: +1-718-270-3141
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15
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Borey M, Blanc F, Lemonnier G, Leplat JJ, Jardet D, Rossignol MN, Ravon L, Billon Y, Bernard M, Estellé J, Rogel-Gaillard C. Links between fecal microbiota and the response to vaccination against influenza A virus in pigs. NPJ Vaccines 2021; 6:92. [PMID: 34294732 PMCID: PMC8298503 DOI: 10.1038/s41541-021-00351-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/11/2021] [Indexed: 02/06/2023] Open
Abstract
This study describes the associations between fecal microbiota and vaccine response variability in pigs, using 98 piglets vaccinated against the influenza A virus at 28 days of age (D28) with a booster at D49. Immune response to the vaccine is measured at D49, D56, D63, and D146 by serum levels of IAV-specific IgG and assays of hemagglutination inhibition (HAI). Analysis of the pre-vaccination microbiota characterized by 16S rRNA gene sequencing of fecal DNA reveals a higher vaccine response in piglets with a richer microbiota, and shows that 23 operational taxonomic units (OTUs) are differentially abundant between high and low IAV-specific IgG producers at D63. A stronger immune response is linked with OTUs assigned to the genus Prevotella and family Muribaculaceae, and a weaker response is linked with OTUs assigned to the genera Helicobacter and Escherichia-Shigella. A set of 81 OTUs accurately predicts IAV-specific IgG and HAI titer levels at all time points, highlighting early and late associations between pre-vaccination fecal microbiota composition and immune response to the vaccine.
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Affiliation(s)
- Marion Borey
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.
| | - Fany Blanc
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Gaëtan Lemonnier
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | - Deborah Jardet
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | | | | | - Maria Bernard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Jordi Estellé
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
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16
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Soffritti I, D’Accolti M, Fabbri C, Passaro A, Manfredini R, Zuliani G, Libanore M, Franchi M, Contini C, Caselli E. Oral Microbiome Dysbiosis Is Associated With Symptoms Severity and Local Immune/Inflammatory Response in COVID-19 Patients: A Cross-Sectional Study. Front Microbiol 2021; 12:687513. [PMID: 34248910 PMCID: PMC8261071 DOI: 10.3389/fmicb.2021.687513] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/07/2021] [Indexed: 12/14/2022] Open
Abstract
The human oral microbiome (HOM) is the second largest microbial community after the gut and can impact the onset and progression of several localized and systemic diseases, including those of viral origin, especially for viruses entering the body via the oropharynx. However, this important aspect has not been clarified for the new pandemic human coronavirus SARS-CoV-2, causing COVID-19 disease, despite it being one of the many respiratory viruses having the oropharynx as the primary site of replication. In particular, no data are available about the non-bacterial components of the HOM (fungi, viruses), which instead has been shown to be crucial for other diseases. Consistent with this, this study aimed to define the HOM in COVID-19 patients, to evidence any association between its profile and the clinical disease. Seventy-five oral rinse samples were analyzed by Whole Genome Sequencing (WGS) to simultaneously identify oral bacteria, fungi, and viruses. To correlate the HOM profile with local virus replication, the SARS-CoV-2 amount in the oral cavity was quantified by digital droplet PCR. Moreover, local inflammation and secretory immune response were also assessed, respectively by measuring the local release of pro-inflammatory cytokines (L-6, IL-17, TNFα, and GM-CSF) and the production of secretory immunoglobulins A (sIgA). The results showed the presence of oral dysbiosis in COVID-19 patients compared to matched controls, with significantly decreased alpha-diversity value and lower species richness in COVID-19 subjects. Notably, oral dysbiosis correlated with symptom severity (p = 0.006), and increased local inflammation (p < 0.01). In parallel, a decreased mucosal sIgA response was observed in more severely symptomatic patients (p = 0.02), suggesting that local immune response is important in the early control of virus infection and that its correct development is influenced by the HOM profile. In conclusion, the data presented here suggest that the HOM profile may be important in defining the individual susceptibility to SARS-CoV-2 infection, facilitating inflammation and virus replication, or rather, inducing a protective IgA response. Although it is not possible to determine whether the alteration in the microbial community is the cause or effect of the SARS-CoV-2 replication, these parameters may be considered as markers for personalized therapy and vaccine development.
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Affiliation(s)
- Irene Soffritti
- Section of Microbiology, CIAS Research Center and LTTA, Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | - Maria D’Accolti
- Section of Microbiology, CIAS Research Center and LTTA, Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | - Chiara Fabbri
- Section of Dentistry, Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Angela Passaro
- Unit of Internal Medicine, Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Roberto Manfredini
- Medical Clinic Unit, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Giovanni Zuliani
- Unit of Internal Medicine, Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Marco Libanore
- Unit of Infectious Diseases, University Hospital of Ferrara, Ferrara, Italy
| | - Maurizio Franchi
- Section of Dentistry, Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Carlo Contini
- Section of Infectious Diseases and Dermatology, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Elisabetta Caselli
- Section of Microbiology, CIAS Research Center and LTTA, Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
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17
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Zenobia C, Herpoldt KL, Freire M. Is the oral microbiome a source to enhance mucosal immunity against infectious diseases? NPJ Vaccines 2021; 6:80. [PMID: 34078913 PMCID: PMC8172910 DOI: 10.1038/s41541-021-00341-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/24/2021] [Indexed: 12/14/2022] Open
Abstract
Mucosal tissues act as a barrier throughout the oral, nasopharyngeal, lung, and intestinal systems, offering first-line protection against potential pathogens. Conventionally, vaccines are applied parenterally to induce serotype-dependent humoral response but fail to drive adequate mucosal immune protection for viral infections such as influenza, HIV, and coronaviruses. Oral mucosa, however, provides a vast immune repertoire against specific microbial pathogens and yet is shaped by an ever-present microbiome community that has co-evolved with the host over thousands of years. Adjuvants targeting mucosal T-cells abundant in oral tissues can promote soluble-IgA (sIgA)-specific protection to confer increased vaccine efficacy. Th17 cells, for example, are at the center of cell-mediated immunity and evidence demonstrates that protection against heterologous pathogen serotypes is achieved with components from the oral microbiome. At the point of entry where pathogens are first encountered, typically the oral or nasal cavity, the mucosal surfaces are layered with bacterial cohabitants that continually shape the host immune profile. Constituents of the oral microbiome including their lipids, outer membrane vesicles, and specific proteins, have been found to modulate the Th17 response in the oral mucosa, playing important roles in vaccine and adjuvant designs. Currently, there are no approved adjuvants for the induction of Th17 protection, and it is critical that this research is included in the preparedness for the current and future pandemics. Here, we discuss the potential of oral commensals, and molecules derived thereof, to induce Th17 activity and provide safer and more predictable options in adjuvant engineering to prevent emerging infectious diseases.
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Affiliation(s)
| | | | - Marcelo Freire
- Departments of Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, USA.
- Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
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18
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Reens AL, Cabral DJ, Liang X, Norton JE, Therien AG, Hazuda DJ, Swaminathan G. Immunomodulation by the Commensal Microbiome During Immune-Targeted Interventions: Focus on Cancer Immune Checkpoint Inhibitor Therapy and Vaccination. Front Immunol 2021; 12:643255. [PMID: 34054810 PMCID: PMC8155485 DOI: 10.3389/fimmu.2021.643255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/22/2021] [Indexed: 12/11/2022] Open
Abstract
Emerging evidence in clinical and preclinical studies indicates that success of immunotherapies can be impacted by the state of the microbiome. Understanding the role of the microbiome during immune-targeted interventions could help us understand heterogeneity of treatment success, predict outcomes, and develop additional strategies to improve efficacy. In this review, we discuss key studies that reveal reciprocal interactions between the microbiome, the immune system, and the outcome of immune interventions. We focus on cancer immune checkpoint inhibitor treatment and vaccination as two crucial therapeutic areas with strong potential for immunomodulation by the microbiota. By juxtaposing studies across both therapeutic areas, we highlight three factors prominently involved in microbial immunomodulation: short-chain fatty acids, microbe-associate molecular patterns (MAMPs), and inflammatory cytokines. Continued interrogation of these models and pathways may reveal critical mechanistic synergies between the microbiome and the immune system, resulting in novel approaches designed to influence the efficacy of immune-targeted interventions.
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Affiliation(s)
- Abigail L. Reens
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, United States
| | - Damien J. Cabral
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, United States
| | - Xue Liang
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, United States
| | - James E. Norton
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, United States
| | - Alex G. Therien
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, United States
| | - Daria J. Hazuda
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, United States
- Infectious Disease and Vaccine Research, Merck & Co., Inc., West Point, PA, United States
| | - Gokul Swaminathan
- Exploratory Science Center, Merck & Co., Inc., Cambridge, MA, United States
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19
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de Steenhuijsen Piters WAA, Binkowska J, Bogaert D. Early Life Microbiota and Respiratory Tract Infections. Cell Host Microbe 2021; 28:223-232. [PMID: 32791114 DOI: 10.1016/j.chom.2020.07.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/02/2020] [Accepted: 07/07/2020] [Indexed: 12/18/2022]
Abstract
Over the last decade, it has become clear that respiratory and intestinal tract microbiota are related to pathogenesis of respiratory tract infections (RTIs). Host and environmental factors can drive respiratory microbiota maturation in early life, which in turn is related to consecutive susceptibility to RTIs. Moreover, during RTIs, including viral bronchiolitis, the local microbiome appears to play an immunomodulatory role through complex interactions, though causality has not yet been fully demonstrated. The microbiota is subsequently associated with recovery after RTIs and can be related to persistent or long-term sequelae. In this Review, we explore the epidemiological evidence supporting these associations and link to mechanistic insights. The long-term consequences of childhood RTIs and the comprehensive role of the microbiota at various stages in RTI pathogenesis call for early life preventative and therapeutic interventions to promote respiratory health.
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Affiliation(s)
- Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands
| | - Justyna Binkowska
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, the Netherlands; National Institute for Public Health and the Environment, Antonie van Leeuwenhoeklaan 9, 3721 MA Bilthoven, the Netherlands; University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK.
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20
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From the Role of Microbiota in Gut-Lung Axis to SARS-CoV-2 Pathogenesis. Mediators Inflamm 2021; 2021:6611222. [PMID: 33953641 PMCID: PMC8059477 DOI: 10.1155/2021/6611222] [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: 11/03/2020] [Revised: 03/04/2021] [Accepted: 04/07/2021] [Indexed: 12/21/2022] Open
Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is responsible for the outbreak of a new viral respiratory infection. It has been demonstrated that the microbiota has a crucial role in establishing immune responses against respiratory infections, which are controlled by a bidirectional cross-talk, known as the “gut-lung axis.” The effects of microbiota on antiviral immune responses, including dendritic cell (DC) function and lymphocyte homing in the gut-lung axis, have been reported in the recent literature. Additionally, the gut microbiota composition affects (and is affected by) the expression of angiotensin-converting enzyme-2 (ACE2), which is the main receptor for SARS-CoV-2 and contributes to regulate inflammation. Several studies demonstrated an altered microbiota composition in patients infected with SARS-CoV-2, compared to healthy individuals. Furthermore, it has been shown that vaccine efficacy against viral respiratory infection is influenced by probiotics pretreatment. Therefore, the importance of the gut microbiota composition in the lung immune system and ACE2 expression could be valuable to provide optimal therapeutic approaches for SARS-CoV-2 and to preserve the symbiotic relationship of the microbiota with the host.
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Carniel BF, Marcon F, Rylance J, German EL, Zaidi S, Reiné J, Negera E, Nikolaou E, Pojar S, Solórzano C, Collins AM, Connor V, Bogaert D, Gordon SB, Nakaya HI, Ferreira DM, Jochems SP, Mitsi E. Pneumococcal colonization impairs mucosal immune responses to live attenuated influenza vaccine. JCI Insight 2021; 6:141088. [PMID: 33497364 PMCID: PMC7934923 DOI: 10.1172/jci.insight.141088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 01/15/2021] [Indexed: 12/16/2022] Open
Abstract
Influenza virus infections affect millions of people annually, and current available vaccines provide varying rates of protection. However, the way in which the nasal microbiota, particularly established pneumococcal colonization, shape the response to influenza vaccination is not yet fully understood. In this study, we inoculated healthy adults with live Streptococcuspneumoniae and vaccinated them 3 days later with either tetravalent-inactivated influenza vaccine (TIV) or live attenuated influenza vaccine (LAIV). Vaccine-induced immune responses were assessed in nose, blood, and lung. Nasal pneumococcal colonization had no impact upon TIV-induced antibody responses to influenza, which manifested in all compartments. However, experimentally induced pneumococcal colonization dampened LAIV-mediated mucosal antibody responses, primarily IgA in the nose and IgG in the lung. Pulmonary influenza-specific cellular responses were more apparent in the LAIV group compared with either the TIV or an unvaccinated group. These results indicate that TIV and LAIV elicit differential immunity to adults and that LAIV immunogenicity is diminished by the nasal presence of S. pneumoniae. Therefore, nasopharyngeal pneumococcal colonization may affect LAIV efficacy.
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Affiliation(s)
- Beatriz F Carniel
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Fernando Marcon
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Jamie Rylance
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Esther L German
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Seher Zaidi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Jesus Reiné
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Edessa Negera
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Elissavet Nikolaou
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Sherin Pojar
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Carla Solórzano
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Andrea M Collins
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom.,Royal Liverpool and Broadgreen University Hospital, Liverpool, United Kingdom
| | - Victoria Connor
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Debbie Bogaert
- Centre for Inflammation Research, Edinburgh Medical School, University of Edinburgh, Edinburgh, United Kingdom.,Department of Paediatric Immunology and Infectious Diseases, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Stephen B Gordon
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, Blantyre, Malawi
| | - Helder I Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paolo, Brazil
| | - Daniela M Ferreira
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Simon P Jochems
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Elena Mitsi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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22
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Beirão BCB, Ingberman M, Mesa D, Salles GBC, Muniz EC, Caron LF. Effects of aroA deleted E. coli vaccine on intestinal microbiota and mucosal immunity. Comp Immunol Microbiol Infect Dis 2021; 75:101612. [PMID: 33477024 DOI: 10.1016/j.cimid.2021.101612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/10/2021] [Accepted: 01/10/2021] [Indexed: 01/16/2023]
Abstract
E. coli infection of broilers can result in systemic diseases and productivity losses. Use of antimicrobials against this condition is common but other approaches, such as vaccination, are gaining ground. Anecdotal field reports indicate that intestinal health is improved unspecifically following E. coli live vaccination. We hypothesized that the intestine may be an important site for the functionality of the vaccine. Vaccine effects on the intestine were assessed. Spray vaccination induced marked alterations of the caecum microbiota of broilers within 3 days, and this effect gradually waned. However, T cell activation occurred in the spleen, but not in caecal tonsils, and anti-E. coli IgA was concentrated in the respiratory mucosae. Accordingly, IL-6 mRNA was produced in the lungs following immunization. Overall, these data are an initial indication that any vaccine-induced effects on the intestine are greatly associated with the microbiota. However, immunity conferred by vaccination is not primarily induced in gut-associated lymphoid tissues.
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Affiliation(s)
- Breno C B Beirão
- Imunova Análises Biológicas, Setor de Ciências Biológicas UFPR, Curitiba, PR, 81531-980, Brazil; Universidade Federal do Paraná, Setor de Ciências Biológicas UFPR, Curitiba, 81531-980, Brazil.
| | - Max Ingberman
- Imunova Análises Biológicas, Setor de Ciências Biológicas UFPR, Curitiba, PR, 81531-980, Brazil
| | - Dany Mesa
- Universidade Federal do Paraná, Setor de Ciências Biológicas UFPR, Curitiba, 81531-980, Brazil
| | - Gleidson B C Salles
- Zoetis Indústria de Produtos Veterinários Ltda, São Paulo, SP, 04709-111, Brazil
| | - Eduardo C Muniz
- Zoetis Indústria de Produtos Veterinários Ltda, São Paulo, SP, 04709-111, Brazil
| | - Luiz Felipe Caron
- Universidade Federal do Paraná, Setor de Ciências Biológicas UFPR, Curitiba, 81531-980, Brazil
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23
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Thibeault C, Suttorp N, Opitz B. The microbiota in pneumonia: From protection to predisposition. Sci Transl Med 2021; 13:13/576/eaba0501. [PMID: 33441423 DOI: 10.1126/scitranslmed.aba0501] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 06/30/2020] [Indexed: 12/12/2022]
Abstract
Mucosal surfaces of the upper respiratory tract and gut are physiologically colonized with their own collection of microbes, the microbiota. The normal upper respiratory tract and gut microbiota protects against pneumonia by impeding colonization by potentially pathogenic bacteria and by regulating immune responses. However, antimicrobial therapy and critical care procedures perturb the microbiota, thus compromising its function and predisposing to lung infections (pneumonia). Interindividual variations and age-related alterations in the microbiota also affect vulnerability to pneumonia. We discuss how the healthy microbiota protects against pneumonia and how host factors and medical interventions alter the microbiota, thus influencing susceptibility to pneumonia.
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Affiliation(s)
- Charlotte Thibeault
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Norbert Suttorp
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Bastian Opitz
- Department of Internal Medicine/Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany.
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24
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Di Stadio A, Costantini C, Renga G, Pariano M, Ricci G, Romani L. The Microbiota/Host Immune System Interaction in the Nose to Protect from COVID-19. Life (Basel) 2020; 10:life10120345. [PMID: 33322584 PMCID: PMC7763594 DOI: 10.3390/life10120345] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 12/12/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and is characterized by variable clinical presentation that ranges from asymptomatic to fatal multi-organ damage. The site of entry and the response of the host to the infection affect the outcomes. The role of the upper airways and the nasal barrier in the prevention of infection is increasingly being recognized. Besides the epithelial lining and the local immune system, the upper airways harbor a community of microorganisms, or microbiota, that takes an active part in mucosal homeostasis and in resistance to infection. However, the role of the upper airway microbiota in COVID-19 is not yet completely understood and likely goes beyond protection from viral entry to include the regulation of the immune response to the infection. Herein, we discuss the hypothesis that restoring endogenous barriers and anti-inflammatory pathways that are defective in COVID-19 patients might represent a valid strategy to reduce infectivity and ameliorate clinical symptomatology.
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Affiliation(s)
- Arianna Di Stadio
- Department of Otolaryngology, University of Perugia, 06132 Perugia, Italy;
- Correspondence: (A.D.S.); (L.R.)
| | - Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.C.); (G.R.); (M.P.)
| | - Giorgia Renga
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.C.); (G.R.); (M.P.)
| | - Marilena Pariano
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.C.); (G.R.); (M.P.)
| | - Giampietro Ricci
- Department of Otolaryngology, University of Perugia, 06132 Perugia, Italy;
| | - Luigina Romani
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy; (C.C.); (G.R.); (M.P.)
- Correspondence: (A.D.S.); (L.R.)
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25
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Bonato M, Borges LL, Ingberman M, Fávaro C, Mesa D, Caron LF, Beirão BC. Effects of yeast cell wall on immunity, microbiota, and intestinal integrity of Salmonella-infected broilers. J APPL POULTRY RES 2020. [DOI: 10.1016/j.japr.2020.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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26
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Tsang TK, Lee KH, Foxman B, Balmaseda A, Gresh L, Sanchez N, Ojeda S, Lopez R, Yang Y, Kuan G, Gordon A. Association Between the Respiratory Microbiome and Susceptibility to Influenza Virus Infection. Clin Infect Dis 2020; 71:1195-1203. [PMID: 31562814 PMCID: PMC7442850 DOI: 10.1093/cid/ciz968] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 09/26/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Previous studies suggest that the nose/throat microbiome may play an important role in shaping host immunity and modifying the risk of respiratory infection. Our aim is to quantify the association between the nose/throat microbiome and susceptibility to influenza virus infection. METHODS In this household transmission study, index cases with confirmed influenza virus infection and their household contacts were followed for 9-12 days to identify secondary influenza infections. Respiratory swabs were collected at enrollment to identify and quantify bacterial species via high-performance sequencing. Data were analyzed by an individual hazard-based transmission model that was adjusted for age, vaccination, and household size. RESULTS We recruited 115 index cases with influenza A(H3N2) or B infection and 436 household contacts. We estimated that a 10-fold increase in the abundance in Streptococcus spp. and Prevotella salivae was associated with 48% (95% credible interval [CrI], 9-69%) and 25% (95% CrI, 0.5-42%) lower susceptibility to influenza A(H3N2) infection, respectively. In contrast, for influenza B infection, a 10-fold increase in the abundance in Streptococcus vestibularis and Prevotella spp. was associated with 63% (95% CrI, 17-83%) lower and 83% (95% CrI, 15-210%) higher susceptibility, respectively. CONCLUSIONS Susceptibility to influenza infection is associated with the nose/throat microbiome at the time of exposure. The effects of oligotypes on susceptibility differ between influenza A(H3N2) and B viruses. Our results suggest that microbiome may be a useful predictor of susceptibility, with the implication that microbiome could be modulated to reduce influenza infection risk, should these associations be causal.
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Affiliation(s)
- Tim K Tsang
- Department of Biostatistics, University of Florida, Gainesville, Florida, USA
| | - Kyu Han Lee
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Betsy Foxman
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Angel Balmaseda
- Sustainable Sciences Institute, Managua, Nicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Lionel Gresh
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Nery Sanchez
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Sergio Ojeda
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Roger Lopez
- Sustainable Sciences Institute, Managua, Nicaragua
- Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Yang Yang
- Department of Biostatistics, University of Florida, Gainesville, Florida, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
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27
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Gosens R, Hiemstra PS, Adcock IM, Bracke KR, Dickson RP, Hansbro PM, Krauss-Etschmann S, Smits HH, Stassen FRM, Bartel S. Host-microbe cross-talk in the lung microenvironment: implications for understanding and treating chronic lung disease. Eur Respir J 2020; 56:13993003.02320-2019. [PMID: 32430415 PMCID: PMC7439216 DOI: 10.1183/13993003.02320-2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/20/2020] [Indexed: 12/15/2022]
Abstract
Chronic respiratory diseases are highly prevalent worldwide and will continue to rise in the foreseeable future. Despite intensive efforts over recent decades, the development of novel and effective therapeutic approaches has been slow. However, there is new and increasing evidence that communities of micro-organisms in our body, the human microbiome, are crucially involved in the development and progression of chronic respiratory diseases. Understanding the detailed mechanisms underlying this cross-talk between host and microbiota is critical for development of microbiome- or host-targeted therapeutics and prevention strategies. Here we review and discuss the most recent knowledge on the continuous reciprocal interaction between the host and microbes in health and respiratory disease. Furthermore, we highlight promising developments in microbiome-based therapies and discuss the need to employ more holistic approaches of restoring both the pulmonary niche and the microbial community. The reciprocal interaction between microbes and host in the lung is increasingly recognised as an important determinant of health. The complexity of this cross-talk needs to be taken into account when studying diseases and developing future new therapies.https://bit.ly/2VKYUfT
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Affiliation(s)
- Reinoud Gosens
- University of Groningen, Dept of Molecular Pharmacology, GRIAC Research Institute, Groningen, The Netherlands
| | - Pieter S Hiemstra
- Dept of Pulmonology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - Ian M Adcock
- Airways Disease, National Heart and Lung Institute, Imperial College London, London, UK
| | - Ken R Bracke
- Dept of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Dept of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.,Michigan Center for Integrative Research in Critical Care, Ann Arbor, MI, USA
| | - Philip M Hansbro
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and the University of Newcastle, Newcastle, Australia.,Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
| | - Susanne Krauss-Etschmann
- Early Life Origins of Chronic Lung Disease, Research Center Borstel, Leibniz Lung Center, Airway Research Center North, Member of the German Center for Lung Research (DZL), Borstel, Germany.,Institute for Experimental Medicine, Christian-Albrechts-Universitaet zu Kiel, Kiel, Germany
| | - Hermelijn H Smits
- Dept of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Frank R M Stassen
- Dept of Medical Microbiology, NUTRIM - School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Sabine Bartel
- Early Life Origins of Chronic Lung Disease, Research Center Borstel, Leibniz Lung Center, Airway Research Center North, Member of the German Center for Lung Research (DZL), Borstel, Germany .,University of Groningen, University Medical Center Groningen, Dept of Pathology and Medical Biology, GRIAC Research Institute, Groningen, The Netherlands
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28
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Munyaka PM, Blanc F, Estellé J, Lemonnier G, Leplat JJ, Rossignol MN, Jardet D, Plastow G, Billon Y, Willing BP, Rogel-Gaillard C. Discovery of Predictors of Mycoplasma hyopneumoniae Vaccine Response Efficiency in Pigs: 16S rRNA Gene Fecal Microbiota Analysis. Microorganisms 2020; 8:E1151. [PMID: 32751315 PMCID: PMC7464067 DOI: 10.3390/microorganisms8081151] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/22/2020] [Accepted: 07/27/2020] [Indexed: 01/18/2023] Open
Abstract
The gut microbiota comprises a large and diverse community of bacteria that play a significant role in swine health. Indeed, there is a tight association between the enteric immune system and the overall composition and richness of the microbiota, which is key in the induction, training and function of the host immunity, and may therefore, influence the immune response to vaccination. Using vaccination against Mycoplasma hyopneumoniae (M. hyo) as a model, we investigated the potential of early-life gut microbiota in predicting vaccine response and explored the post-vaccination dynamics of fecal microbiota at later time points. At 28 days of age (0 days post-vaccination; dpv), healthy piglets were vaccinated, and a booster vaccine was administered at 21 dpv. Blood samples were collected at 0, 21, 28, 35, and 118 dpv to measure M. hyo-specific IgG levels. Fecal samples for 16S rRNA gene amplicon sequencing were collected at 0, 21, 35, and 118 dpv. The results showed variability in antibody response among individual pigs, whilst pre-vaccination operational taxonomic units (OTUs) primarily belonging to Prevotella, [Prevotella], Anaerovibrio, and Sutterella appeared to best-predict vaccine response. Microbiota composition did not differ between the vaccinated and non-vaccinated pigs at post-vaccination time points, but the time effect was significant irrespective of the animals' vaccination status. Our study provides insight into the role of pre-vaccination gut microbiota composition in vaccine response and emphasizes the importance of studies on full metagenomes and microbial metabolites aimed at deciphering the role of specific bacteria and bacterial genes in the modulation of vaccine response.
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Affiliation(s)
- Peris M. Munyaka
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France; (P.M.M.); (F.B.); (J.E.); (G.L.); (J.-J.L.); (M.-N.R.); (D.J.)
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada; (G.P.); (B.P.W.)
| | - Fany Blanc
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France; (P.M.M.); (F.B.); (J.E.); (G.L.); (J.-J.L.); (M.-N.R.); (D.J.)
| | - Jordi Estellé
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France; (P.M.M.); (F.B.); (J.E.); (G.L.); (J.-J.L.); (M.-N.R.); (D.J.)
| | - Gaëtan Lemonnier
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France; (P.M.M.); (F.B.); (J.E.); (G.L.); (J.-J.L.); (M.-N.R.); (D.J.)
| | - Jean-Jacques Leplat
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France; (P.M.M.); (F.B.); (J.E.); (G.L.); (J.-J.L.); (M.-N.R.); (D.J.)
| | - Marie-Noëlle Rossignol
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France; (P.M.M.); (F.B.); (J.E.); (G.L.); (J.-J.L.); (M.-N.R.); (D.J.)
| | - Déborah Jardet
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France; (P.M.M.); (F.B.); (J.E.); (G.L.); (J.-J.L.); (M.-N.R.); (D.J.)
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada; (G.P.); (B.P.W.)
- Livestock Gentec, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | | | - Benjamin P. Willing
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB T6G 2R3, Canada; (G.P.); (B.P.W.)
| | - Claire Rogel-Gaillard
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France; (P.M.M.); (F.B.); (J.E.); (G.L.); (J.-J.L.); (M.-N.R.); (D.J.)
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Saso A, Kampmann B. Maternal Immunization: Nature Meets Nurture. Front Microbiol 2020; 11:1499. [PMID: 32849319 PMCID: PMC7396522 DOI: 10.3389/fmicb.2020.01499] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/09/2020] [Indexed: 12/17/2022] Open
Abstract
Vaccinating women in pregnancy (i.e., maternal immunization) has emerged as a promising tool to tackle infant morbidity and mortality worldwide. This approach nurtures a 'gift of nature,' whereby antibody is transferred from mother to fetus transplacentally during pregnancy, or postnatally in breast milk, thereby providing passive, antigen-specific protection against infections in the first few months of life, a period of increased immune vulnerability for the infant. In this review, we briefly summarize the rationale for maternal immunization programs and the landscape of vaccines currently in use or in the pipeline. We then direct the focus to the underlying biological phenomena, including the main mechanisms by which maternally derived antibody is transferred efficiently to the infant, at the placental interface or in breast milk; important research models and methodological approaches to interrogate these processes, particularly in the context of recent advances in systems vaccinology; the potential biological and clinical impact of high maternal antibody titres on neonatal ontogeny and subsequent infant vaccine responses; and key vaccine- and host-related factors influencing the maternal-infant dyad across different environments. Finally, we outline important gaps in knowledge and suggest future avenues of research on this topic, proposing potential strategies to ensure optimal testing, delivery and implementation of maternal vaccination programs worldwide.
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Affiliation(s)
- Anja Saso
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Vaccines and Immunity Theme, MRC Unit The Gambia at LSHTM, Banjul, Gambia
| | - Beate Kampmann
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Vaccines and Immunity Theme, MRC Unit The Gambia at LSHTM, Banjul, Gambia
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30
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Wait LF, Dobson AP, Graham AL. Do parasite infections interfere with immunisation? A review and meta-analysis. Vaccine 2020; 38:5582-5590. [DOI: 10.1016/j.vaccine.2020.06.064] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 05/12/2020] [Accepted: 06/21/2020] [Indexed: 12/18/2022]
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31
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Dimitri-Pinheiro S, Soares R, Barata P. The Microbiome of the Nose-Friend or Foe? ALLERGY & RHINOLOGY 2020; 11:2152656720911605. [PMID: 32206384 PMCID: PMC7074508 DOI: 10.1177/2152656720911605] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recently, multiple studies regarding the human microbiota and its role on the development of disease have emerged. Current research suggests that the nasal cavity is a major reservoir for opportunistic pathogens, which can then spread to other sections of the respiratory tract and be involved in the development of conditions such as allergic rhinitis, chronic rhinosinusitis, asthma, pneumonia, and otitis media. However, our knowledge of how nasal microbiota changes originate nasopharyngeal and respiratory conditions is still incipient. Herein, we describe how the nasal microbiome in healthy individuals varies with age and explore the effect of nasal microbiota changes in a range of infectious and immunological conditions. We also describe the potential health benefits of human microbiota modulation through probiotic use, both in disease prevention and as adjuvant therapy. Current research suggests that patients with different chronic rhinosinusitis phenotypes possess distinct nasal microbiota profiles, which influence immune response and may be used in the future as biomarkers of disease progression. Probiotic intervention may also have a promising role in the prevention and adjunctive treatment of acute respiratory tract infections and allergic rhinitis, respectively. However, further studies are needed to define the role of probiotics in the chronic rhinosinusitis.
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Affiliation(s)
- Sofia Dimitri-Pinheiro
- Hospital Centre of Vila Nova de Gaia/Espinho, Vila Nova de Gaia, Portugal.,Department of Biomedicine, Unit of Biochemistry, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Raquel Soares
- Department of Biomedicine, Unit of Biochemistry, Faculty of Medicine, University of Porto, Porto, Portugal.,I3S-Institute for Innovation and Health Research, University of Porto, Porto, Portugal
| | - Pedro Barata
- I3S-Institute for Innovation and Health Research, University of Porto, Porto, Portugal.,Faculty of Health Sciences, University of Fernando Pessoa, Porto, Portugal
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Marsh RL, Aho C, Beissbarth J, Bialasiewicz S, Binks M, Cervin A, Kirkham LAS, Lemon KP, Slack MPE, Smith-Vaughan HC. Panel 4: Recent advances in understanding the natural history of the otitis media microbiome and its response to environmental pressures. Int J Pediatr Otorhinolaryngol 2020; 130 Suppl 1:109836. [PMID: 31879084 PMCID: PMC7085411 DOI: 10.1016/j.ijporl.2019.109836] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To perform a comprehensive review of otitis media microbiome literature published between 1st July 2015 and 30th June 2019. DATA SOURCES PubMed database, National Library of Medicine. REVIEW METHODS Key topics were assigned to each panel member for detailed review. Draft reviews were collated and circulated for discussion when the panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019. The final draft was prepared with input from all panel members. CONCLUSIONS Much has been learned about the different types of bacteria (including commensals) present in the upper respiratory microbiome, but little is known about the virome and mycobiome. A small number of studies have investigated the middle ear microbiome; however, current data are often limited by small sample sizes and methodological heterogeneity between studies. Furthermore, limited reporting of sample collection methods mean that it is often difficult to determine whether bacteria detected in middle ear fluid specimens originated from the middle ear or the external auditory canal. Recent in vitro studies suggest that bacterial interactions in the nasal/nasopharyngeal microbiome may affect otitis media pathogenesis by modifying otopathogen behaviours. Impacts of environmental pressures (e.g. smoke, nutrition) and clinical interventions (e.g. vaccination, antibiotics) on the upper respiratory and middle ear microbiomes remain poorly understood as there are few data. IMPLICATIONS FOR PRACTICE Advances in understanding bacterial dynamics in the upper airway microbiome are driving development of microbiota-modifying therapies to prevent or treat disease (e.g. probiotics). Further advances in otitis media microbiomics will likely require technological improvements that overcome the current limitations of OMICs technologies when applied to low volume and low biomass specimens that potentially contain high numbers of host cells. Improved laboratory models are needed to elucidate mechanistic interactions among the upper respiratory and middle ear microbiomes. Minimum reporting standards are critically needed to improve inter-study comparisons and enable future meta-analyses.
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Affiliation(s)
- Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia.
| | - Celestine Aho
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Jemima Beissbarth
- Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia
| | - Seweryn Bialasiewicz
- The University of Queensland, Australian Centre for Ecogenomics, Queensland, Australia; Children's Health Queensland, Centre for Children's Health Research, Queensland, Australia
| | - Michael Binks
- Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia
| | - Anders Cervin
- The University of Queensland Centre for Clinical Research, Royal Brisbane & Women's Hospital, Queensland, Australia
| | - Lea-Ann S Kirkham
- Centre for Child Health Research, University of Western Australia, Western Australia, Australia; Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Western Australia, Australia
| | - Katherine P Lemon
- Forsyth Institute (Microbiology), USA and Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Massachusetts, USA; Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology and Pediatrics, Infectious Diseases Section, Texas Children's Hospital, Baylor College of Medicine, Texas, USA
| | - Mary P E Slack
- School of Medicine, Griffith University, Gold Coast Campus, Queensland, Australia
| | - Heidi C Smith-Vaughan
- Menzies School of Health Research, Charles Darwin University, Northern Territory, Australia; School of Medicine, Griffith University, Gold Coast Campus, Queensland, Australia
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Effects of 10-valent pneumococcal conjugate (PCV10) vaccination on the nasopharyngeal microbiome. Vaccine 2020; 38:1436-1443. [DOI: 10.1016/j.vaccine.2019.11.079] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 11/19/2019] [Accepted: 11/28/2019] [Indexed: 01/02/2023]
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Rowe HM, Rosch JW. Close Encounters of the Viral Kind: Cross-Kingdom Synergies at the Host-Pathogen Interface. Bioessays 2019; 41:e1900128. [PMID: 31693223 PMCID: PMC7050635 DOI: 10.1002/bies.201900128] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/27/2019] [Indexed: 12/29/2022]
Abstract
The synergies between viral and bacterial infections are well established. Most studies have been focused on the indirect mechanisms underlying this phenomenon, including immune modulation and alterations to the mucosal structures that promote pathogen outgrowth. A growing body of evidence implicates direct binding of virus to bacterial surfaces being an additional mechanism of synergy at the host-pathogen interface. These cross-kingdom interactions enhance bacterial and viral adhesion and can alter tissue tropism. These bacterial-viral complexes play unique roles in pathogenesis and can alter virulence potential. The bacterial-viral complexes may also play important roles in pathogen transmission. Additionally, the complexes are recognized by the host immune system in a distinct manner, thus presenting novel routes for vaccine development. These synergies are active for multiple species in both the respiratory and gastrointestinal tract, indicating that direct interactions between bacteria and virus to modulate host interactions are used by a diverse array of species.
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Affiliation(s)
- Hannah M Rowe
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jason W Rosch
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
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Vlasova AN, Takanashi S, Miyazaki A, Rajashekara G, Saif LJ. How the gut microbiome regulates host immune responses to viral vaccines. Curr Opin Virol 2019; 37:16-25. [PMID: 31163292 PMCID: PMC6863389 DOI: 10.1016/j.coviro.2019.05.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 02/07/2023]
Abstract
The co-evolution of the microbiota and immune system has forged a mutually beneficial relationship. This relationship allows the host to maintain the balance between active immunity to pathogens and vaccines and tolerance to self-antigens and food antigens. In children living in low-income and middle-income countries, undernourishment and repetitive gastrointestinal infections are associated with the failure of oral vaccines. Intestinal dysbiosis associated with these environmental influences, as well as some host-related factors, compromises immune responses and negatively impacts vaccine efficacy. To understand how immune responses to viral vaccines can be optimally modulated, mechanistic studies of the relationship between the microbiome, host genetics, viral infections and the development and function of the immune system are needed. We discuss the potential role of the microbiome in modulating vaccine responses in the context of a growing understanding of the relationship between the gastrointestinal microbiota, host related factors (including histo-blood group antigens) and resident immune cell populations.
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Affiliation(s)
- Anastasia N Vlasova
- Food Animal Health Research Program, CFAES, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA.
| | - Sayaka Takanashi
- Food Animal Health Research Program, CFAES, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA; Department of Developmental Medical Sciences, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ayako Miyazaki
- Division of Viral Disease and Epidemiology, National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-0856, Japan
| | - Gireesh Rajashekara
- Food Animal Health Research Program, CFAES, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA
| | - Linda J Saif
- Food Animal Health Research Program, CFAES, Ohio Agricultural Research and Development Center, Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Wooster, OH 44691, USA.
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de Steenhuijsen Piters WAA, Jochems SP, Mitsi E, Rylance J, Pojar S, Nikolaou E, German EL, Holloway M, Carniel BF, Chu MLJN, Arp K, Sanders EAM, Ferreira DM, Bogaert D. Interaction between the nasal microbiota and S. pneumoniae in the context of live-attenuated influenza vaccine. Nat Commun 2019; 10:2981. [PMID: 31278315 PMCID: PMC6611866 DOI: 10.1038/s41467-019-10814-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 05/15/2019] [Indexed: 12/21/2022] Open
Abstract
Streptococcus pneumoniae is the main bacterial pathogen involved in pneumonia. Pneumococcal acquisition and colonization density is probably affected by viral co-infections, the local microbiome composition and mucosal immunity. Here, we report the interactions between live-attenuated influenza vaccine (LAIV), successive pneumococcal challenge, and the healthy adult nasal microbiota and mucosal immunity using an experimental human challenge model. Nasal microbiota profiles at baseline are associated with consecutive pneumococcal carriage outcome (non-carrier, low-dense and high-dense pneumococcal carriage), independent of LAIV co-administration. Corynebacterium/Dolosigranulum-dominated profiles are associated with low-density colonization. Lowest rates of natural viral co-infection at baseline and post-LAIV influenza replication are detected in the low-density carriers. Also, we detected the fewest microbiota perturbations and mucosal cytokine responses in the low-density carriers compared to non-carriers or high-density carriers. These results indicate that the complete respiratory ecosystem affects pneumococcal behaviour following challenge, with low-density carriage representing the most stable ecological state.
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Affiliation(s)
- Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
- Medical Research Council/University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom
| | - Simon P Jochems
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Elena Mitsi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Jamie Rylance
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Sherin Pojar
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Elissavet Nikolaou
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Esther L German
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Mark Holloway
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Beatriz F Carniel
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Mei Ling J N Chu
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Kayleigh Arp
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands
| | - Elisabeth A M Sanders
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands
| | - Daniela M Ferreira
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, United Kingdom
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Lundlaan 6, Utrecht, 3584 EA, The Netherlands.
- Department of Medical Microbiology, University Medical Center Utrecht, Heidelberglaan 100, Utrecht, 3584 CX, The Netherlands.
- Medical Research Council/University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, United Kingdom.
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Microbial Composition of the Human Nasopharynx Varies According to Influenza Virus Type and Vaccination Status. mBio 2019; 10:mBio.01296-19. [PMID: 31266874 PMCID: PMC6606809 DOI: 10.1128/mbio.01296-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Our results suggest that there is a significant association between the composition of the microbiota in the nasopharynx and the influenza virus type causing the infection. We observe that vaccination status, especially in more senior individuals, also has an association with the microbial community profile. This indicates that vaccination against influenza, even when ineffective to prevent disease, could play a role in controlling secondary bacterial complications. Factors that contribute to enhanced susceptibility to severe bacterial disease after influenza virus infection are not well defined but likely include the microbiome of the respiratory tract. Vaccination against influenza, while having variable effectiveness, could also play a role in microbial community stability. We collected nasopharyngeal samples from 215 individuals infected with influenza A/H3N2 or influenza B virus and profiled the microbiota by target sequencing of the 16S rRNA gene. We identified signature taxonomic groups by performing linear discriminant analysis and effective size comparisons (LEfSe) and defined bacterial community types using Dirichlet multinomial mixture (DMM) models. Influenza infection was shown to be significantly associated with microbial composition of the nasopharynx according to the virus type and the vaccination status of the patient. We identified four microbial community types across the combined cohort of influenza patients and healthy individuals with one community type most representative of the influenza virus-infected group. We also identified microbial taxa for which relative abundance was significantly higher in the unvaccinated elderly group; these taxa include species known to be associated with pneumonia.
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Abstract
The use of next-generation sequencing and multiomic analysis reveals new insights on the identity of microbes in the lower airways blurring the lines between commensals and pathogens. Microbes are not found in isolation; rather they form complex metacommunities where microbe-host and microbe-microbe interactions play important roles on the host susceptibility to pathogens. In addition, the lower airway microbiota exert significant effects on host immune tone. Thus, this review highlights the roles that microbes in the respiratory tract play in the development of pneumonia.
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Affiliation(s)
- Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, NYU Human Microbiome Program, New York University School of Medicine, New York, NY 10028, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, NYU Human Microbiome Program, New York University School of Medicine, New York, NY 10028, USA.
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Abstract
Pneumonia is a highly prevalent disease with considerable morbidity and mortality. However, diagnosis and therapy still rely on antiquated methods, leading to the vast overuse of antimicrobials, which carries risks for both society and the individual. Furthermore, outcomes in severe pneumonia remain poor. Genomic techniques have the potential to transform the management of pneumonia through deep characterization of pathogens as well as the host response to infection. This characterization will enable the delivery of selective antimicrobials and immunomodulatory therapy that will help to offset the disorder associated with overexuberant immune responses.
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Affiliation(s)
- Samir Gautam
- Pulmonary Critical Care and Sleep Medicine, Center for Pulmonary Infection Research and Treatment, Yale University, 300 Cedar Street, TACS441, New Haven, CT 06520-8057, USA
| | - Lokesh Sharma
- Pulmonary Critical Care and Sleep Medicine, Center for Pulmonary Infection Research and Treatment, Yale University, 300 Cedar Street, TACS441, New Haven, CT 06520-8057, USA
| | - Charles S Dela Cruz
- Pulmonary Critical Care and Sleep Medicine, Center for Pulmonary Infection Research and Treatment, Yale University, 300 Cedar Street, TACS441, New Haven, CT 06520-8057, USA.
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40
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Abstract
There is substantial variation between individuals in the immune response to vaccination. In this review, we provide an overview of the plethora of studies that have investigated factors that influence humoral and cellular vaccine responses in humans. These include intrinsic host factors (such as age, sex, genetics, and comorbidities), perinatal factors (such as gestational age, birth weight, feeding method, and maternal factors), and extrinsic factors (such as preexisting immunity, microbiota, infections, and antibiotics). Further, environmental factors (such as geographic location, season, family size, and toxins), behavioral factors (such as smoking, alcohol consumption, exercise, and sleep), and nutritional factors (such as body mass index, micronutrients, and enteropathy) also influence how individuals respond to vaccines. Moreover, vaccine factors (such as vaccine type, product, adjuvant, and dose) and administration factors (schedule, site, route, time of vaccination, and coadministered vaccines and other drugs) are also important. An understanding of all these factors and their impacts in the design of vaccine studies and decisions on vaccination schedules offers ways to improve vaccine immunogenicity and efficacy.
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Characterization of whole blood transcriptome and early-life fecal microbiota in high and low responder pigs before, and after vaccination for Mycoplasma hyopneumoniae. Vaccine 2019; 37:1743-1755. [PMID: 30808565 DOI: 10.1016/j.vaccine.2019.02.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 02/01/2019] [Accepted: 02/11/2019] [Indexed: 12/29/2022]
Abstract
We investigated gene expression patterns in whole blood and fecal microbiota profile as potential predictors of immune response to vaccination, using healthy M. hyopneumoniae infection free piglets (n = 120). Eighty piglets received a dose of prophylactic antibiotics during the first two days of life, whereas the remaining 40 did not. Blood samples for RNA-Seq analysis were collected on experimental Day 0 (D0; 28 days of age) just prior to vaccination, D2, and D6 post-vaccination. A booster vaccine was given at D24. Fecal samples for microbial 16SrRNA sequencing were collected at 7 days of age, and at D0 and D35 post-vaccination. Pigs were ranked based on the levels of M. hyopneumoniae-specific antibodies in serum samples collected at D35, and groups of 'high' (HR) and 'low' (LR) responder pigs (n = 15 each) were selected. Prophylactic antibiotics did not influence antibody titer levels and differential expression analysis did not reveal differences between HR and LR at any time-point (FDR > 0.05); however, based on functional annotation with Ingenuity Pathway Analysis, D2 post-vaccination, HR pigs were enriched for biological terms relating to increased activation of immune cells. In contrast, the immune activation decreased in HR, 6 days post-vaccination. No significant differences were observed prior to vaccination (D0). Two days post-vaccination, multivariate analysis revealed that ADAM8, PROSER3, B4GALNT1, MAP7D1, SPP1, HTRA4, and ENO3 genes were the most promising potential biomarkers. At D0, OTUs annotated to Prevotella, CF21, Bacteroidales and S24-7 were more abundant in HR, whereas Fibrobacter, Paraprevotella, Anaerovibrio, [Prevotella], YRC22, and Helicobacter positively correlated with the antibody titer as well as MYL1, SPP1, and ENO3 genes. Our study integrates gene differential expression and gut microbiota to predict vaccine response in pigs. The results indicate that post-vaccination gene-expression and early-life gut microbiota profile could potentially predict vaccine response in pigs, and inform a direction for future research.
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42
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Frasca D, McElhaney J. Influence of Obesity on Pneumococcus Infection Risk in the Elderly. Front Endocrinol (Lausanne) 2019; 10:71. [PMID: 30814978 PMCID: PMC6381016 DOI: 10.3389/fendo.2019.00071] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/24/2019] [Indexed: 12/16/2022] Open
Abstract
Obesity negatively affects immune function and host defense mechanisms. Obesity is associated with chronic activation of the innate immune system and consequent local and systemic inflammation which contribute to pathologic conditions such as type-2 diabetes mellitus, cancer, psoriasis, atherosclerosis, and inflammatory bowel disease. Individuals with obesity have increased susceptibility to contract viral, bacterial, and fungal infections and respond sub-optimally to vaccination. In this review, we summarize research findings on the effects of obesity on immune responses to respiratory tract infections (RTI), focusing on Streptococcus pneumoniae ("pneumococcus") infection, which is a major cause of morbidity and mortality in the US, causing community-acquired infections such as pneumonia, otitis media and meningitis. We show that the risk of infection is higher in elderly individuals and also in individuals of certain ethnic groups, although in a few reports obesity has been associated with better survival of individuals admitted to hospital with pneumococcus infection, a phenomenon known as "obesity paradox." We discuss factors that are associated with increased risk of pneumococcal infection, such as recent infection with RTI, chronic medical conditions, and immunosuppressive medications.
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Affiliation(s)
- Daniela Frasca
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Janet McElhaney
- Health Sciences North Research Institute, Sudbury, ON, Canada
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Huda MN, Ahmad SM, Alam MJ, Khanam A, Kalanetra KM, Taft DH, Raqib R, Underwood MA, Mills DA, Stephensen CB. Bifidobacterium Abundance in Early Infancy and Vaccine Response at 2 Years of Age. Pediatrics 2019; 143:peds.2018-1489. [PMID: 30674610 PMCID: PMC6361348 DOI: 10.1542/peds.2018-1489] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/07/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The intestinal microbiome in early infancy affects immunologic development and thus may affect vaccine memory, though few prospective studies have examined such associations. We examined the association of Bifidobacterium levels in early infancy with memory responses to early vaccination measured at 2 years of age. METHODS In this prospective observational study, we examined the association of Bifidobacterium abundance in the stool of healthy infants at 6 to 15 weeks of age, near the time of vaccination, with T-cell and antibody responses measured at 6 weeks, 15 weeks, and 2 years of age. Infants were vaccinated with Bacillus Calmette-Guérin (BCG) (at birth), oral polio virus (at birth and at 6, 10, and 14 weeks), tetanus toxoid (TT) (at 6, 10, and 14 weeks), and hepatitis B virus (at 6, 10, and 14 weeks). Fecal Bifidobacterium was measured at 6, 11, and 15 weeks. Bifidobacterium species and subspecies were measured at 6 weeks. RESULTS Mean Bifidobacterium abundance in early infancy was positively associated with the CD4 T-cell responses to BCG, TT, and hepatitis B virus at 15 weeks, with CD4 responses to BCG and TT at 2 years, and with plasma TT-specific immunoglobulin G and stool polio-specific immunoglobulin A at 2 years. Similar associations were seen for the predominant subspecies, Bifidobacterium longum subspecies infantis. CONCLUSIONS Bifidobacterium abundance in early infancy may increase protective efficacy of vaccines by enhancing immunologic memory. This hypothesis could be tested in clinical trials of interventions to optimize Bifidobacterium abundance in appropriate populations.
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Affiliation(s)
- M. Nazmul Huda
- Nutrition Department and,Western Human Nutrition Research Center, US Department of Agriculture, Davis, California;,Enteric and Respiratory Infections Unit, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh; and
| | - Shaikh M. Ahmad
- Enteric and Respiratory Infections Unit, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh; and
| | - M. Jahangir Alam
- Enteric and Respiratory Infections Unit, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh; and
| | - Afsana Khanam
- Enteric and Respiratory Infections Unit, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh; and
| | | | | | - Rubhana Raqib
- Enteric and Respiratory Infections Unit, Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh; and
| | - Mark A. Underwood
- Department of Pediatrics, University of California, Davis, Sacramento, California
| | - David A. Mills
- Departments of Food Science and Technology and,Viticulture and Enology, University of California, Davis, Davis, California
| | - Charles B. Stephensen
- Nutrition Department and,Western Human Nutrition Research Center, US Department of Agriculture, Davis, California
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Lee KH, Gordon A, Shedden K, Kuan G, Ng S, Balmaseda A, Foxman B. The respiratory microbiome and susceptibility to influenza virus infection. PLoS One 2019; 14:e0207898. [PMID: 30625134 PMCID: PMC6326417 DOI: 10.1371/journal.pone.0207898] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/06/2018] [Indexed: 12/27/2022] Open
Abstract
Influenza is a major cause of morbidity and mortality worldwide. However, vaccine effectiveness has been low to moderate in recent years and vaccine coverage remains low, especially in low- and middle-income countries. Supplementary methods of prevention should be explored to reduce the high burden of influenza. A potential target is the respiratory tract microbiome, complex microbial communities which envelop the respiratory epithelium and play an important role in shaping host immunity. Using a household transmission study, we examined whether the nose/throat microbiota was associated with influenza susceptibility among participants exposed to influenza virus in the household. Further, we characterized changes in the nose/throat microbiota to explore whether community stability was influenced by influenza virus infection. Using a generalized linear mixed effects model, we found a nasal/oropharyngeal community state type (CST) associated with decreased susceptibility to influenza. The CST was rare and transitory among young children but a prevalent and stable CST among adults. Using boosting and linear mixed effects models, we found associations between the nose/throat microbiota and influenza also existed at the taxa level, specifically with the relative abundance of Alloprevotella, Prevotella, and Bacteroides oligotypes. We found high rates of change between bacterial community states among both secondary cases and household contacts who were not infected during follow up. Further work is needed to separate the effect of influenza virus infection from the considerable short-term changes that occur even in the absence of virus. Lastly, age was strongly associated with susceptibility to influenza and the nose/throat bacterial community structure. Although additional studies are needed to determine causality, our results suggest the nose/throat microbiome may be a potential target for reducing the burden of influenza.
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Affiliation(s)
- Kyu Han Lee
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Aubree Gordon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Kerby Shedden
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Statistics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua
- Sustainable Sciences Institute, Managua, Nicaragua
| | - Sophia Ng
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Angel Balmaseda
- Sustainable Sciences Institute, Managua, Nicaragua
- National Virology Laboratory, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Betsy Foxman
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
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Hanada S, Pirzadeh M, Carver KY, Deng JC. Respiratory Viral Infection-Induced Microbiome Alterations and Secondary Bacterial Pneumonia. Front Immunol 2018; 9:2640. [PMID: 30505304 PMCID: PMC6250824 DOI: 10.3389/fimmu.2018.02640] [Citation(s) in RCA: 293] [Impact Index Per Article: 48.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/26/2018] [Indexed: 12/18/2022] Open
Abstract
Influenza and other respiratory viral infections are the most common type of acute respiratory infection. Viral infections predispose patients to secondary bacterial infections, which often have a more severe clinical course. The mechanisms underlying post-viral bacterial infections are complex, and include multifactorial processes mediated by interactions between viruses, bacteria, and the host immune system. Studies over the past 15 years have demonstrated that unique microbial communities reside on the mucosal surfaces of the gastrointestinal tract and the respiratory tract, which have both direct and indirect effects on host defense against viral infections. In addition, antiviral immune responses induced by acute respiratory infections such as influenza are associated with changes in microbial composition and function (“dysbiosis”) in the respiratory and gastrointestinal tract, which in turn may alter subsequent immune function against secondary bacterial infection or alter the dynamics of inter-microbial interactions, thereby enhancing the proliferation of potentially pathogenic bacterial species. In this review, we summarize the literature on the interactions between host microbial communities and host defense, and how influenza, and other acute respiratory viral infections disrupt these interactions, thereby contributing to the pathogenesis of secondary bacterial infections.
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Affiliation(s)
- Shigeo Hanada
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, United States.,Toranomon Hospital, Tokyo, Japan
| | - Mina Pirzadeh
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, United States.,Veterans Affairs Healthcare System, Ann Arbor, MI, United States
| | - Kyle Y Carver
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, United States.,Veterans Affairs Healthcare System, Ann Arbor, MI, United States
| | - Jane C Deng
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, United States.,Veterans Affairs Healthcare System, Ann Arbor, MI, United States
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Ramakrishnan VR, Holt J, Nelson LF, Ir D, Robertson CE, Frank DN. Determinants of the Nasal Microbiome: Pilot Study of Effects of Intranasal Medication Use. ALLERGY & RHINOLOGY 2018; 9:2152656718789519. [PMID: 30128169 PMCID: PMC6088474 DOI: 10.1177/2152656718789519] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Introduction A role for bacteria and other microbes has long been suspected in the chronic
inflammatory sinonasal diseases. Recent studies utilizing
culture-independent, sequence-based identification have demonstrated
aberrant shifts in the sinus microbiota of chronic rhinosinusitis subjects,
compared with ostensibly healthy controls. Examining how such microbiota
shifts occur and the potential for physician-prescribed interventions to
influence microbiota dynamics are the topics of the current article. Methods The nasal cavity microbiota of 5 subjects was serially examined over an
8-week period using pan-bacterial 16S rRNA gene sequencing. Four of the
subjects were administered topical mometasone furoate spray, while 1 subject
underwent a mupirocin decolonization procedure in anticipation of orthopedic
surgery. Results Measures of microbial diversity were unaffected by intranasal treatment in 2
patients and were markedly increased in the remaining 3. The increase in
microbial diversity was related to clearance of Moraxella
spp. and a simultaneous increase in members of the phylum Actinobacteria.
Both effects persisted at least 2 weeks beyond cessation of treatment.
Transient changes in the relative abundance of several bacterial genera,
including Staphylococcus and
Priopionibacteria, were also observed during
treatment. Conclusions The effects of intranasal steroids on the sinonasal microbiome are poorly
understood, despite their widespread use in treating chronic sinonasal
inflammatory disorders. In this longitudinal study, administration of
intranasal mometasone furoate or mupirocin resulted in shifts in microbial
diversity that persisted to some degree following treatment cessation.
Further characterization of these effects as well as elucidation of the
mechanism(s) underlying these changes is needed.
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Affiliation(s)
- Vijay R Ramakrishnan
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado School of Medicine, Aurora, Colorado
| | - Justin Holt
- Department of Otolaryngology-Head and Neck Surgery, University of Colorado School of Medicine, Aurora, Colorado.,Department of Otolaryngology-Head and Neck Surgery, Oregon Health & Science University, Portland, Oregon
| | - Leah F Nelson
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado
| | - Diana Ir
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado
| | - Charles E Robertson
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado
| | - Daniel N Frank
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, Colorado
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Role of nutrition, infection, and the microbiota in the efficacy of oral vaccines. Clin Sci (Lond) 2018; 132:1169-1177. [PMID: 29925624 DOI: 10.1042/cs20171106] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/15/2018] [Accepted: 05/21/2018] [Indexed: 12/11/2022]
Abstract
Oral vaccines (OVs), provide protection against pathogens that infect mucosal surfaces and their potency relies on their capacity to elicit T- and B-cell responses directed to these surfaces. Oral vaccination efficacy has been found to vary considerably with differences in geographical locations and socioeconomic status. Specifically, in children living in resource-poor countries, undernourishment and chronic gastrointestinal (GI) infection are associated with the failure of OVs, which is a tragic outcome for the children who would benefit most from mucosal-based protection from infection. Both undernutrition and GI infection have been shown to profoundly affect the microbiota, inducing 'dysbiosis' characterized by narrowed bacterial diversity and increased frequency of bacterial clades associated with the induction of inflammation. Recent studies have demonstrated that the microbiota exerts a profound effect on the development of mucosal immune responses. Therefore, it seems likely that OV failure in resource-poor regions is affected by alterations to the immune response driven by dysbiotic changes to the microbiota. Here, we review the contribution of the microbiota to OV efficacy in the context of diet and GI infection.
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48
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Microbiota Composition and the Integration of Exogenous and Endogenous Signals in Reactive Nasal Inflammation. J Immunol Res 2018; 2018:2724951. [PMID: 29967798 PMCID: PMC6008798 DOI: 10.1155/2018/2724951] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/09/2018] [Accepted: 04/19/2018] [Indexed: 02/06/2023] Open
Abstract
The prevalence of reactive nasal inflammatory conditions, for example, allergic rhinitis and chronic rhinosinusitis, is steadily increasing in parallel with significant environmental changes worldwide. Allergens and as yet undefined environmental agents may trigger these conditions via the involvement of host intrinsic factors, including the innate and adaptive immune system, the nasal epithelium, and the nasal nervous system. The critical role of the nasal microbiota in coordinating these components has emerged in recent studies documenting a significant association between microbial composition and the onset and progression of allergic or nonallergic inflammation. It is now clear that the local microbiota is a major player in the development of the mucosa-associated lymphoid tissue and in the regulation of such adaptive responses as IgA production and the function of effector and regulatory T cells. Microbial components also play a major role in the regulation of epithelial barrier functions, including mucus production and the control of paracellular transport across tight junctions. Bacterial components, including lipopolysaccharide, have also been shown to induce or amplify neuroinflammatory responses by engaging specific nociceptors. Finally, bacterial products may promote tissue remodeling processes, including nasal polyp formation, by interacting with formyl peptide receptors and inducing the expression of angiogenic factors and matrix-degrading enzymes.
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49
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Beirão BCB, Ingberman M, Fávaro C, Mesa D, Bittencourt LC, Fascina VB, Caron LF. Effect of an Enterococcus faecium probiotic on specific IgA following live Salmonella Enteritidis vaccination of layer chickens. Avian Pathol 2018. [PMID: 29534604 DOI: 10.1080/03079457.2018.1450487] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Probiotics and immunization are being widely adopted by the poultry industry with the goal of controlling Salmonella enterica. However, the interaction between these two management protocols has been sparsely studied. The present study aimed to understand the role of an Enterococcus faecium probiotic in the production of salmonella-specific IgA in layers immunized with a live vaccine. Four groups were used: "Control" (no vaccine or probiotic); "Probiotic" (which received an E. faecium product); "Vaccine" (immunized with two doses of a live attenuated S. Enteritidis vaccine); and "Vaccine + probiotic". Faecal salmonella-specific IgA was analysed 7 and 20 days post-vaccination (dpv) boost. At 7 dpv, the "Vaccine" and "Vaccine + probiotic" groups had similar IgA levels. However, at 20 dpv, IgA levels were two times higher in the "Vaccine + probiotic" group compared to the "Vaccine" group. To understand the role of the intestinal microbiota in this finding, bacterial diversity in faeces was analysed by 16S rRNA gene sequencing. The improvement in IgA production in probiotic-treated birds was accompanied by marked changes in the faecal microbiome. Some of the main differences between the "Vaccine" and "Vaccine + probiotic" groups included reduction of Escherichia-Shigella and increases in Blautia, Anaerotruncus and Lactobacillus in the latter group. Although no direct causal link can be established from this study design, it is possible that the E. faecium probiotic induces improved antibody production following vaccination via modulation of the intestinal microbiota.
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Affiliation(s)
- Breno C B Beirão
- a Imunova Análises Biológicas , Setor de Ciências Biológicas UFPR , Curitiba , Brazil
| | - Max Ingberman
- a Imunova Análises Biológicas , Setor de Ciências Biológicas UFPR , Curitiba , Brazil
| | - Celso Fávaro
- a Imunova Análises Biológicas , Setor de Ciências Biológicas UFPR , Curitiba , Brazil
| | - Dany Mesa
- b Setor de Ciências Biológicas UFPR, Universidade Federal do Paraná , Curitiba , Brazil
| | | | | | - Luiz Felipe Caron
- b Setor de Ciências Biológicas UFPR, Universidade Federal do Paraná , Curitiba , Brazil
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50
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Lynn DJ, Pulendran B. The potential of the microbiota to influence vaccine responses. J Leukoc Biol 2017; 103:225-231. [PMID: 28864446 DOI: 10.1189/jlb.5mr0617-216r] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/21/2017] [Accepted: 08/01/2017] [Indexed: 12/25/2022] Open
Abstract
After clean water, vaccines are the primary public health intervention providing protection against serious infectious diseases. Antigen-specific antibody-mediated responses play a critical role in the protection conferred by vaccination; however these responses are highly variable among individuals. In addition, vaccine immunogenicity is frequently impaired in developing world populations, for reasons that are poorly understood. Although the factors that are associated with interindividual variation in vaccine responses are likely manifold, emerging evidence from mouse models and studies in human populations now suggests that the gut microbiome plays a key role in shaping systemic immune responses to both orally and parenterally administered vaccines. Herein, we review the evidence to date that the microbiota can influence vaccine responses and discuss the potential mechanisms through which these effects may be mediated. In addition, we highlight the gaps in this evidence and suggest future directions for research.
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Affiliation(s)
- David J Lynn
- Infection and Immunity Theme, South Australian Health and Medical Research Institute, North Terrace, Adelaide, South Australia, Australia.,School of Medicine, Flinders University, Bedford Park, South Australia, Australia
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
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