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Hilliam Y, Armbruster CR, Rapsinski GJ, Marshall CW, Moore J, Koirala J, Krainz L, Gaston JR, Cooper VS, Lee SE, Bomberger JM. Cystic fibrosis pathogens persist in the upper respiratory tract following initiation of elexacaftor/tezacaftor/ivacaftor therapy. Microbiol Spectr 2024; 12:e0078724. [PMID: 38916354 PMCID: PMC11302335 DOI: 10.1128/spectrum.00787-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/06/2024] [Indexed: 06/26/2024] Open
Abstract
Elexacaftor/tezacaftor/ivacaftor (ETI) therapy has revolutionized the treatment of cystic fibrosis (CF) for most affected individuals but the effects of treatment on sinus microbiota are still unknown. Changes to the airway microbiota in CF are associated with disease state and alterations to the bacterial community after ETI initiation may require changes to clinical management regimens. We collected sinus swab samples from the middle meatus in an observational study of 38 adults with CF and chronic rhinosinusitis (CRS) from 2017 to 2021 and captured the initiation of ETI therapy. We performed 16S and custom amplicon sequencing to characterize the sinus microbiota pre- and post-ETI. Real-time quantitative PCR (RT-qPCR) was performed to estimate total bacterial abundance. Sinus samples from people with CF (pwCF) clustered into three community types, dependent on the dominant bacterial organism: a Pseudomonas-dominant, Staphylococcus-dominant, and mixed dominance cluster. Shannon's diversity index was low and not significantly altered post-ETI. Total bacterial load was not significantly lowered post-ETI. Pseudomonas spp. abundance was significantly reduced post-ETI, but eradication was not observed. Staphylococcus spp. became the dominant organism in most individuals post-ETI and we showed the presence of methicillin-resistant Staphylococcus aureus (MRSA) in the sinus both pre- and post-ETI. We also demonstrated that the sinus microbiome is predictive of the presence of Pseudomonas spp., Staphylococcus spp., and Serratia spp. in the sputum. Pseudomonas spp. and Staphylococcus spp., including MRSA, persist in the sinuses of pwCF after ETI therapy, indicating that these pathogens will continue to be important in CF airway disease management in the era of highly effective modulator therapies (HEMT).IMPORTANCEHighly effective modulator therapies (HEMT), such as elexacaftor/tezacaftor/ivacaftor (ETI), for cystic fibrosis (CF) have revolutionized patient care and quality of life for most affected individuals. The effects of these therapies on the microbiota of the airways are still unclear, though work has already been published on changes to microbiota in the sputum. Our study presents evidence for reduced relative abundance of Pseudomonas spp. in the sinuses following ETI therapy. We also show that Staphylococcus spp. becomes the dominant organism in the sinus communities of most individuals in this cohort after ETI therapy. We identified methicillin-resistant Staphylococcus aureus (MRSA) in the sinus microbiota both pre- and post-therapy. These findings demonstrate that pathogen monitoring and treatment will remain a vital part of airway disease management for people with cystic fibrosis (pwCF) in the era of HEMT.
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Affiliation(s)
- Yasmin Hilliam
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Catherine R. Armbruster
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Glenn J. Rapsinski
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - John Moore
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Junu Koirala
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Leah Krainz
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jordan R. Gaston
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Vaughn S. Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Stella E. Lee
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Jennifer M. Bomberger
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Luo C, Ye Y, Lv A, Zuo W, Yang Y, Jiang C, Ke J. The impact of Astragaloside IV on the inflammatory response and gut microbiota in cases of acute lung injury is examined through the utilization of the PI3K/AKT/mTOR pathway. PLoS One 2024; 19:e0305058. [PMID: 38954702 PMCID: PMC11218977 DOI: 10.1371/journal.pone.0305058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/22/2024] [Indexed: 07/04/2024] Open
Abstract
OBJECTIVES Astragaloside IV (AS-IV) is a natural triterpenoid saponin compound with a variety of pharmacological effects, and several studies have clarified its anti-inflammatory effects, which may make it an effective alternative treatment against inflammation. In the study, we aimed to investigate whether AS-IV could attenuate the inflammatory response to acute lung injury and its mechanisms. METHODS Different doses of AS-IV (20mg·kg-1, 40mg·kg-1, and 80mg·kg-1) were administered to the ALI rat model, followed by collection of serum and broncho alveolar lavage fluid (BALF) for examination of the inflammatory response, and HE staining of the lung and colon tissues, and interpretation of the potential molecular mechanisms by quantitative real-time PCR (qRT-PCR), Western blotting (WB). In addition, fecal samples from ALI rats were collected and analyzed by 16S rRNA sequencing. RESULTS AS-IV decreased the levels of TNF-α, IL-6, and IL-1β in serum and BALF of mice with Acute lung injury (ALI). Lung and colon histopathology confirmed that AS-IV alleviated inflammatory infiltration, tissue edema, and structural changes. qRT-PCR and WB showed that AS-IV mainly improved inflammation by inhibiting the expression of PI3K, AKT and mTOR mRNA, and improved the disorder of intestinal microflora by increasing the number of beneficial bacteria and reducing the number of harmful bacteria. CONCLUSION AS-IV reduces the expression of inflammatory factors by inhibiting the PI3K/AKT/mTOR pathway and optimizes the composition of the gut microflora in AIL rats.
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Affiliation(s)
- Cheng Luo
- Clinical College of traditional Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Yuanhang Ye
- Clinical College of traditional Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Anqi Lv
- Clinical College of traditional Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Wanzhao Zuo
- Clinical College of traditional Chinese Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Yi Yang
- Hubei Provincial Hospital of Traditional Chinese Medicine, Hubei Academy of Traditional Chinese Medicine, Affiliated Hospital of Hubei University of Traditional Chinese Medicine, Wuhan, China
| | - Cheng Jiang
- Hubei Provincial Hospital of Traditional Chinese Medicine, Hubei Academy of Traditional Chinese Medicine, Affiliated Hospital of Hubei University of Traditional Chinese Medicine, Wuhan, China
| | - Jia Ke
- Hubei Provincial Hospital of Traditional Chinese Medicine, Hubei Academy of Traditional Chinese Medicine, Affiliated Hospital of Hubei University of Traditional Chinese Medicine, Wuhan, China
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Song X, Liang J, Lin S, Xie Y, Ke C, Ao D, Lu J, Chen X, He Y, Liu X, Li W. Gut-lung axis and asthma: A historical review on mechanism and future perspective. Clin Transl Allergy 2024; 14:e12356. [PMID: 38687096 PMCID: PMC11060082 DOI: 10.1002/clt2.12356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 03/24/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Gut microbiota are closely related to the development and regulation of the host immune system by regulating the maturation of immune cells and the resistance to pathogens, which affects the host immunity. Early use of antibiotics disrupts the homeostasis of gut microbiota and increases the risk of asthma. Gut microbiota actively interact with the host immune system via the gut-lung axis, a bidirectional communication pathway between the gut and lung. The manipulation of gut microbiota through probiotics, helminth therapy, and fecal microbiota transplantation (FMT) to combat asthma has become a hot research topic. BODY: This review mainly describes the current immune pathogenesis of asthma, gut microbiota and the role of the gut-lung axis in asthma. Moreover, the potential of manipulating the gut microbiota and its metabolites as a treatment strategy for asthma has been discussed. CONCLUSION The gut-lung axis has a bidirectional effect on asthma. Gut microecology imbalance contributes to asthma through bacterial structural components and metabolites. Asthma, in turn, can also cause intestinal damage through inflammation throughout the body. The manipulation of gut microbiota through probiotics, helminth therapy, and FMT can inform the treatment strategies for asthma by regulating the maturation of immune cells and the resistance to pathogens.
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Affiliation(s)
- Xiu‐Ling Song
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Juan Liang
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Shao‐Zhu Lin
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Yu‐Wei Xie
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Chuang‐Hong Ke
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Dang Ao
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Jun Lu
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Xue‐Mei Chen
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Ying‐Zhi He
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Xiao‐Hua Liu
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
| | - Wen Li
- Department of PediatricsAffiliated Hospital of Guangdong Medical UniversityZhanjiangChina
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Yang W, Yang T, Huang B, Chen Z, Liu H, Huang C. Berberine improved the microbiota in lung tissue of colon cancer and reversed the bronchial epithelial cell changes caused by cancer cells. Heliyon 2024; 10:e24405. [PMID: 38312643 PMCID: PMC10835176 DOI: 10.1016/j.heliyon.2024.e24405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/21/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
Objective The lung is a common organ for colon cancer metastasis, and the objective of this experiment was to explore the protective effect of berberine on lung tissue or alveolar epithelial cells induced by colon cancer. Methods Thirty-six BALB/c nude mice were used to establish a xenograft model of colon cancer with the HT29 cell line and were treated with berberine and probiotics. Human bronchial epithelial BEAS-2B cells were induced by conditioned medium (CM) from the colon cancer cell lines HT29 and RKO and were treated with berberine. Lung tissues were collected to detect the changes in the microbiota using 16S rDNA sequencing and the expression of inflammatory cytokines. The expression of E-cadherin and N-cadherin in BEAS-2B cells was detected by cellular immunofluorescence. The changes in cell proliferation were detected by the CCK-8 assay. Western blotting was used to detect E-cadherin, N-cadherin, collagen I, fibronectin, PDGF-β, and RAD51 expression in BEAS-2B cells. Results The richness and evenness of the microbiota in the lung tissues of mice with colon cancer were significantly lower than those of the control group. Berberine significantly increased the abundances of Bacteroidetes, Bacteroidia, Bacteroidales, Lactobacillaceae, Lactobacillus and Acinetobacter in the lung tissue of mice with colon cancer, with reduced abundances of Actinobacteria, Bacillales, Staphylococcaceae and Staphylococcus. Berberine or probiotics significantly increased the alpha diversity of the lung microbiota. Compared with probiotics, berberine significantly enhanced the abundance of microbiota involved in the metabolism of lysosomes, flavone and flavonol biosynthesis, glycosaminoglycan degradation, and glycosphingolipid biosynthesis-ganglio. Berberine increased IL-6 and IL-10 and decreased IL-17 and IFN-γ expression in lung tissue (P > 0.05), but berberine-probiotics significantly decreased IL-17 and IFN-γ and increased IL-10 expression (P < 0.05). Colon cancer cells could not induce BEAS-2B proliferation but decreased the expression of the epithelial marker E-cadherin and altered the expression of extracellular matrix-related proteins (collagen I, fibronectin, and PDGF-β), which were reversed by berberine. Berberine increased RAD51 expression in BEAS-2B cells, which had been decreased by HT29 and RKO CM treatment. Conclusion Berberine can selectively regulate the abundance of some microbiomes of lung tissue in colon cancer, improve the inflammatory response in lung tissue, and antagonize the cancerous stimulation of colon cancer cells to lung tissue cells by regulating the bronchial epithelial cell phenotype, extracellular matrix remodelling and the expression of the repair gene RAD51.
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Affiliation(s)
- Wei Yang
- Pediatric Department, The Second Affiliated Hospital of Shenzhen University (People's Hospital of Shenzhen Baoan District), Shenzhen, 518100, China
| | - Ting Yang
- Gastroenterology Department, The Second Affiliated Hospital of Shenzhen University (People's Hospital of Shenzhen Baoan District), Shenzhen, 518100, China
| | - Bo Huang
- General Surgery Department, The Second Affiliated Hospital of Shenzhen University (People's Hospital of Shenzhen Baoan District), Shenzhen, 518100, China
| | - Zhanjun Chen
- Department of Cardiology, The Second Affiliated Hospital of Shenzhen University (People's Hospital of Shenzhen Baoan District), Shenzhen, 518100, China
| | - Haosheng Liu
- Department of Traditional Chinese Medicine, The Second Affiliated Hospital of Shenzhen University (People's Hospital of Shenzhen Baoan District), Shenzhen, 518100, China
| | - Chao Huang
- Department of Traditional Chinese Medicine, The Second Affiliated Hospital of Shenzhen University (People's Hospital of Shenzhen Baoan District), Shenzhen, 518100, China
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Souza VGP, Forder A, Pewarchuk ME, Telkar N, de Araujo RP, Stewart GL, Vieira J, Reis PP, Lam WL. The Complex Role of the Microbiome in Non-Small Cell Lung Cancer Development and Progression. Cells 2023; 12:2801. [PMID: 38132121 PMCID: PMC10741843 DOI: 10.3390/cells12242801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
In recent years, there has been a growing interest in the relationship between microorganisms in the surrounding environment and cancer cells. While the tumor microenvironment predominantly comprises cancer cells, stromal cells, and immune cells, emerging research highlights the significant contributions of microbial cells to tumor development and progression. Although the impact of the gut microbiome on treatment response in lung cancer is well established, recent investigations indicate complex roles of lung microbiota in lung cancer. This article focuses on recent findings on the human lung microbiome and its impacts in cancer development and progression. We delve into the characteristics of the lung microbiome and its influence on lung cancer development. Additionally, we explore the characteristics of the intratumoral microbiome, the metabolic interactions between lung tumor cells, and how microorganism-produced metabolites can contribute to cancer progression. Furthermore, we provide a comprehensive review of the current literature on the lung microbiome and its implications for the metastatic potential of tumor cells. Additionally, this review discusses the potential for therapeutic modulation of the microbiome to establish lung cancer prevention strategies and optimize lung cancer treatment.
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Affiliation(s)
- Vanessa G. P. Souza
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil (P.P.R.)
| | - Aisling Forder
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | | | - Nikita Telkar
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- British Columbia Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Rachel Paes de Araujo
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil (P.P.R.)
| | - Greg L. Stewart
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Juliana Vieira
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Patricia P. Reis
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil (P.P.R.)
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil
| | - Wan L. Lam
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
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Zhao Y, Sun H, Chen Y, Niu Q, Dong Y, Li M, Yuan Y, Yang X, Sun Q. Butyrate protects against MRSA pneumonia via regulating gut-lung microbiota and alveolar macrophage M2 polarization. mBio 2023; 14:e0198723. [PMID: 37754570 PMCID: PMC10653920 DOI: 10.1128/mbio.01987-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/08/2023] [Indexed: 09/28/2023] Open
Abstract
IMPORTANCE Pneumonia caused by methicillin-resistant Staphylococcus aureus (MRSA) continues to carry a high burden in terms of mortality. With the roles of gut microbiota in mediating lung diseases being gradually uncovered, the details of the molecular mechanism of the "gut-lung axis" mediated by beneficial microorganisms and small-molecule metabolites have gradually attracted the attention of researchers. However, further studies are still necessary to determine the efficacy of microbial-based interventions. Our findings indicate that sodium butyrate (NaB) alleviates MRSA-induced pulmonary inflammation by improving gut-lung microbiota and promoting M2 polarization of alveolar macrophages. Therefore, the preventive administration of NaB might be explored as an effective strategy to control MRSA pneumonia.
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Affiliation(s)
- Yan Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Haoming Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yiwei Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qiang Niu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yiting Dong
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Mei Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Ye Yuan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaojun Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qingzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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Gao J, Yi X, Wang Z. The application of multi-omics in the respiratory microbiome: Progresses, challenges and promises. Comput Struct Biotechnol J 2023; 21:4933-4943. [PMID: 37867968 PMCID: PMC10585227 DOI: 10.1016/j.csbj.2023.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/24/2023] Open
Abstract
The study of the respiratory microbiome has entered a multi-omic era. Through integrating different omic data types such as metagenome, metatranscriptome, metaproteome, metabolome, culturome and radiome surveyed from respiratory specimens, holistic insights can be gained on the lung microbiome and its interaction with host immunity and inflammation in respiratory diseases. The power of multi-omics have moved the field forward from associative assessment of microbiome alterations to causative understanding of the lung microbiome in the pathogenesis of chronic, acute and other types of respiratory diseases. However, the application of multi-omics in respiratory microbiome remains with unique challenges from sample processing, data integration, and downstream validation. In this review, we first introduce the respiratory sample types and omic data types applicable to studying the respiratory microbiome. We next describe approaches for multi-omic integration, focusing on dimensionality reduction, multi-omic association and prediction. We then summarize progresses in the application of multi-omics to studying the microbiome in respiratory diseases. We finally discuss current challenges and share our thoughts on future promises in the field.
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Affiliation(s)
- Jingyuan Gao
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Zhang Wang
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
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Chen IL, Huang F, Li SC, Huang HC. Salivary microbiome and asthma risk in children with orofacial defects. Pediatr Pulmonol 2023; 58:2777-2785. [PMID: 37470110 DOI: 10.1002/ppul.26582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Patients with congenital orofacial defects, cleft lip (CL), cleft palate (CP), and cleft lip and palate (CLP) have continuous exposure of the respiratory system to the microbiome from the oral environment, offering opportunities to develop mucosal immunity in the airway. This two-part study aims to analyze data on asthma occurrence in CL, CP, and CLP infants and the composition of the salivary microbiome, and to evaluate the oral microbiota and its association with the risk of developing childhood asthma. METHODS Patient data from the research database of Chang Gung Memorial Hospital from 2004 to 2015 were retrospectively analyzed by multivariable regression. Diseases diagnoses were defined by ICD codes. Asthma must also meet the criteria for receiving selective β2 agonistic or/and inhaled corticosteroid treatments twice within 1 year. Analysis of the saliva microbiome was performed prospectively from 2016 to 2020 in 10 healthy term infants and 10 CLP infants on postnatal 7th day, 1 month, and 6 months by next-generation sequencing. RESULTS Asthma and nonasthma groups included 988 and 3952 patients, respectively. The incidence of asthma development was higher in patients with CP than in CL and CLP groups (aOR: 5.644, CI: 1.423-22.376). The species composition of the microbiome at 1 and 6 months was significantly different between infants with CLP and healthy infants. CONCLUSION Children with orofacial defects have a higher risk of developing asthma with a possible contribution from oral microbiota in the early months of life.
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Affiliation(s)
- I-Lun Chen
- Department of Pediatrics, College of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, Kaohsiung, Taiwan
- School of Traditional Chinese Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Faye Huang
- Department of Plastic Surgery, College of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, Kaohsiung, Taiwan
| | - Sung-Chou Li
- Department of Medical Research, College of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, Kaohsiung, Taiwan
| | - Hsin-Chun Huang
- Department of Pediatrics, College of Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University, Kaohsiung, Taiwan
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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Werner M, Weeger J, Hörner-Schmid L, Weber K, Palić J, Shih J, Suchodolski JS, Pilla R, Schulz B. Comparison of the respiratory bacterial microbiome in cats with feline asthma and chronic bronchitis. Front Vet Sci 2023; 10:1148849. [PMID: 37051512 PMCID: PMC10083293 DOI: 10.3389/fvets.2023.1148849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/13/2023] [Indexed: 03/28/2023] Open
Abstract
ObjectivesWhile feline chronic bronchitis (CB) is known as neutrophilic bronchial inflammation (NI), feline asthma (FA) is defined as an eosinophilic airway inflammation (EI). Feline chronic bronchial disease refers to both syndromes, with similar clinical presentations and applied treatment strategies. Recent studies described alterations of the microbiota composition in cats with FA, but little is known about the comparison of the lung microbiota between different types of feline bronchial disease. The study aimed to describe the bacterial microbiota of the lower respiratory tracts of cats with FA and CB and to identify potential differences.MethodsTwenty-two client-owned cats with FA (n = 15) or CB (n = 7) confirmed via bronchoalveolar-lavage (BALF)-cytology were included. Next-generation sequencing analysis of 16S rRNA genes was performed on bacterial DNA derived from BALF samples. QIIME was used to compare microbial composition and diversity between groups.ResultsEvenness and alpha-diversity-indices did not significantly differ between cats with FA and CB (Shannon p = 0.084, Chao 1 p = 0.698, observed ASVs p = 0.944). Based on a PERMANOVA analysis, no significant differences were observed in microbial composition between animals of both groups (Bray-Curtis metric, R-value 0.086, p = 0.785; unweighted UniFrac metric, R-value −0.089, p = 0.799; weighted Unifrac metric, R-value −0.072, p = 0.823). Regarding taxonomic composition, significant differences were detected for Actinobacteria on the phylum level (p = 0.026), Mycoplasma spp. (p = 0.048), and Acinetobacteria (p = 0.049) on the genus level between cats with FA and CB, with generally strong interindividual differences seen. There was a significant difference in the duration of clinical signs before diagnosis in animals dominated by Bacteriodetes (median 12 months, range 2–58 months) compared to animals dominated by Proteobacteria (median 1 month, range 1 day to 18 months; p = 0.003).Conclusions and relevanceLung microbiota composition is very similar in cat populations with spontaneous FA and CB besides small differences in some bacterial groups. However, with disease progression, the lung microbiome of cats with both diseases appears to shift away from dominantly Proteobacteria to a pattern more dominated by Bacteriodetes. A substantial proportion of cats tested positive for Mycoplasma spp. via sequencing, while none of them tested positive using classical PCR.
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Affiliation(s)
- Melanie Werner
- Clinic of Small Animal Internal Medicine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilian-University, Munich, Germany
- Clinic for Small Animal Internal Medicine, Vetsuisse Faculty, Zurich, Switzerland
| | - Jasmin Weeger
- Clinic of Small Animal Internal Medicine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilian-University, Munich, Germany
| | - Lina Hörner-Schmid
- Clinic of Small Animal Internal Medicine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilian-University, Munich, Germany
| | - Karin Weber
- Clinic of Small Animal Internal Medicine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilian-University, Munich, Germany
| | - Jelena Palić
- Vet Med Labor GmbH, Division of IDEXX Laboratories, Kornwestheim, Germany
| | - Jonathan Shih
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX, United States
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX, United States
| | - Rachel Pilla
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, Texas A&M University, College Station, TX, United States
| | - Bianka Schulz
- Clinic of Small Animal Internal Medicine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilian-University, Munich, Germany
- *Correspondence: Bianka Schulz
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Bentouhami H, Bungwa MK, Casas L, Coenen S, Weyler J. Asthma occurrence in children and early life systemic antibiotic use: an incidence density study. ALLERGY, ASTHMA, AND CLINICAL IMMUNOLOGY : OFFICIAL JOURNAL OF THE CANADIAN SOCIETY OF ALLERGY AND CLINICAL IMMUNOLOGY 2023; 19:18. [PMID: 36879341 PMCID: PMC9987135 DOI: 10.1186/s13223-023-00773-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 02/13/2023] [Indexed: 03/08/2023]
Abstract
BACKGROUND Results of studies evaluating the relationship between asthma occurrence and early life antibiotic use have been conflicting. The aim of this study was to investigate the relationship between occurrence of asthma in children and systemic antibiotic use in the first year of life based on an incidence density study with careful consideration of the temporal aspects of the determinant-outcome relationship. METHODS We conducted an incidence density study nested in a data collection project with information on 1128 mother-child pairs. Systemic antibiotic use in the first year of life was defined as excessive (≥ 4 courses) vs. non-excessive (< 4 courses) use based on information from weekly diaries. Events (cases) were defined as the first parent-reported occurrence of asthma in a child between 1 and 10 years of age. Population time 'at risk' was probed by sampling population moments (controls). Missing data were imputed. Multiple logistic regression was used to assess the association between current first asthma occurrence (incidence density) and systemic antibiotic use in the first year of life, to evaluate effect modification and adjust for confounding. RESULTS Forty-seven first asthma events and 147 population moments were included. Excessive systemic antibiotic use in the first year of life showed more than twice the incidence density of asthma compared to non-excessive use (adjusted IDR [95% CI]: 2.18 [0.98, 4.87], p = 0.06). The association was more pronounced in children who have had lower respiratory tract infections (LRTIs) in the first year of life compared to children who had no LRTIs in the first year of life (adjusted IDR [95% CI]: 5.17 [1.19, 22.52] versus 1.49 [0.54, 4.14]). CONCLUSIONS Excessive use of systemic antibiotics in the first year of life may play a role in the genesis of asthma in children. This effect is modified by the occurrence of LRTIs in the first year of life, with a stronger association observed in children experiencing LRTIs in the first year of life.
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Affiliation(s)
- Hayat Bentouhami
- Department of Family Medicine & Population Health (FAMPOP), Social Epidemiology and Health Policy (SEHPO), University of Antwerp, Antwerp, Belgium.
| | - Milcah Kahkelam Bungwa
- Department of Family Medicine & Population Health (FAMPOP), Social Epidemiology and Health Policy (SEHPO), University of Antwerp, Antwerp, Belgium
| | - Lidia Casas
- Department of Family Medicine & Population Health (FAMPOP), Social Epidemiology and Health Policy (SEHPO), University of Antwerp, Antwerp, Belgium
| | - Samuel Coenen
- Department of Family Medicine & Population Health (FAMPOP), Social Epidemiology and Health Policy (SEHPO), University of Antwerp, Antwerp, Belgium.,Department of Family Medicine & Population Health (FAMPOP), Primary Care & Interdisciplinary Care Antwerp (ELIZA), University of Antwerp, Antwerp, Belgium.,Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, Antwerp, Belgium
| | - Joost Weyler
- Department of Family Medicine & Population Health (FAMPOP), Social Epidemiology and Health Policy (SEHPO), University of Antwerp, Antwerp, Belgium.,StatUa Statistics Centre, University of Antwerp, Antwerp, Belgium
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11
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The Lung Microbiome: A New Frontier for Lung and Brain Disease. Int J Mol Sci 2023; 24:ijms24032170. [PMID: 36768494 PMCID: PMC9916971 DOI: 10.3390/ijms24032170] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Due to the limitations of culture techniques, the lung in a healthy state is traditionally considered to be a sterile organ. With the development of non-culture-dependent techniques, the presence of low-biomass microbiomes in the lungs has been identified. The species of the lung microbiome are similar to those of the oral microbiome, suggesting that the microbiome is derived passively within the lungs from the oral cavity via micro-aspiration. Elimination, immigration, and relative growth within its communities all contribute to the composition of the lung microbiome. The lung microbiome is reportedly altered in many lung diseases that have not traditionally been considered infectious or microbial, and potential pathways of microbe-host crosstalk are emerging. Recent studies have shown that the lung microbiome also plays an important role in brain autoimmunity. There is a close relationship between the lungs and the brain, which can be called the lung-brain axis. However, the problem now is that it is not well understood how the lung microbiota plays a role in the disease-specifically, whether there is a causal connection between disease and the lung microbiome. The lung microbiome includes bacteria, archaea, fungi, protozoa, and viruses. However, fungi and viruses have not been fully studied compared to bacteria in the lungs. In this review, we mainly discuss the role of the lung microbiome in chronic lung diseases and, in particular, we summarize the recent progress of the lung microbiome in multiple sclerosis, as well as the lung-brain axis.
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12
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Micrococcus luteus-derived extracellular vesicles attenuate neutrophilic asthma by regulating miRNAs in airway epithelial cells. Exp Mol Med 2023; 55:196-204. [PMID: 36639716 PMCID: PMC9898544 DOI: 10.1038/s12276-022-00910-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/10/2022] [Accepted: 11/15/2022] [Indexed: 01/15/2023] Open
Abstract
Bacterial extracellular vesicles (EVs) have been shown to regulate various pulmonary diseases, but their functions in asthma remain uncertain. To demonstrate the clinical significance of Micrococcus luteus-derived EVs (MlEVs) in asthma, we enrolled 45 asthmatic patients (20 patients with neutrophilic asthma [NA], 25 patients with eosinophilic asthma [EA]) and 40 healthy controls (HCs). When the prevalence of IgG1 and IgG4 specific to MlEVs was evaluated in serum by ELISA, lower levels of MlEV-specific IgG4 (but not IgG1) were noted in asthmatic patients than in HCs. Among asthmatic patients, significantly lower levels of MIEV-specific IgG4 were noted in patients with NA than in those with EA. Moreover, there was a positive correlation between serum MlEV-specific IgG4 levels and FEV1 (%) values. In asthmatic C57BL/6 mice, MlEVs significantly attenuated neutrophilic airway inflammation by reducing the production of IL-1β and IL-17 in bronchoalveolar lavage fluid as well as the number of group 3 innate lymphoid cells (ILC3s) in lung tissues. To clarify the functional mechanism of MlEVs in NA, the effect of MlEVs on airway epithelial cells (AECs) and immune cells was investigated ex vivo. According to microarray analysis, MlEVs upregulated hsa-miR-4517 expression in AECs. Moreover, this miRNA could suppress IL-1β production by monocytes, resulting in the inhibition of ILC3 activation and neutrophil recruitment. These findings suggest that MlEVs could be a novel therapeutic agent for managing unresolved NA by regulating miRNA expression in AECs.
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13
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Abstract
Metabolomics is an expanding field of systems biology that is gaining significant attention in respiratory research. As a unique approach to understanding and diagnosing diseases, metabolomics provides a snapshot of all metabolites present in biological samples such as exhaled breath condensate, bronchoalveolar lavage, plasma, serum, urine, and other specimens that may be obtained from patients with respiratory diseases. In this article, we review the rapidly expanding field of metabolomics in its application to respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), pneumonia, and acute lung injury, along with its more severe form, adult respiratory disease syndrome. We also discuss the potential applications of metabolomics for monitoring exposure to aerosolized occupational and environmental materials. With the latest advances in our understanding of the microbiome, we discuss microbiome-derived metabolites that arise from the gut and lung in asthma and COPD that have mechanistic implications for these diseases. Recent literature has suggested that metabolomics analysis using nuclear magnetic resonance (NMR) and mass spectrometry (MS) approaches may provide clinicians with the opportunity to identify new biomarkers that may predict progression to more severe diseases which may be fatal for many patients each year.
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Affiliation(s)
- Subhabrata Moitra
- Department of Medicine, Alberta Respiratory Centre (ARC), University of Alberta, Edmonton, AB, Canada
| | - Arghya Bandyopadhyay
- Department of Medicine, Alberta Respiratory Centre (ARC), University of Alberta, Edmonton, AB, Canada
| | - Paige Lacy
- Department of Medicine, Alberta Respiratory Centre (ARC), University of Alberta, Edmonton, AB, Canada.
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14
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Machine-learning algorithms for asthma, COPD, and lung cancer risk assessment using circulating microbial extracellular vesicle data and their application to assess dietary effects. EXPERIMENTAL & MOLECULAR MEDICINE 2022; 54:1586-1595. [PMID: 36180580 PMCID: PMC9534896 DOI: 10.1038/s12276-022-00846-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 06/17/2022] [Accepted: 07/12/2022] [Indexed: 11/08/2022]
Abstract
Although mounting evidence suggests that the microbiome has a tremendous influence on intractable disease, the relationship between circulating microbial extracellular vesicles (EVs) and respiratory disease remains unexplored. Here, we developed predictive diagnostic models for COPD, asthma, and lung cancer by applying machine learning to microbial EV metagenomes isolated from patient serum and coded by their accumulated taxonomic hierarchy. All models demonstrated high predictive strength with mean AUC values ranging from 0.93 to 0.99 with various important features at the genus and phylum levels. Application of the clinical models in mice showed that various foods reduced high-fat diet-associated asthma and lung cancer risk, while COPD was minimally affected. In conclusion, this study offers a novel methodology for respiratory disease prediction and highlights the utility of serum microbial EVs as data-rich features for noninvasive diagnosis. Artificial intelligence (AI) has enabled researchers to intercept microbial messages bearing clinically useful information about of a variety of respiratory disorders. The organisms that comprise our microbiome communicate via the release of tiny, biomolecule-laden membrane bubbles called ‘extracellular vesicles’ (EVs) into the bloodstream. EVs are also influenced by human disease. South Korean researchers led by Yoon-Keun Kim of MD Healthcare, Seoul, and Young-Koo Jee of Dankook University College of Medicine, Cheonan, have used an AI algorithm to assemble EV-based profiles that can discriminate between healthy people and those with conditions like asthma or lung cancer. Their analysis of 1727 patient serum samples revealed microbial signatures that enabled accurate diagnosis of several respiratory disorders. Preliminary experiments in mice suggest that certain dietary changes could help shift the microbiome of high-risk individuals towards a healthier profile.
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15
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Costantini C, Nunzi E, Romani L. From the nose to the lungs: the intricate journey of airborne pathogens amidst commensal bacteria. Am J Physiol Cell Physiol 2022; 323:C1036-C1043. [PMID: 36036448 PMCID: PMC9529274 DOI: 10.1152/ajpcell.00287.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The recent COVID-19 pandemic has dramatically brought the pitfalls of airborne pathogens to the attention of the scientific community. Not only viruses but also bacteria and fungi may exploit air transmission to colonize and infect potential hosts and be the cause of significant morbidity and mortality in susceptible populations. The efforts to decipher the mechanisms of pathogenicity of airborne microbes have brought to light the delicate equilibrium that governs the homeostasis of mucosal membranes. The microorganisms already thriving in the permissive environment of the respiratory tract represent a critical component of this equilibrium and a potent barrier to infection by means of direct competition with airborne pathogens or indirectly via modulation of the immune response. Moving down the respiratory tract, physicochemical and biological constraints promote site-specific expansion of microbes that engage in cross talk with the local immune system to maintain homeostasis and promote protection. In this review, we critically assess the site-specific microbial communities that an airborne pathogen encounters in its hypothetical travel along the respiratory tract and discuss the changes in the composition and function of the microbiome in airborne diseases by taking fungal and SARS-CoV-2 infections as examples. Finally, we discuss how technological and bioinformatics advancements may turn microbiome analysis into a valuable tool in the hands of clinicians to predict the risk of disease onset, the clinical course, and the response to treatment of individual patients in the direction of personalized medicine implementation.
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Affiliation(s)
- Claudio Costantini
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Emilia Nunzi
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Luigina Romani
- Department of Medicine and Surgery, University of Perugia, Perugia, Italy
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16
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Giron LB, Peluso MJ, Ding J, Kenny G, Zilberstein NF, Koshy J, Hong KY, Rasmussen H, Miller GE, Bishehsari F, Balk RA, Moy JN, Hoh R, Lu S, Goldman AR, Tang HY, Yee BC, Chenna A, Winslow JW, Petropoulos CJ, Kelly JD, Wasse H, Martin JN, Liu Q, Keshavarzian A, Landay A, Deeks SG, Henrich TJ, Abdel-Mohsen M. Markers of fungal translocation are elevated during post-acute sequelae of SARS-CoV-2 and induce NF-κB signaling. JCI Insight 2022; 7:e160989. [PMID: 35727635 PMCID: PMC9462470 DOI: 10.1172/jci.insight.160989] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/17/2022] [Indexed: 11/24/2022] Open
Abstract
Long COVID, a type of post-acute sequelae of SARS-CoV-2 (PASC), has been associated with sustained elevated levels of immune activation and inflammation. However, the mechanisms that drive this inflammation remain unknown. Inflammation during acute coronavirus disease 2019 could be exacerbated by microbial translocation (from the gut and/or lung) to blood. Whether microbial translocation contributes to inflammation during PASC is unknown. We did not observe a significant elevation in plasma markers of bacterial translocation during PASC. However, we observed higher levels of fungal translocation - measured as β-glucan, a fungal cell wall polysaccharide - in the plasma of individuals experiencing PASC compared with those without PASC or SARS-CoV-2-negative controls. The higher β-glucan correlated with higher inflammation and elevated levels of host metabolites involved in activating N-methyl-d-aspartate receptors (such as metabolites within the tryptophan catabolism pathway) with established neurotoxic properties. Mechanistically, β-glucan can directly induce inflammation by binding to myeloid cells (via Dectin-1) and activating Syk/NF-κB signaling. Using a Dectin-1/NF-κB reporter model, we found that plasma from individuals experiencing PASC induced higher NF-κB signaling compared with plasma from negative controls. This higher NF-κB signaling was abrogated by piceatannol (Syk inhibitor). These data suggest a potential targetable mechanism linking fungal translocation and inflammation during PASC.
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Affiliation(s)
| | | | - Jianyi Ding
- The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Grace Kenny
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | | | - Jane Koshy
- The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Kai Ying Hong
- The Wistar Institute, Philadelphia, Pennsylvania, USA
| | | | | | - Faraz Bishehsari
- Department of Internal Medicine, Rush University, Chicago, Illinois, USA
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, Illinois, USA
| | - Robert A. Balk
- Department of Internal Medicine, Rush University, Chicago, Illinois, USA
| | - James N. Moy
- Department of Internal Medicine, Rush University, Chicago, Illinois, USA
| | | | - Scott Lu
- UCSF, San Francisco, California, USA
| | | | - Hsin-Yao Tang
- The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Brandon C. Yee
- Monogram Biosciences, Inc., Labcorp, South San Francisco, California, USA
| | - Ahmed Chenna
- Monogram Biosciences, Inc., Labcorp, South San Francisco, California, USA
| | - John W. Winslow
- Monogram Biosciences, Inc., Labcorp, South San Francisco, California, USA
| | | | | | - Haimanot Wasse
- Department of Internal Medicine, Rush University, Chicago, Illinois, USA
| | | | - Qin Liu
- The Wistar Institute, Philadelphia, Pennsylvania, USA
| | - Ali Keshavarzian
- Department of Internal Medicine, Rush University, Chicago, Illinois, USA
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, Illinois, USA
| | - Alan Landay
- Department of Internal Medicine, Rush University, Chicago, Illinois, USA
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17
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Klosinska K, Reece E, Kenny E, Renwick J. Reducing human DNA bias in cystic fibrosis airway specimens for microbiome analysis. J Microbiol Methods 2022; 200:106540. [PMID: 35853495 DOI: 10.1016/j.mimet.2022.106540] [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: 05/26/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 12/27/2022]
Abstract
Next generation sequencing (NGS) has transformed our understanding of airway microbiology, however there are methodology limitations that require consideration. The presence of high concentrations of human DNA in clinical specimens can significantly impact sequencing of the microbiome, especially in low biomass samples. Here we compared three different methods (0.025% saponin, NEBNext Microbiome DNA enrichment kit, QIAamp DNA microbiome kit) for the reduction of human DNA from six CF sputum samples and determined the impact on the microbiome detected using 16S rRNA gene sequencing. Human DNA in undepleted CF sputum accounted for 94.3% of the total DNA. Saponin, the NEBNext kit and the QIAamp kit reduced human DNA levels by an average of 38.7%, 61.8% and 94.8%, respectively. None of the depletion methods reduced total bacterial DNA concentrations. QIAamp depletion did not influence taxa richness or alpha diversity however alterations to the core genera were noted following depletion. While all methods reduced human DNA in the CF sputum samples, the QIAamp DNA microbiome kit reduced Human DNA levels significantly while leaving bacterial DNA levels unchanged. Human DNA depletion in low biomass, human DNA-dense CF sputum samples is vital for improving bacterial resolution in the CF airway microbiome.
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Affiliation(s)
- Karolina Klosinska
- Clinical Microbiology Department, Trinity College Dublin, Trinity Centre for Health Sciences, Tallaght University Hospital, Dublin, Ireland
| | - Emma Reece
- Clinical Microbiology Department, Trinity College Dublin, Trinity Centre for Health Sciences, Tallaght University Hospital, Dublin, Ireland
| | - Elaine Kenny
- ELDA Biotech, Naas, Kildare, Ireland; TrinSeq, Trinity Translational Medicine Institute, Trinity College Dublin, Ireland
| | - Julie Renwick
- Clinical Microbiology Department, Trinity College Dublin, Trinity Centre for Health Sciences, Tallaght University Hospital, Dublin, Ireland.
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18
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Birla P, Shaikh FY. De- "bug"-ing the microbiome in lung cancer. Cancer Metastasis Rev 2022; 41:335-346. [PMID: 35588337 DOI: 10.1007/s10555-022-10036-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/30/2022] [Indexed: 12/12/2022]
Abstract
The identification of microbes enriched in the healthy lung has led to the compelling discovery that microbes may contribute to lung cancer pathogenesis. Here, we review the recent literature showing microbial associations with lung cancer as well as the functional features that have been identified in human and murine studies. Most biomarker data remain limited due to variable findings. However, multiple studies have found that lung tumors or ipsilateral airway samples have decreased α diversity compared to normal tissue. Specific genera, such as Veillonella and Streptococcus, were also found in association with lung tumors using multiple sampling methodologies. These microbes, which are generally found in the upper respiratory track, are associated with an IL-17 signature in the lung, potentially resulting in a pro-tumorigenic environment. Studies detailing these immune mechanisms are limited, and further investigation is necessary to delineate how these bacteria, their metabolites, and potentially tumor-associated neoantigens modulate the immune response in cancer.
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Affiliation(s)
- Pakhi Birla
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, 1650 Orleans Street CRB1 Bldg, Suite 4M 441, Baltimore, MD, 21231, USA
| | - Fyza Y Shaikh
- The Bloomberg-Kimmel Institute of Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Oncology, Johns Hopkins University School of Medicine, 1650 Orleans Street CRB1 Bldg, Suite 4M 441, Baltimore, MD, 21231, USA.
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19
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Functional, transcriptional, and microbial shifts associated with healthy pulmonary aging in rhesus macaques. Cell Rep 2022; 39:110725. [PMID: 35443183 PMCID: PMC9096119 DOI: 10.1016/j.celrep.2022.110725] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/09/2022] [Accepted: 03/30/2022] [Indexed: 01/04/2023] Open
Abstract
Older individuals are at increased risk of developing severe respiratory infections. However, our understanding of the impact of aging on the respiratory tract remains limited as samples from healthy humans are challenging to obtain and results can be confounded by variables such as smoking and diet. Here, we carry out a comprehensive cross-sectional study (n = 34 adult, n = 49 aged) to define the consequences of aging on the lung using the rhesus macaque model. Pulmonary function testing establishes similar age and sex differences as humans. Additionally, we report increased abundance of alveolar and infiltrating macrophages and a concomitant decrease in T cells were in aged animals. scRNAseq reveals shifts from GRZMB to IFN expressing CD8+ T cells in the lungs. These data provide insight into age-related changes in the lungs’ functional, microbial, and immunological landscape that explain increased prevalence and severity of respiratory diseases in the elderly. Rhoades et al. describe age-associated functional, microbial, and immunological changes in the lung using the rhesus macaque model. These data will support further studies aimed at designing and testing interventions to mitigate the impact of age-associated shifts in the lung environment to reduce age-related pulmonary disease in the elderly.
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20
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Busse WW, Melén E, Menzies-Gow AN. Holy Grail: the journey towards disease modification in asthma. Eur Respir Rev 2022; 31:31/163/210183. [PMID: 35197266 PMCID: PMC9488532 DOI: 10.1183/16000617.0183-2021] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/28/2021] [Indexed: 12/12/2022] Open
Abstract
At present, there is no cure for asthma, and treatment typically involves therapies that prevent or reduce asthma symptoms, without modifying the underlying disease. A “disease-modifying” treatment can be classed as able to address the pathogenesis of a disease, preventing progression or leading to a long-term reduction in symptoms. Such therapies have been investigated and approved in other indications, e.g. rheumatoid arthritis and immunoglobulin E-mediated allergic disease. Asthma's heterogeneous nature has made the discovery of similar therapies in asthma more difficult, although novel therapies (e.g. biologics) may have the potential to exhibit disease-modifying properties. To investigate the disease-modifying potential of a treatment, study design considerations can be made, including: appropriate end-point selection, length of trial, age of study population (key differences between adults/children in physiology, pathology and drug metabolism) and comorbidities in the patient population. Potential future focus areas for disease-modifying treatments in asthma include early assessments (e.g. to detect patterns of remodelling) and interventions for patients genetically susceptible to asthma, interventions to prevent virally induced asthma and therapies to promote a healthy microbiome. This review explores the pathophysiology of asthma, the disease-modifying potential of current asthma therapies and the direction future research may take to achieve full disease remission or prevention. Asthma is a complex, heterogeneous disease, which currently has no cure; this review explores the disease-modifying potential of asthma therapies and the direction future research may take to achieve disease remission or prevention.https://bit.ly/31AxYou
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Affiliation(s)
- William W Busse
- Dept of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Erik Melén
- Dept of Clinical Science and Education Södersjukhuset, Karolinska Institutet and Sachs' Children's Hospital, Stockholm, Sweden
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21
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Logotheti M, Agioutantis P, Katsaounou P, Loutrari H. Microbiome Research and Multi-Omics Integration for Personalized Medicine in Asthma. J Pers Med 2021; 11:jpm11121299. [PMID: 34945771 PMCID: PMC8707330 DOI: 10.3390/jpm11121299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/13/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
Asthma is a multifactorial inflammatory disorder of the respiratory system characterized by high diversity in clinical manifestations, underlying pathological mechanisms and response to treatment. It is generally established that human microbiota plays an essential role in shaping a healthy immune response, while its perturbation can cause chronic inflammation related to a wide range of diseases, including asthma. Systems biology approaches encompassing microbiome analysis can offer valuable platforms towards a global understanding of asthma complexity and improving patients' classification, status monitoring and therapeutic choices. In the present review, we summarize recent studies exploring the contribution of microbiota dysbiosis to asthma pathogenesis and heterogeneity in the context of asthma phenotypes-endotypes and administered medication. We subsequently focus on emerging efforts to gain deeper insights into microbiota-host interactions driving asthma complexity by integrating microbiome and host multi-omics data. One of the most prominent achievements of these research efforts is the association of refractory neutrophilic asthma with certain microbial signatures, including predominant pathogenic bacterial taxa (such as Proteobacteria phyla, Gammaproteobacteria class, especially species from Haemophilus and Moraxella genera). Overall, despite existing challenges, large-scale multi-omics endeavors may provide promising biomarkers and therapeutic targets for future development of novel microbe-based personalized strategies for diagnosis, prevention and/or treatment of uncontrollable asthma.
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Affiliation(s)
- Marianthi Logotheti
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
| | - Panagiotis Agioutantis
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
| | - Paraskevi Katsaounou
- Pulmonary Dept First ICU, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, Ipsilantou 45-7, 10675 Athens, Greece;
| | - Heleni Loutrari
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
- Correspondence:
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22
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Jeong J, Lee HK. The Role of CD4 + T Cells and Microbiota in the Pathogenesis of Asthma. Int J Mol Sci 2021; 22:11822. [PMID: 34769255 PMCID: PMC8584410 DOI: 10.3390/ijms222111822] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 12/22/2022] Open
Abstract
Asthma, a chronic respiratory disease involving variable airflow limitations, exhibits two phenotypes: eosinophilic and neutrophilic. The asthma phenotype must be considered because the prognosis and drug responsiveness of eosinophilic and neutrophilic asthma differ. CD4+ T cells are the main determinant of asthma phenotype. Th2, Th9 and Tfh cells mediate the development of eosinophilic asthma, whereas Th1 and Th17 cells mediate the development of neutrophilic asthma. Elucidating the biological roles of CD4+ T cells is thus essential for developing effective asthma treatments and predicting a patient's prognosis. Commensal bacteria also play a key role in the pathogenesis of asthma. Beneficial bacteria within the host act to suppress asthma, whereas harmful bacteria exacerbate asthma. Recent literature indicates that imbalances between beneficial and harmful bacteria affect the differentiation of CD4+ T cells, leading to the development of asthma. Correcting bacterial imbalances using probiotics reportedly improves asthma symptoms. In this review, we investigate the effects of crosstalk between the microbiota and CD4+ T cells on the development of asthma.
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Affiliation(s)
| | - Heung Kyu Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea;
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Boutin S, Hildebrand D, Boulant S, Kreuter M, Rüter J, Pallerla SR, Velavan TP, Nurjadi D. Host factors facilitating SARS-CoV-2 virus infection and replication in the lungs. Cell Mol Life Sci 2021; 78:5953-5976. [PMID: 34223911 PMCID: PMC8256233 DOI: 10.1007/s00018-021-03889-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 06/01/2021] [Accepted: 06/18/2021] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 is the virus causing the major pandemic facing the world today. Although, SARS-CoV-2 primarily causes lung infection, a variety of symptoms have proven a systemic impact on the body. SARS-CoV-2 has spread in the community quickly infecting humans from all age, ethnicities and gender. However, fatal outcomes have been linked to specific host factors and co-morbidities such as age, hypertension, immuno-deficiencies, chronic lung diseases or metabolic disorders. A major shift in the microbiome of patients suffering of the coronavirus disease 2019 (COVID-19) have also been observed and is linked to a worst outcome of the disease. As many co-morbidities are already known to be associated with a dysbiosis of the microbiome such as hypertension, diabetes and metabolic disorders. Host factors and microbiome changes are believed to be involved as a network in the acquisition of the infection and the development of the diseases. We will review in detail in this manuscript, the immune response toward SARS-CoV-2 infection as well as the host factors involved in the facilitation and worsening of the infection. We will also address the impact of COVID-19 on the host's microbiome and secondary infection which also worsen the disease.
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Affiliation(s)
- Sébastien Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany.
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany.
| | - Dagmar Hildebrand
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
| | - Steeve Boulant
- Division of Cellular Polarity and Viral Infection, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Kreuter
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), University of Heidelberg, Heidelberg, Germany
- Center for Interstitial and Rare Lung Diseases, Pneumology, Thoraxklinik, University of Heidelberg, Heidelberg, Germany
| | - Jule Rüter
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
| | | | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
| | - Dennis Nurjadi
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University Hospital Heidelberg, Im Neuenheimer Feld 324, 69120, Heidelberg, Germany
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Hsieh CS, Rengarajan S, Kau A, Tarazona-Meza C, Nicholson A, Checkley W, Romero K, Hansel NN. Altered IgA Response to Gut Bacteria Is Associated with Childhood Asthma in Peru. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:398-407. [PMID: 34193598 PMCID: PMC8516662 DOI: 10.4049/jimmunol.2001296] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/28/2021] [Indexed: 12/24/2022]
Abstract
Alterations in gut microbiota in early life have been associated with the development of asthma; however, the role of gut bacteria or the IgA response to gut bacteria in school-aged children with asthma is unclear. To address this question, we profiled the microbial populations in fecal and nasal swab samples by 16S rRNA sequencing from 40 asthma and 40 control children aged 9-17 y from Peru. Clinical history and laboratory evaluation of asthma and allergy were obtained. Fecal samples were analyzed by flow cytometry and sorted into IgA+ and IgA- subsets for 16S rRNA sequencing. We found that the fecal or nasal microbial 16S rRNA diversity and frequency of IgA+ fecal bacteria did not differ between children with or without asthma. However, the α diversity of fecal IgA+ bacteria was decreased in asthma compared with control. Machine learning analysis of fecal bacterial IgA-enrichment data revealed loss of IgA binding to the Blautia, Ruminococcus, and Lachnospiraceae taxa in children with asthma compared with controls. In addition, this loss of IgA binding was associated with worse asthma control (Asthma Control Test) and increased odds of severe as opposed to mild to moderate asthma. Thus, despite little to no change in the microbiota, children with asthma exhibit an altered host IgA response to gut bacteria compared with control participants. Notably, the signature of altered IgA responses is loss of IgA binding, in particular to members of Clostridia spp., which is associated with greater severity of asthma.
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Affiliation(s)
- Chyi-Song Hsieh
- Division of Rheumatology, John T. Milliken Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO;
| | - Sunaina Rengarajan
- Division of Rheumatology, John T. Milliken Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO
| | - Andrew Kau
- Division of Allergy and Immunology, John T. Milliken Department of Internal Medicine, Washington University School of Medicine, Saint Louis, MO
| | - Carla Tarazona-Meza
- Asociacion Benefica Prisma, PRISMA, Lima, Peru
- Center for Global Non-Communicable Disease Research and Training, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Andrew Nicholson
- Program in Global Disease Epidemiology and Control, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; and
| | - William Checkley
- Center for Global Non-Communicable Disease Research and Training, Johns Hopkins University School of Medicine, Baltimore, MD
- Program in Global Disease Epidemiology and Control, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; and
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Karina Romero
- Asociacion Benefica Prisma, PRISMA, Lima, Peru
- Center for Global Non-Communicable Disease Research and Training, Johns Hopkins University School of Medicine, Baltimore, MD
- Program in Global Disease Epidemiology and Control, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; and
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Nadia N Hansel
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
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Dzhambov AM, Lercher P, Rüdisser J, Browning MHEM, Markevych I. Allergic symptoms in association with naturalness, greenness, and greyness: A cross-sectional study in schoolchildren in the Alps. ENVIRONMENTAL RESEARCH 2021; 198:110456. [PMID: 33188758 DOI: 10.1016/j.envres.2020.110456] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/02/2020] [Accepted: 11/07/2020] [Indexed: 05/16/2023]
Abstract
BACKGROUND Greenness may protect from or contribute to allergy risk by influencing air pollution and human-microbe interactions. However, existing research on the issue is heterogeneous and produced conflicting results. Less in known about the effects of greyness. This study investigated the association between different characteristics of residential and school environment and allergic symptoms in schoolchildren. METHODS The present cross-sectional survey was undertaken in 2004/2005 among 1251 schoolchildren (8-12 years old) in several alpine valleys in Austria and Italy. Children's mothers completed a questionnaire that asked about allergic symptoms (International Study of Asthma and Allergies in Childhood questionnaire), sociodemographic information, lifestyle, perinatal data, and housing conditions. We constructed four aggregate outcome variables: current asthma symptoms, ever asthma symptoms, ever allergic rhinitis (AR) symptoms, and ever eczema symptoms. We employed well-known greenness and greyness exposure indicators (Normalized Difference Vegetation Index, tree canopy cover, agricultural cover, imperviousness cover, and industrial cover), as well as an alternative naturalness index (Distance to Nature, D2N). Adjusted logistic regressions were used to explore associations between each exposure-outcome pair. Air pollution (NO2), traffic noise and time spent outdoors were tested as potential mediators in causal mediation analysis. RESULTS Decrease in naturalness in a 500-m buffer around the home was associated with higher prevalence of AR symptoms. Associations with asthma symptoms were in the same direction but marginally significant. Residential NDVI and tree cover were marginally associated with lower prevalence of asthma and AR symptoms. Having a domestic garden was associated with lower prevalence of asthma symptoms. School greenness in a 100-m buffer was associated with lower prevalence of AR symptoms. Residential greyness was associated with higher prevalence of AR and asthma symptoms. We observed stronger associations for greenness and greyness in non-movers and in children without a family history of allergies. Mediation by NO2 and time spent outdoors was present in some of the exposure-outcome pairs. CONCLUSIONS Schoolchildren residing in places with lower naturalness and higher greyness may be more likely to have allergic rhinitis and possibly asthma. Considering more comprehensive indicators than greenness and greyness and conducting research in children without a family history of allergic diseases may be key to better understanding who can profit from natural landscapes.
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Affiliation(s)
- Angel M Dzhambov
- Department of Hygiene, Faculty of Public Health, Medical University of Plovdiv, Plovdiv, Bulgaria; Institute for Highway Engineering and Transport Planning, Graz University of Technology, Graz, Austria.
| | - Peter Lercher
- Institute for Highway Engineering and Transport Planning, Graz University of Technology, Graz, Austria
| | | | - Matthew H E M Browning
- Department of Parks , Recreation, and Tourism Management, Clemson University, Clemson, USA
| | - Iana Markevych
- Institute of Psychology, Jagiellonian University, Krakow, Poland
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26
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Extracellular vesicle-derived microbiome obtained from exhaled breath condensate in patients with asthma. Ann Allergy Asthma Immunol 2021; 126:729-731. [PMID: 33713805 DOI: 10.1016/j.anai.2021.02.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/09/2021] [Accepted: 02/28/2021] [Indexed: 12/20/2022]
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Magryś A. Microbiota: A Missing Link in The Pathogenesis of Chronic Lung Inflammatory Diseases. Pol J Microbiol 2021; 70:25-32. [PMID: 33815524 PMCID: PMC8008760 DOI: 10.33073/pjm-2021-013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 12/21/2022] Open
Abstract
Chronic respiratory diseases account for high morbidity and mortality, with asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis (CF) being the most prevalent globally. Even though the diseases increase in prevalence, the exact underlying mechanisms have still not been fully understood. Despite their differences in nature, pathophysiologies, and clinical phenotypes, a growing body of evidence indicates that the presence of lung microbiota can shape the pathogenic processes underlying chronic inflammation, typically observed in the course of the diseases. Therefore, the characterization of the lung microbiota may shed new light on the pathogenesis of these diseases. Specifically, in chronic respiratory tract diseases, the human microbiota may contribute to the disease’s development and severity. The present review explores the role of the microbiota in the area of chronic pulmonary diseases, especially COPD, asthma, and CF.
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Affiliation(s)
- Agnieszka Magryś
- Chair and Department of Medical Microbiology, Medical University of Lublin, Lublin, Poland
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28
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Shi J, Xiao Y, Zhang Y, Geng D, Cong D, Shi KX, Knapp RJ. Challenges of drug development during the COVID-19 pandemic: Key considerations for clinical trial designs. Br J Clin Pharmacol 2020; 87:2170-2185. [PMID: 33119136 DOI: 10.1111/bcp.14629] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/14/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022] Open
Abstract
There is an urgent need for targeted and effective COVID-19 treatments. Several medications, including hydroxychloroquine, remdesivir, lopinavir-ritonavir, favipiravir, tocilizumab and others have been identified as potential treatments for COVID-19. Bringing these repurposed medications to the public for COVID-19 requires robust and high-quality clinical trials that must be conducted under extremely challenging pandemic conditions. This article reviews translational science principles and strategies for conducting clinical trials in a pandemic and evaluates recent trials for different drug candidates. We hope that this knowledge will help focus efforts during this crisis and lead to the expedited development and approval of COVID-19 therapies.
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Affiliation(s)
| | | | | | | | | | - Kevin X Shi
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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Lee JH, Choi JP, Yang J, Won HK, Park CS, Song WJ, Kwon HS, Kim TB, Kim YK, Park HS, Cho YS. Metagenome analysis using serum extracellular vesicles identified distinct microbiota in asthmatics. Sci Rep 2020; 10:15125. [PMID: 32934287 PMCID: PMC7492258 DOI: 10.1038/s41598-020-72242-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023] Open
Abstract
Different patterns of bacterial communities have been reported in the airways and gastrointestinal tract of asthmatics when compared to healthy controls. However, the blood microbiome of asthmatics is yet to be investigated. Therefore, we aimed to determine whether a distinct serum microbiome is observed in asthmatics by metagenomic analysis of serum extracellular vesicles (EVs). We obtained serum from 190 adults with asthma and 260 healthy controls, from which EVs were isolated and analyzed. The bacterial composition of asthmatics was significantly different from that of healthy controls. Chao 1 index was significantly higher in the asthma group, while Shannon and Simpson indices were higher in the control group. At the phylum level, Bacteroidetes was more abundant in asthmatics, while Actinobacter, Verrucomicrobia, and Cyanobacteria were more abundant in healthy controls. At the genus level, 24 bacterial genera showed differences in relative abundance between asthmatics and controls, with linear discriminant analysis scores greater than 3. Further, in a diagnostic model based on these differences, a high predictive value with a sensitivity of 0.92 and a specificity of 0.93 was observed. In conclusion, we demonstrated distinct blood microbiome in asthma indicating the role of microbiome as a potential diagnostic marker of asthma.
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Affiliation(s)
- Ji-Hyang Lee
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Jun-Pyo Choi
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jinho Yang
- MD Healthcare Inc, Seoul, Republic of Korea
| | - Ha-Kyeong Won
- Department of Internal Medicine, Veterans Health Service Medical Center, Seoul, Republic of Korea
| | - Chan Sun Park
- Department of Internal Medicine, Inje University Haeundae Paik Hospital, Busan, Republic of Korea
| | - Woo-Jung Song
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Hyouk-Soo Kwon
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Tae-Bum Kim
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | | | - Hae-Sim Park
- Department of Allergy and Clinical Immunology, Ajou University Medical Center, Suwon, Republic of Korea
| | - You Sook Cho
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea.
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30
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Vandenborght LE, Enaud R, Urien C, Coron N, Girodet PO, Ferreira S, Berger P, Delhaes L. Type 2-high asthma is associated with a specific indoor mycobiome and microbiome. J Allergy Clin Immunol 2020; 147:1296-1305.e6. [PMID: 32926879 PMCID: PMC7486598 DOI: 10.1016/j.jaci.2020.08.035] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 12/17/2022]
Abstract
Background The links between microbial environmental exposures and asthma are well documented, but no study has combined deep sequencing results from pulmonary and indoor microbiomes of patients with asthma with spirometry, clinical, and endotype parameters. Objective The goal of this study was to investigate the links between indoor microbial exposures and pulmonary microbial communities and to document the role of microbial exposures on inflammatory and clinical outcomes of patients with severe asthma (SA). Methods A total of 55 patients with SA from the national Cohort of Bronchial Obstruction and Asthma cohort were enrolled for analyzing their indoor microbial flora through the use of electrostatic dust collectors (EDCs). Among these patients, 22 were able to produce sputum during “stable” or pulmonary “exacerbation” periods and had complete pairs of EDC and sputum samples, both collected and analyzed. We used amplicon targeted metagenomics to compare microbial communities from EDC and sputum samples of patients according to type 2 (T2)-asthma endotypes. Results Compared with patients with T2-low SA, patients with T2-high SA exhibited an increase in bacterial α-diversity and a decrease in fungal α-diversity of their indoor microbial florae, the latter being significantly correlated with fraction of exhaled nitric oxide levels. The β-diversity of the EDC mycobiome clustered significantly according to T2 endotypes. Moreover, the proportion of fungal taxa in common between the sputum and EDC samples was significantly higher when patients exhibited acute exacerbation. Conclusion These results illustrated, for the first time, a potential association between the indoor mycobiome and clinical features of patients with SA, which should renew interest in deciphering the interactions between indoor environment, fungi, and host in asthma.
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Affiliation(s)
- Louise-Eva Vandenborght
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, F-33000 Bordeaux, France; Centre de Recherche Cardio-thoracique de Bordeaux, INSERM, U1045, CIC 1401, F-33000 Bordeaux, France; Microbiota Team, Research and Development Department, GenoScreen, Lille, France
| | - Raphaël Enaud
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, F-33000 Bordeaux, France; Centre de Recherche Cardio-thoracique de Bordeaux, INSERM, U1045, CIC 1401, F-33000 Bordeaux, France; Laboratoire de Parasitologie-Mycologie, Service D'exploration Fonctionnelle Respiratoire, Service de pharmacologie, CIC 1401, CHU de Bordeaux, F-33604 Pessac, France
| | - Charlotte Urien
- Microbiota Team, Research and Development Department, GenoScreen, Lille, France
| | - Noémie Coron
- Laboratoire de Parasitologie-Mycologie, Service D'exploration Fonctionnelle Respiratoire, Service de pharmacologie, CIC 1401, CHU de Bordeaux, F-33604 Pessac, France
| | - Pierre-Olivier Girodet
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, F-33000 Bordeaux, France; Centre de Recherche Cardio-thoracique de Bordeaux, INSERM, U1045, CIC 1401, F-33000 Bordeaux, France; Laboratoire de Parasitologie-Mycologie, Service D'exploration Fonctionnelle Respiratoire, Service de pharmacologie, CIC 1401, CHU de Bordeaux, F-33604 Pessac, France
| | - Stéphanie Ferreira
- Microbiota Team, Research and Development Department, GenoScreen, Lille, France
| | - Patrick Berger
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, F-33000 Bordeaux, France; Centre de Recherche Cardio-thoracique de Bordeaux, INSERM, U1045, CIC 1401, F-33000 Bordeaux, France; Laboratoire de Parasitologie-Mycologie, Service D'exploration Fonctionnelle Respiratoire, Service de pharmacologie, CIC 1401, CHU de Bordeaux, F-33604 Pessac, France
| | - Laurence Delhaes
- Univ-Bordeaux, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, F-33000 Bordeaux, France; Centre de Recherche Cardio-thoracique de Bordeaux, INSERM, U1045, CIC 1401, F-33000 Bordeaux, France; Laboratoire de Parasitologie-Mycologie, Service D'exploration Fonctionnelle Respiratoire, Service de pharmacologie, CIC 1401, CHU de Bordeaux, F-33604 Pessac, France.
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Wallace RK. The Microbiome in Health and Disease from the Perspective of Modern Medicine and Ayurveda. ACTA ACUST UNITED AC 2020; 56:medicina56090462. [PMID: 32932766 PMCID: PMC7559905 DOI: 10.3390/medicina56090462] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 08/28/2020] [Accepted: 09/09/2020] [Indexed: 02/07/2023]
Abstract
The role of the microbiome in health and disease helps to provide a scientific understanding of key concepts in Ayurveda. We now recognize that virtually every aspect of our physiology and health is influenced by the collection of microorganisms that live in various parts of our body, especially the gut microbiome. There are many external factors which influence the composition of the gut microbiome but one of the most important is diet and digestion. Ayurveda and other systems of traditional health have for thousands of years focused on diet and digestion. Recent research has helped us understand the connection between the microbiome and the many different prevention and therapeutic treatment approaches of Ayurveda.
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Affiliation(s)
- Robert Keith Wallace
- Department of Physiology and Health, Maharishi International University, Fairfield, IA 52556, USA
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32
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Actis GC, Pellicano R, Ribaldone DG. Inflammation: an all-season phenomenon in human pathology. GAZZETTA MEDICA ITALIANA ARCHIVIO PER LE SCIENZE MEDICHE 2020. [DOI: 10.23736/s0393-3660.20.04349-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
PURPOSE OF REVIEW The purpose of this review is to integrate recent research on the respiratory immune effects of e-cigarettes with the pathogenesis of asthma to better understand how e-cigarettes may affect asthmatics and to note critical knowledge gaps regarding the effects of e-cigarettes on asthmatics. RECENT FINDINGS Human, rodent, and cell culture studies show that key cellular functions of epithelial cells, macrophages, and neutrophils are altered by e-cigarette exposure. Because respiratory immunity is already dysregulated in asthma, further alteration of cellular function by e-cigarettes could impact asthma development, severity, and/or exacerbations. Future research is needed to more directly investigate this relationship using controlled human exposure studies and exposure of cell culture or animal models of asthma to e-cigarettes.
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The Gut Microbiota and Respiratory Diseases: New Evidence. J Immunol Res 2020; 2020:2340670. [PMID: 32802893 PMCID: PMC7415116 DOI: 10.1155/2020/2340670] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/13/2020] [Accepted: 06/18/2020] [Indexed: 12/14/2022] Open
Abstract
Human body surfaces, such as the skin, intestines, and respiratory and urogenital tracts, are colonized by a large number of microorganisms, including bacteria, fungi, and viruses, with the gut being the most densely and extensively colonized organ. The microbiome plays an essential role in immune system development and tissue homeostasis. Gut microbiota dysbiosis not only modulates the immune responses of the gastrointestinal (GI) tract but also impacts the immunity of distal organs, such as the lung, further affecting lung health and respiratory diseases. Here, we review the recent evidence of the correlations and underlying mechanisms of the relationship between the gut microbiota and common respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF), lung cancer, and respiratory infection, and probiotic development as a therapeutic intervention for these diseases.
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Zhuge A, Li B, Yuan Y, Lv L, Li Y, Wu J, Yang L, Bian X, Wang K, Wang Q, Yan R, Zhu X, Li L. Lactobacillus salivarius LI01 encapsulated in alginate-pectin microgels ameliorates D-galactosamine-induced acute liver injury in rats. Appl Microbiol Biotechnol 2020; 104:7437-7455. [PMID: 32666187 DOI: 10.1007/s00253-020-10749-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/01/2020] [Accepted: 06/16/2020] [Indexed: 12/13/2022]
Abstract
Acute liver failure is a clinical emergency associated with high mortality. Accumulating evidence indicates that gut microbiota participates in the progression of liver injury, and preventive therapies based on altering gut microbiota are of great interest. Previous studies demonstrated that Lactobacillus salivarius LI01 attenuates hepatic injury, though efficiency in curtailed in the harsh environment in the gastrointestinal tract. In this study, a system to encapsulate LI01 in alginate-pectin (AP) microgels was investigated. Encapsulation significantly enhances probiotic viability for long-term storage and heat treatment, and in simulated gastrointestinal fluids (SGF or SIF) and bile salt solutions. Acute liver injury was induced in Sprague-Dawley (SD) rats by D-galactosamine (D-GaIN) injection following pretreatment with probiotics. Liver and gut barrier function, cytokines, liver and gut histology, bacterial translocation, and gut microbiota were assessed. Administration of encapsulated LI01 more effectively upregulates hepatic anti-inflammatory cytokine IL-10 and TLR-3, restores expressions of gut barrier biomarkers Claudin-1 and MUC2 and attenuates destruction of mucosal ultrastructure compared with unencapsulated probiotics pretreatment. Pretreatment with AP-LI01 microgels altered the microbial community, decreasing the abundance of pathogenic taxa Ruminiclostridium, Dorea and Ruminococcaceae_UCG-004 and enriching beneficial taxa Ruminococcaceae_UCG-014, Eubacterium, and Prevotella_1 that produce short-chain fatty acids. These results suggest that AP encapsulation of LI01 boosts viability and attenuates liver injury by reducing inflammation and restoring intestinal barrier function. These beneficial effects are probably due to alternation of gut flora. These findings provide new insight into encapsulation technology and prevention of liver failure. KEY POINTS: • Alginate-pectin encapsulation enhances the viability of Lactobacillus salivarius LI01 under simulated commercial conditions and simulated gastrointestinal environment. • AP-LI01 microgel attenuates hepatic and intestinal inflammation and restores gut barrier function. • AP-LI01 microgel alters gut microbial community with increased SCFAs producers and decreased pathogenic microbes. • Beneficial improvements after administration of probiotics are highly associated with alternation of gut microbial community.
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Affiliation(s)
- Aoxiang Zhuge
- State Key Laboratory for Diagnosis, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innocation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Bo Li
- State Key Laboratory for Diagnosis, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innocation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Yin Yuan
- State Key Laboratory for Diagnosis, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innocation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Longxian Lv
- State Key Laboratory for Diagnosis, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innocation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Yating Li
- State Key Laboratory for Diagnosis, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innocation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jingjing Wu
- State Key Laboratory for Diagnosis, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innocation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Liya Yang
- State Key Laboratory for Diagnosis, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innocation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xiaoyuan Bian
- State Key Laboratory for Diagnosis, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innocation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Kaicen Wang
- State Key Laboratory for Diagnosis, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innocation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Qiangqiang Wang
- State Key Laboratory for Diagnosis, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innocation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Ren Yan
- State Key Laboratory for Diagnosis, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innocation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Xueling Zhu
- State Key Laboratory for Diagnosis, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Collaborative Innocation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
- Collaborative Innocation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.
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Kim YY, Joh JS, Lee JY. Importance of microbial extracellular vesicle in the pathogenesis of asthma and chronic obstructive pulmonary disease and its diagnostic potential. Asia Pac Allergy 2020; 10:e25. [PMID: 32789110 PMCID: PMC7402947 DOI: 10.5415/apallergy.2020.10.e25] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022] Open
Abstract
There are rising evidences of the human microbiome as a potentially influential player that is actively engaged in shaping the pathogenetic processes and other unresolved issues both in asthma and other chronic respiratory diseases, particularly of the airways. The biological components such as microbiome in inhaled air can induce immune dysfunction and inflammation, leading to inflammatory pulmonary disorders such as asthma and chronic obstructive pulmonary disease (COPD). Microbe-derived extracellular vesicles (EVs) with biologically active information or functions can reprogram their respective target cells and EV may have a role for the development of asthma and COPD. To evaluate the role of microbe-derived EV in the pathogenesis of asthma and COPD and its role in diagnosis, the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) statement method was used for the study. An electronic search was performed using PubMed, PubMed Central, and Embase up to 2020. EVs serve as an intercellular transporter of miRNAs for cell-to-cell communication in the lungs. Bacteria-derived EVs have distinctive characteristics in the lungs of patients with asthma and COPD compared to healthy controls. Furthermore, bacterial EV IgG antibody titers in serum were significantly higher in patients with asthma and COPD than in healthy controls, suggesting that antibacterial EV antibodies titers can be used as a diagnostic tool for lung disease. Taken together, microbial EVs and miRNAs have important roles in the pathogenesis of asthma and COPD and they can provide novel diagnostic biomarkers for asthma and COPD.
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Affiliation(s)
- You-Young Kim
- Asthma Allergy Center, National Medical Center, Seoul, Korea
| | - Joon Sung Joh
- Department of Respiratory Medicine, National Medical Center, Seoul, Korea
| | - Ji Yeon Lee
- Department of Respiratory Medicine, National Medical Center, Seoul, Korea
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Cumpanas AA, Bratu OG, Bardan RT, Ferician OC, Cumpanas AD, Horhat FG, Licker M, Pricop C, Cretu OM. Urinary Microbiota-Are We Ready for Prime Time? A Literature Review of Study Methods' Critical Steps in Avoiding Contamination and Minimizing Biased Results. Diagnostics (Basel) 2020; 10:diagnostics10060343. [PMID: 32471022 PMCID: PMC7345871 DOI: 10.3390/diagnostics10060343] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/20/2020] [Accepted: 05/25/2020] [Indexed: 12/11/2022] Open
Abstract
Within the last few years, there have been an increased number of clinical studies involving urinary microbiota. Low-biomass microbiome sequencing (e.g., urine, lung, placenta, blood) is easily biased by contamination or cross-contamination. So far, a few critical steps, from sampling urine to processing and analyzing, have been described (e.g., urine collection modality, sample volume size, snap freezing, negative controls usage, laboratory risks for contamination assessment, contamination of negative results reporting, exploration and discussion of the impact of contamination for the final results, etc.) We performed a literature search (Pubmed, Scopus and Embase) and reviewed the published articles related to urinary microbiome, evaluating how the aforementioned critical steps to obtain unbiased, reliable results have been taken or have been reported. We identified different urinary microbiome evaluation protocols, with non-homogenous reporting systems, which can make gathering results into consistent data for similar topics difficult and further burden the already so complex emerging field of urinary microbiome. We concluded that to ease the progress in this field, a joint approach from researchers, authors and publishers would be necessary in order to create mandatory reporting systems which would allow to recognize pitfalls and avoid compromising a promising field of research.
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Affiliation(s)
- Alin Adrian Cumpanas
- Department of Urology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (A.A.C.); (R.T.B.); (O.C.F.)
| | - Ovidiu Gabriel Bratu
- Department of Urology, Emergency Military Central Hospital, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania;
| | - Razvan Tiberiu Bardan
- Department of Urology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (A.A.C.); (R.T.B.); (O.C.F.)
| | - Ovidiu Catalin Ferician
- Department of Urology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (A.A.C.); (R.T.B.); (O.C.F.)
| | - Andrei Dragos Cumpanas
- Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
- Correspondence:
| | - Florin George Horhat
- Department of Microbiology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (F.G.H.); (M.L.)
| | - Monica Licker
- Department of Microbiology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (F.G.H.); (M.L.)
| | - Catalin Pricop
- Department of Urology, Gr.Tr.Popa University of Medicine and Pharmacy, 700115 Iasi, Romania;
| | - Octavian Marius Cretu
- Department of Surgery, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
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Demoruelle MK, Wilson TM, Deane KD. Lung inflammation in the pathogenesis of rheumatoid arthritis. Immunol Rev 2020; 294:124-132. [DOI: 10.1111/imr.12842] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 12/21/2022]
Affiliation(s)
| | - Timothy M. Wilson
- Division of Rheumatology University of Colorado Denver Aurora CO USA
| | - Kevin D. Deane
- Division of Rheumatology University of Colorado Denver Aurora CO USA
- Denver Veterans Affairs Medical Center Denver CO USA
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