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Gu Z, Sun J, Wang L. mRNA expression insights: Unraveling the relationship between COPD and lung cancer. J Gene Med 2024; 26:e3728. [PMID: 39183385 DOI: 10.1002/jgm.3728] [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: 03/18/2024] [Revised: 06/09/2024] [Accepted: 07/29/2024] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND Lung cancer is a prevalent form of cancer worldwide. A possible link between lung cancer and chronic obstructive pulmonary disease (COPD) has been suggested by recent studies. The objective of our research was to analyze the mRNA expression patterns in both situations, with a specific emphasis on their biological functions and the pathways they are linked to. METHOD Data on COPD mRNA expression was collected from the NCBI-GEO database, while information regarding lung cancer mRNA was acquired from The Cancer Genome Atlas database. To examine the association of COPD-related scores in lung cancer patients, we utilized the ssGSEA algorithm for single sample gene set enrichment analysis. The possible routes were examined through the utilization of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Risk models were developed using Cox and least absolute shrinkage and selection operator (LASSO) regression analyses. Moreover, a GSEA was performed to investigate significant pathways among various risk groups. RESULT After identifying 17 genes that were differentially expressed and linked to COPD, we found that they met the criteria of having a false discovery rate < 0.05 and an absolute log2 fold change > 0.585. By utilizing the ssGSEA algorithm, it became possible to classify individuals with lung cancer into two distinct groups based on their COPD status. Consequently, a seven-gene risk model was developed specifically for these patients. The risk score was determined by applying the given formula: risk score = AC022784.1 × 0.0423737993775888 + CRISP3 × 0.0415322046890524 + MELTF × 0.0661848418476596 + MT2P1 × 0.111843227536117 + FAM83A-AS1 × 0.045295939710361 + ZNF506 × -0.309489953363417 + ITGA6 × 0.01813978449589. The risk model associated with COPD showed a notable connection with different immune cells found in the lung cancer sample, including macrophages of M0/M1/M2 types, hematopoietic stem cells, mast cells, NK T cells and regulatory T cells. Overexpression of crucial genes was seen to enhance cell proliferation and invasive potential in the lung cancer sample. In the lung cancer sample, it was observed that an increase in ZNF506 expression enhanced both cell proliferation and invasion. CONCLUSION In conclusion, this study effectively examines the potential correlation between COPD and lung cancer. A prognostic model based on seven COPD-associated genes demonstrated robust predictive potential in the lung cancer sample. Our analysis offers comprehensive insights for lung cancer patients.
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Affiliation(s)
- Zhan Gu
- Department of Integrative Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jijia Sun
- Department of Mathematics and Physics, School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lixin Wang
- Department of Integrative Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
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Opron K, Begley LA, Erb-Downward JR, Li G, Alexis NE, Barjaktarevic I, Barr RG, Bleecker ER, Boucher R, Bowler RP, Christenson SA, Comellas AP, Criner G, Cooper CB, Couper D, Galban CJ, Han MK, Hastie A, Hatt C, Hoffman EA, Kaner RJ, Kesimer M, Krishnan JA, LaFon DC, Martinez FJ, Ortega VE, Peters SP, Paine R, Putcha N, Woodruff PG, Huffnagle GB, Kozik AJ, Curtis JL, Huang YJ. Loss of Airway Phylogenetic Diversity Is Associated with Clinical and Pathobiological Markers of Disease Development in Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2024; 210:186-200. [PMID: 38261629 PMCID: PMC11273318 DOI: 10.1164/rccm.202303-0489oc] [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: 03/15/2023] [Accepted: 01/23/2024] [Indexed: 01/25/2024] Open
Abstract
Rationale: The airway microbiome has the potential to shape chronic obstructive pulmonary disease (COPD) pathogenesis, but its relationship to outcomes in milder disease is unestablished. Objectives: To identify sputum microbiome characteristics associated with markers of COPD in participants of the Subpopulations and Intermediate Outcome Measures of COPD Study (SPIROMICS). Methods: Sputum DNA from 877 participants was analyzed using 16S ribosomal RNA gene sequencing. Relationships between baseline airway microbiota composition and clinical, radiographic, and mucoinflammatory markers, including longitudinal lung function trajectory, were examined. Measurements and Main Results: Participant data represented predominantly milder disease (Global Initiative for Chronic Obstructive Lung Disease stage 0-2 obstruction in 732 of 877 participants). Phylogenetic diversity (i.e., range of different species within a sample) correlated positively with baseline lung function, decreased with higher Global Initiative for Chronic Obstructive Lung Disease stage, and correlated negatively with symptom burden, radiographic markers of airway disease, and total mucin concentrations (P < 0.001). In covariate-adjusted regression models, organisms robustly associated with better lung function included Alloprevotella, Oribacterium, and Veillonella species. Conversely, lower lung function, greater symptoms, and radiographic measures of small airway disease were associated with enrichment in members of Streptococcus, Actinobacillus, Actinomyces, and other genera. Baseline sputum microbiota features were also associated with lung function trajectory during SPIROMICS follow-up (stable/improved, decline, or rapid decline groups). The stable/improved group (slope of FEV1 regression ⩾66th percentile) had greater bacterial diversity at baseline associated with enrichment in Prevotella, Leptotrichia, and Neisseria species. In contrast, the rapid decline group (FEV1 slope ⩽33rd percentile) had significantly lower baseline diversity associated with enrichment in Streptococcus species. Conclusions: In SPIROMICS, baseline airway microbiota features demonstrate divergent associations with better or worse COPD-related outcomes.
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Affiliation(s)
- Kristopher Opron
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Lesa A. Begley
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | | | - Gen Li
- Department of Biostatistics, School of Public Health
| | - Neil E. Alexis
- Center for Environmental Medicine, Asthma, and Lung Biology, Division of Allergy and Immunology
| | | | - R. Graham Barr
- Department of Medicine, Division of General Medicine and
- Department of Epidemiology, Columbia University Medical Center, New York, New York
| | | | - Richard Boucher
- Marsico Lung Institute/Cystic Fibrosis and Pulmonary Research Center, and
| | | | | | - Alejandro P. Comellas
- Department of Radiology
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, and
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | | | | | - David Couper
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | | - MeiLan K. Han
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
| | - Annette Hastie
- Wake Forest School of Medicine, Winston-Salem, North Carolina
| | | | - Eric A. Hoffman
- Department of Radiology
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, and
- Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa
| | - Robert J. Kaner
- Weill Cornell, Division of Pulmonary and Critical Care Medicine, New York, New York
| | - Mehmet Kesimer
- Marsico Lung Institute/Cystic Fibrosis and Pulmonary Research Center, and
| | - Jerry A. Krishnan
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Breathe Chicago Center, University of Illinois Chicago, Chicago, Illinois
| | - David C. LaFon
- Division of Pulmonary, Allergy and Critical Care, University of Alabama at Birmingham, Alabama
| | - Fernando J. Martinez
- Weill Cornell, Division of Pulmonary and Critical Care Medicine, New York, New York
| | | | | | - Robert Paine
- Division of Respiratory, Critical Care, Occupational Pulmonary Medicine, University of Utah, Salt Lake City, Utah
| | - Nirupama Putcha
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Johns Hopkins University, Baltimore, Maryland; and
| | - Prescott G. Woodruff
- Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Gary B. Huffnagle
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Department of Molecular, Cellular and Developmental Biology and
| | - Ariangela J. Kozik
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Department of Molecular, Cellular and Developmental Biology and
| | - Jeffrey L. Curtis
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Medical Service, Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, Michigan
| | - Yvonne J. Huang
- Department of Medicine, Division of Pulmonary and Critical Care Medicine
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan
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Laiman V, Chuang HC, Lo YC, Yuan TH, Chen YY, Heriyanto DS, Yuliani FS, Chung KF, Chang JH. Cigarette smoke-induced dysbiosis: comparative analysis of lung and intestinal microbiomes in COPD mice and patients. Respir Res 2024; 25:204. [PMID: 38730440 PMCID: PMC11088139 DOI: 10.1186/s12931-024-02836-9] [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: 01/03/2024] [Accepted: 05/04/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND The impact of cigarette smoke (CS) on lung diseases and the role of microbiome dysbiosis in chronic obstructive pulmonary disease (COPD) have been previously reported; however, the relationships remain unclear. METHODS Our research examined the effects of 20-week cigarette smoke (CS) exposure on the lung and intestinal microbiomes in C57BL/6JNarl mice, alongside a comparison with COPD patients' intestinal microbiome data from a public dataset. RESULTS The study found that CS exposure significantly decreased forced vital capacity (FVC), thickened airway walls, and induced emphysema. Increased lung damage was observed along with higher lung keratinocyte chemoattractant (KC) levels by CS exposure. Lung microbiome analysis revealed a rise in Actinobacteriota, while intestinal microbiome showed significant diversity changes, indicating dysbiosis. Principal coordinate analysis highlighted distinct intestinal microbiome compositions between control and CS-exposed groups. In the intestinal microbiome, notable decreases in Patescibacteria, Campilobacterota, Defferibacterota, Actinobacteriota, and Desulfobacterota were observed. We also identified correlations between lung function and dysbiosis in both lung and intestinal microbiomes. Lung interleukins, interferon-ɣ, KC, and 8-isoprostane levels were linked to lung microbiome dysbiosis. Notably, dysbiosis patterns in CS-exposed mice were similar to those in COPD patients, particularly of Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage 4 patients. This suggests a systemic impact of CS exposure. CONCLUSION In summary, CS exposure induces significant dysbiosis in lung and intestinal microbiomes, correlating with lung function decline and injury. These results align with changes in COPD patients, underscoring the important role of microbiome in smoke-related lung diseases.
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Affiliation(s)
- Vincent Laiman
- Department of Radiology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada - Dr. Sardjito Hospital, Yogyakarta, Indonesia
- Collaboration Research Center for Precision Oncology based Omics- PKR Promics, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Hsiao-Chi Chuang
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
- Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Yu-Chun Lo
- The Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Tzu-Hsuen Yuan
- Department of Health and Welfare, College of City Management, University of Taipei, Taipei, Taiwan
| | - You-Yin Chen
- The Ph.D. Program for Neural Regenerative Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Industrial Ph.D. Program of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Biomedical Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Didik Setyo Heriyanto
- Department of Anatomical Pathology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada - Dr. Sardjito Hospital, Yogyakarta, Indonesia
| | - Fara Silvia Yuliani
- Department of Pharmacology and Therapy, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Jer-Hwa Chang
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, 250 Wuxing Street, Taipei, 11031, Taiwan.
- Division of Pulmonary Medicine, Departments of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
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Varzakas T, Antoniadou M. A Holistic Approach for Ethics and Sustainability in the Food Chain: The Gateway to Oral and Systemic Health. Foods 2024; 13:1224. [PMID: 38672896 PMCID: PMC11049237 DOI: 10.3390/foods13081224] [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: 03/28/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Food production is a complex matter, affecting people's lives, organizations' profits, and the well-being of the whole planet, and has multifaceted ethical considerations surrounding its production, distribution, and consumption. This paper addresses the pressing need to confront ethical challenges within the food system, encompassing issues such as environmental sustainability, food security, and individual food choices for better oral and systemic health of all individuals around the globe. From agricultural practices to global trade and food waste, ethical implications are addressed across various domains, highlighting the interconnectedness of ethical decision-making in the food industry. Central themes explored include the ethical dimensions of food production methods, the impact of global trade on food ethics, and the role of individuals in making ethically informed food choices. Additionally, this paper considers the spiritual and physical significance of food, particularly through the lens of oral health as a gateway to holistic well-being. Recognizing the complexity of the food and mouth ecosystem, this paper calls for serious interventions in legislation and economics to promote ethical protocols and techniques for sustainability reasons. It emphasizes the importance of ethical considerations in food safety management systems, regulatory frameworks, and quality standards. Moreover, this paper underlines the need for a comprehensive approach to address ethical dilemmas and moral values inherent in the food industry and oral health policies, adopting the precautionary principle and ethical decision-making frameworks. This article finally aims to serve as a call to action for stakeholders across the food industry and the healthcare sector, to prioritize ethical practices, promote transparency, rearrange economic parameters, and work towards a more sustainable and equitable food system for inner and outer oral and systemic health and human sustainability for all.
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Affiliation(s)
- Theodoros Varzakas
- Department Food Science and Technology, University of the Peloponnese, 24100 Kalamata, Greece
| | - Maria Antoniadou
- Department of Dentistry, School of Health Sciences, National and Kapodistrian University of Athens, 11527 Athens, Greece
- Certified Systemic Analyst Program in Systemic Management (CSAP), University of Piraeus, 18534 Piraeus, Greece
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Hibbert T, Krpetic Z, Latimer J, Leighton H, McHugh R, Pottenger S, Wragg C, James CE. Antimicrobials: An update on new strategies to diversify treatment for bacterial infections. Adv Microb Physiol 2024; 84:135-241. [PMID: 38821632 DOI: 10.1016/bs.ampbs.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
Ninety-five years after Fleming's discovery of penicillin, a bounty of antibiotic compounds have been discovered, modified, or synthesised. Diversification of target sites, improved stability and altered activity spectra have enabled continued antibiotic efficacy, but overwhelming reliance and misuse has fuelled the global spread of antimicrobial resistance (AMR). An estimated 1.27 million deaths were attributable to antibiotic resistant bacteria in 2019, representing a major threat to modern medicine. Although antibiotics remain at the heart of strategies for treatment and control of bacterial diseases, the threat of AMR has reached catastrophic proportions urgently calling for fresh innovation. The last decade has been peppered with ground-breaking developments in genome sequencing, high throughput screening technologies and machine learning. These advances have opened new doors for bioprospecting for novel antimicrobials. They have also enabled more thorough exploration of complex and polymicrobial infections and interactions with the healthy microbiome. Using models of infection that more closely resemble the infection state in vivo, we are now beginning to measure the impacts of antimicrobial therapy on host/microbiota/pathogen interactions. However new approaches are needed for developing and standardising appropriate methods to measure efficacy of novel antimicrobial combinations in these contexts. A battery of promising new antimicrobials is now in various stages of development including co-administered inhibitors, phages, nanoparticles, immunotherapy, anti-biofilm and anti-virulence agents. These novel therapeutics need multidisciplinary collaboration and new ways of thinking to bring them into large scale clinical use.
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Affiliation(s)
- Tegan Hibbert
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK
| | - Zeljka Krpetic
- School of Science, Engineering, and Environment, University of Salford, Salford, UK
| | - Joe Latimer
- School of Science, Engineering, and Environment, University of Salford, Salford, UK
| | - Hollie Leighton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK
| | - Rebecca McHugh
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Sian Pottenger
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK
| | - Charlotte Wragg
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK
| | - Chloë E James
- School of Science, Engineering, and Environment, University of Salford, Salford, UK.
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van der Bie S, Haaksma ME, Vermin B, van Assema H, van Gorp ECM, Langerak T, Endeman H, Snijders D, van den Akker JPC, van Houten MA, van Lelyveld SFL, Goeijenbier M. A Systematic Review of the Pulmonary Microbiome in Patients with Acute Exacerbation COPD Requiring ICU Admission. J Clin Med 2024; 13:472. [PMID: 38256606 PMCID: PMC10816170 DOI: 10.3390/jcm13020472] [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: 11/30/2023] [Revised: 01/03/2024] [Accepted: 01/13/2024] [Indexed: 01/24/2024] Open
Abstract
Background: Chronic obstructive pulmonary disease (COPD) is a major health concern. Acute exacerbations (AECOPD) may require intensive care unit (ICU) admission and mechanical ventilation. Acute infections and chronic colonization of the respiratory system are known to precipitate AECOPD. Detailed knowledge of the respiratory microbiome could lead to effective treatment and prevention of exacerbations. Objective: The aim of this review is to summarize the available evidence on the respiratory microbiome of patients with a severe AECOPD requiring mechanical ventilation and intensive care admission. Methods: A systematic literature search was conducted to identify the published papers until January 2023. The collected data were then subjected to qualitative analysis. After the first analysis, a secondary focused review of the most recent publications studying the relationship between microbiome and mortality in AECOPD was performed. Results: Out of 120 screened articles six articles were included in this review. Potentially pathogenic microorganisms (PPMs) were identified in 30% to 72% of the patients with community-acquired bacteria, gram-negative enteric bacilli, Stenotrophomonas and Pseudomonas being the most frequently isolated. During hospitalization, 21% of patients experienced colonization by PPMs. Adequate antimicrobial therapy resulted in the eradication of 77% of the identified PPMs. However, 24% of the bacteria displayed multi-drug resistance leading to prolonged or failure of eradication. Conclusion: PPMs are prevalent in a significant proportion of patients experiencing an AECOPD. The most identified PPMs include community-acquired pathogens and gram-negative enteric bacilli. Notably, no differences in mortality or duration of ventilation were observed between patients with and without isolated PPMs. However, the included studies did not investigate the virome of the patients, which may influence the microbiome and the outcome of infection. Therefore, further research is essential to comprehensively investigate the complete microbial and viral composition of the lower respiratory system in COPD patients admitted to the ICU.
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Affiliation(s)
- Sjoerd van der Bie
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
| | - Mark E. Haaksma
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
| | - Ben Vermin
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
| | - Hidde van Assema
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
| | - Eric C. M. van Gorp
- Department of Viroscience, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.C.M.v.G.); (T.L.)
| | - Thomas Langerak
- Department of Viroscience, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.C.M.v.G.); (T.L.)
| | - Henrik Endeman
- Department of Intensive Care Medicine, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (H.E.); (J.P.C.v.d.A.)
| | - Dominic Snijders
- Department of Pulmonology, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands;
| | | | - Marlies A. van Houten
- Department of Pediatric Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands;
| | | | - Marco Goeijenbier
- Department of Intensive Care Medicine, Spaarne Gasthuis Hoofddorp, 2134 TM Hoofddorp, The Netherlands; (S.v.d.B.); (M.E.H.); (B.V.); (H.v.A.)
- Department of Viroscience, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (E.C.M.v.G.); (T.L.)
- Department of Intensive Care Medicine, Erasmus MC, 3000 CA Rotterdam, The Netherlands; (H.E.); (J.P.C.v.d.A.)
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Davies R, Minhas S, Jayasena CN. Next-Generation Sequencing to Elucidate the Semen Microbiome in Male Reproductive Disorders. MEDICINA (KAUNAS, LITHUANIA) 2023; 60:25. [PMID: 38256286 PMCID: PMC10819355 DOI: 10.3390/medicina60010025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024]
Abstract
Mean sperm counts are declining at an accelerated rate and infertility is increasingly becoming a public health concern. It is now understood that human semen, previously considered to be sterile, harbours its own specific microbiome. Via activated leucocytes and the generation of reactive oxygen species, bacteria have the capability of evoking an immune response which may lead to sperm damage. Men with infertility have higher rates of both reactive oxygen species and sperm DNA damage. Due to the lack of sensitivity of routine culture and PCR-based methods, next-generation sequencing technology is being employed to characterise the seminal microbiome. There is a mounting body of studies that share a number of similarities but also a great range of conflicting findings. A lack of stringent decontamination procedures, small sample sizes and heterogeneity in other aspects of methodology makes it difficult to draw firm conclusions from these studies. However, various themes have emerged and evidence of highly conserved clusters of common bacteria can be seen. Depletion or over-representation of specific bacteria may be associated with aberrations in traditional and functional seminal parameters. Currently, the evidence is too limited to inform clinical practice and larger studies are needed.
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Affiliation(s)
- Rhianna Davies
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0HS, UK;
| | - Suks Minhas
- Department of Urology, Charing Cross Hospital, Imperial College NHS Trust, London W6 8RF, UK;
| | - Channa N. Jayasena
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0HS, UK;
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Lin P, Liu A, Tsuchiya Y, Noritake K, Ohsugi Y, Toyoshima K, Tsukahara Y, Shiba T, Nitta H, Aoki A, Iwata T, Katagiri S. Association between periodontal disease and chronic obstructive pulmonary disease. JAPANESE DENTAL SCIENCE REVIEW 2023; 59:389-402. [PMID: 38022389 PMCID: PMC10652094 DOI: 10.1016/j.jdsr.2023.10.004] [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: 08/30/2023] [Revised: 10/15/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) and periodontal disease are chronic inflammatory conditions that significantly affect an individual's overall health and well-being. Generally, the prevalence of periodontitis is higher in patients with COPD than those without COPD, which may partly be attributed to common risk factors in COPD, such as smoking, respiratory infections, and inflammation. In particular, periodontitis may exacerbate the progression of COPD and further deteriorate the respiratory system by promoting inflammatory responses and bacterial infections. Immunocytes, including neutrophils, and microorganisms such as Fusobacterium nucleatum originating from oral biofilms are believed to be crucial factors influencing to COPD. Furthermore, the potential benefits of treating periodontal disease in COPD outcomes have been investigated. Although the relationship between COPD and periodontal disease has been preliminarily studied, there is currently a lack of large-scale clinical studies to validate this association. In addition to clinical examinations, investigating biomarkers and microbiology may contribute to explore the underlying mechanisms involved in the management of these conditions. This review aims to contribute to a better understanding of the clinical and basic research aspects of COPD and periodontitis, allowing for potential therapeutic approaches and interdisciplinary management strategies.
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Affiliation(s)
- Peiya Lin
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Anhao Liu
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yosuke Tsuchiya
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kanako Noritake
- Oral Diagnosis and General Dentistry, Division of Clinical Dentistry, Tokyo Medical and Dental University Hospital, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yujin Ohsugi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Keita Toyoshima
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Yuta Tsukahara
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takahiko Shiba
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Hiroshi Nitta
- Department of General Dentistry, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Akira Aoki
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Sayaka Katagiri
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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Kim HY, Kim TH, Shin JH, Cho K, Ha HK, Lee A, Kim YJ. Navigating the microbial community in the trachea-oropharynx of breast cancer patients with or without neoadjuvant chemotherapy (NAC) via endotracheal tube: has NAC caused any change? PeerJ 2023; 11:e16366. [PMID: 38025669 PMCID: PMC10676715 DOI: 10.7717/peerj.16366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023] Open
Abstract
Background We compare the diversity and niche specificity of the microbiome in the trachea-oropharynx microbiome of malignant breast neoplasm with or without neoadjuvant chemotherapy (NAC) via NGS analysis. Methods We prospectively collected a total of 40 endotracheal tubes intubated from subjects, of whom 20 with NAC treated breast cancer (NAC group) and 20 with breast cancer without NAC (Non-NAC group). We generated 16S rRNA-based microbial profiles in IlluminaTM platform and alpha diversity indices were compared between groups. For the comparison of taxa abundance, linear discriminant analysis effect size method with Kruskal-Wallis test was used. The distribution of variables between the two groups was compared using the Mann-Whitney test. For beta diversity analysis, PERMANOVA was used. Results Among the diversity indices, the NAC group showed significantly lower Chao1, Inverse Simpson, and Shannon indices than the Non-NAC group. The three most frequent taxa of all two groups were Streptococcus (20.4%), followed by Veillonella (11.9%), and Prevorella (10.4%). This order was the same in NAC and non-NAC groups. Conclusion Here, we provide the first comparison data of the respiratory tract microbiome of breast cancer patients with or without NAC via NGS analysis. This study ultimately seeks to contribute to future studies on the lower respiratory tract in cancer patients with cytotoxic chemotherapy by establishing reliable control data.
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Affiliation(s)
- Hee Yeon Kim
- Department of Surgery, Busan Paik Hospital, Inje University, Busan, South Korea
| | - Tae Hyun Kim
- Department of Surgery, Busan Paik Hospital, Inje University, Busan, South Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine and Paik Institute for Clinical Research, Inje University, Busan, South Korea
| | - Kwangrae Cho
- Department of Anesthesiology and Pain Medicine, Busan Paik Hospital, Inje University, Busan, South Korea
| | - Heon-Kyun Ha
- Department of Surgery, Chung-Ang University Gwangmyeong Hospital, Chung-Ang University College of Medicine, Chung-Ang University, Gyeonggi-do, South Korea
| | - Anbok Lee
- Department of Surgery, Chung-Ang University Gwangmyeong Hospital, Chung-Ang University College of Medicine, Chung-Ang University, Gyeonggi-do, South Korea
| | - Young Jin Kim
- Department of Laboratory Medicine, Kyung Hee University College of Medicine, Kyung Hee University Medical Center, Seoul, South Korea
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10
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Kaltsas A, Zachariou A, Markou E, Dimitriadis F, Sofikitis N, Pournaras S. Microbial Dysbiosis and Male Infertility: Understanding the Impact and Exploring Therapeutic Interventions. J Pers Med 2023; 13:1491. [PMID: 37888102 PMCID: PMC10608462 DOI: 10.3390/jpm13101491] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
The human microbiota in the genital tract is pivotal for maintaining fertility, but its disruption can lead to male infertility. This study examines the relationship between microbial dysbiosis and male infertility, underscoring the promise of precision medicine in this field. Through a comprehensive review, this research indicates microbial signatures associated with male infertility, such as altered bacterial diversity, the dominance of pathogenic species, and imbalances in the genital microbiome. Key mechanisms linking microbial dysbiosis to infertility include inflammation, oxidative stress, and sperm structural deterioration. Emerging strategies like targeted antimicrobial therapies, probiotics, prebiotics, and fecal microbiota transplantation have shown potential in adjusting the genital microbiota to enhance male fertility. Notably, the application of precision medicine, which customizes treatments based on individual microbial profiles and specific causes of infertility, emerges as a promising approach to enhance treatment outcomes. Ultimately, microbial dysbiosis is intricately linked to male infertility, and embracing personalized treatment strategies rooted in precision medicine principles could be the way forward in addressing infertility associated with microbial factors.
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Affiliation(s)
- Aris Kaltsas
- Department of Urology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.K.); (A.Z.); (N.S.)
| | - Athanasios Zachariou
- Department of Urology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.K.); (A.Z.); (N.S.)
| | - Eleftheria Markou
- Department of Microbiology, University Hospital of Ioannina, 45500 Ioannina, Greece;
| | - Fotios Dimitriadis
- Department of Urology, Faculty of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Nikolaos Sofikitis
- Department of Urology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece; (A.K.); (A.Z.); (N.S.)
| | - Spyridon Pournaras
- Clinical Microbiology Laboratory, Attikon General University Hospital of Athens, 12462 Athens, Greece
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11
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Maetani T, Tanabe N, Sato A, Shiraishi Y, Sakamoto R, Ogawa E, Sakai H, Matsumoto H, Sato S, Date H, Hirai T, Muro S. Association between blood eosinophil count and small airway eosinophils in smokers with and without COPD. ERJ Open Res 2023; 9:00235-2023. [PMID: 37868149 PMCID: PMC10588801 DOI: 10.1183/23120541.00235-2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 06/27/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction Airway eosinophilic inflammation is a pathological feature in a subgroup of patients with COPD and in some smokers with a high COPD risk. Although blood eosinophil count is used to define eosinophilic COPD, the association between blood eosinophil count and airway eosinophilic inflammation remains controversial. This cross-sectional study tested this association in smokers with and without COPD while considering potential confounders, such as smoking status and comorbidities. Methods Lung specimens were obtained from smokers with and without COPD and non-COPD never-smokers undergoing lung lobectomy. Those with any asthma history were excluded. The infiltration of eosinophils into the small airway wall was quantified on histological sections stained with major basic protein (MBP). Results The number of airway MBP-positive cells was greater in smokers (n=60) than in never-smokers (n=14). Smokers with and without COPD (n=30 each) exhibited significant associations between blood eosinophil count and airway MBP-positive cells (ρ=0.45 and 0.71). When smokers were divided into the high and low airway MBP groups based on their median value, blood eosinophil count was higher in the high-MBP group, with no difference in age, smoking status, comorbidities, emphysema or coronary artery calcification on computed tomography, and inhaled corticosteroid (ICS) use. The association between greater blood eosinophil count and the high-MBP group was confirmed in multivariable models adjusted for smoking status, airflow limitation and ICS use. Conclusion The blood eosinophil count may reflect eosinophilic inflammation in the small airways in smokers with and without COPD.
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Affiliation(s)
- Tomoki Maetani
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Naoya Tanabe
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsuyasu Sato
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Shiraishi
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryo Sakamoto
- Department of Diagnostic Imaging and Nuclear Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Emiko Ogawa
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Division of Respiratory Medicine, Department of Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Hiroaki Sakai
- Department of Thoracic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Thoracic Surgery, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Hisako Matsumoto
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Respiratory Medicine and Allergology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Susumu Sato
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Respiratory Care and Sleep Control Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Date
- Department of Thoracic Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toyohiro Hirai
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shigeo Muro
- Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Respiratory Medicine, Nara Medical University Graduate School of Medicine, Nara, Japan
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12
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Karakasidis E, Kotsiou OS, Gourgoulianis KI. Lung and Gut Microbiome in COPD. J Pers Med 2023; 13:jpm13050804. [PMID: 37240974 DOI: 10.3390/jpm13050804] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/06/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is one of the leading causes of death worldwide. The association between lung and gut microbiomes in the pathogenesis of COPD has been recently uncovered. The goal of this study was to discuss the role of the lung and gut microbiomes in COPD pathophysiology. A systematic search of the PubMed database for relevant articles submitted up to June 2022 was performed. We examined the association between the lung and gut microbiome dysbiosis, reflected in bronchoalveolar lavage (BAL), lung tissue, sputum, and feces samples, and the pathogenesis and progression of COPD. It is evident that the lung and gut microbiomes affect each other and both play a vital role in the pathogenesis of COPD. However, more research needs to be carried out to find the exact associations between microbiome diversity and COPD pathophysiology and exacerbation genesis. Another field that research should focus on is the impact of treatment interventions targeting the human microbiome in preventing COPD genesis and progression.
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Affiliation(s)
- Efstathios Karakasidis
- Department of Respiratory Medicine, School of Health Science, University of Thessaly, Biopolis, 41110 Larissa, Greece
| | - Ourania S Kotsiou
- Department of Respiratory Medicine, School of Health Science, University of Thessaly, Biopolis, 41110 Larissa, Greece
- Department of Human Pathophysiology, Faculty of Nursing, School of Health Science, University of Thessaly, Gaiopolis, 41110 Larissa, Greece
| | - Konstantinos I Gourgoulianis
- Department of Respiratory Medicine, School of Health Science, University of Thessaly, Biopolis, 41110 Larissa, Greece
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13
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Chen D, Zeng Q, Liu L, Zhou Z, Qi W, Yu S, Zhao L. Global Research Trends on the Link Between the Microbiome and COPD: A Bibliometric Analysis. Int J Chron Obstruct Pulmon Dis 2023; 18:765-783. [PMID: 37180751 PMCID: PMC10167978 DOI: 10.2147/copd.s405310] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 04/30/2023] [Indexed: 05/16/2023] Open
Abstract
Background The pathogenesis of chronic obstructive pulmonary disease (COPD) has been studied in relation to the microbiome, providing space for more targeted interventions and new treatments. Numerous papers on the COPD microbiome have been reported in the last 10 years, yet few publications have used bibliometric methods to evaluate this area. Methods We searched the Web of Science Core Collection for all original research articles in the field of COPD microbiome from January 2011 to August 2022 and used CiteSpace for visual analysis. Results A total of 505 relevant publications were obtained, and the number of global publications in this field is steadily increasing every year, with China and the USA occupying the first two spots in international publications. Imperial College London and the University of Leicester produced the most publications. Brightling C from the UK was the most prolific writer, while Huang Y and Sze M from the USA were first and second among the authors cited. The American Journal of Respiratory and Critical Care Medicine had the highest frequency of citations. The top 10 institutions, cited authors and journals are mostly from the UK and the US. In the ranking of citations, the first article was a paper published by Sze M on changes in the lung tissue's microbiota in COPD patients. The keywords "exacerbation", "gut microbiota", "lung microbiome", "airway microbiome", "bacterial colonization", and "inflammation" were identified as cutting-edge research projects for 2011-2022. Conclusion Based on the visualization results, in the future, we can use the gut-lung axis as the starting point to explore the immunoinflammatory mechanism of COPD, and study how to predict the effects of different treatments of COPD by identifying the microbiota, and how to achieve the optimal enrichment of beneficial bacteria and the optimal consumption of harmful bacteria to improve COPD.
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Affiliation(s)
- Daohong Chen
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Qian Zeng
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Lu Liu
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Ziyang Zhou
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Wenchuan Qi
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Shuguang Yu
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
| | - Ling Zhao
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, People’s Republic of China
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14
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Mazumder MHH, Gandhi J, Majumder N, Wang L, Cumming RI, Stradtman S, Velayutham M, Hathaway QA, Shannahan J, Hu G, Nurkiewicz TR, Tighe RM, Kelley EE, Hussain S. Lung-gut axis of microbiome alterations following co-exposure to ultrafine carbon black and ozone. Part Fibre Toxicol 2023; 20:15. [PMID: 37085867 PMCID: PMC10122302 DOI: 10.1186/s12989-023-00528-8] [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: 01/26/2023] [Accepted: 04/17/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Microbial dysbiosis is a potential mediator of air pollution-induced adverse outcomes. However, a systemic comparison of the lung and gut microbiome alterations and lung-gut axis following air pollution exposure is scant. In this study, we exposed male C57BL/6J mice to inhaled air, CB (10 mg/m3), O3 (2 ppm) or CB + O3 mixture for 3 h/day for either one day or four consecutive days and were euthanized 24 h post last exposure. The lung and gut microbiome were quantified by 16 s sequencing. RESULTS Multiple CB + O3 exposures induced an increase in the lung inflammatory cells (neutrophils, eosinophils and B lymphocytes), reduced absolute bacterial load in the lungs and increased load in the gut. CB + O3 exposure was more potent as it decreased lung microbiome alpha diversity just after a single exposure. CB + O3 co-exposure uniquely increased Clostridiaceae and Prevotellaceae in the lungs. Serum short chain fatty acids (SCFA) (acetate and propionate) were increased significantly only after CB + O3 co-exposure. A significant increase in SCFA producing bacterial families (Ruminococcaceae, Lachnospiraceae, and Eubacterium) were also observed in the gut after multiple exposures. Co-exposure induced significant alterations in the gut derived metabolite receptors/mediator (Gcg, Glp-1r, Cck) mRNA expression. Oxidative stress related mRNA expression in lungs, and oxidant levels in the BALF, serum and gut significantly increased after CB + O3 exposures. CONCLUSION Our study confirms distinct gut and lung microbiome alterations after CB + O3 inhalation co-exposure and indicate a potential homeostatic shift in the gut microbiome to counter deleterious impacts of environmental exposures on metabolic system.
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Affiliation(s)
- Md Habibul Hasan Mazumder
- Department of Physiology, Pharmacology, and Toxicology, Center for Inhalation Toxicology (iTOX), School of Medicine, West Virginia University, Morgantown, WV, 26506, USA
- Center for Inhalation Toxicology (iTOX), School of Medicine, West Virginia University, Morgantown, WV, 26506, USA
| | - Jasleen Gandhi
- Department of Microbiology, School of Medicine, West Virginia University, Morgantown, WV, 26506, USA
| | - Nairrita Majumder
- Department of Physiology, Pharmacology, and Toxicology, Center for Inhalation Toxicology (iTOX), School of Medicine, West Virginia University, Morgantown, WV, 26506, USA
- Center for Inhalation Toxicology (iTOX), School of Medicine, West Virginia University, Morgantown, WV, 26506, USA
| | - Lei Wang
- Department of Microbiology, School of Medicine, West Virginia University, Morgantown, WV, 26506, USA
| | - Robert Ian Cumming
- Department of Medicine, Duke University Medical Center, Durham, NC, 2927, USA
| | - Sydney Stradtman
- School of Health Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Murugesan Velayutham
- Department of Physiology, Pharmacology, and Toxicology, Center for Inhalation Toxicology (iTOX), School of Medicine, West Virginia University, Morgantown, WV, 26506, USA
- Center for Inhalation Toxicology (iTOX), School of Medicine, West Virginia University, Morgantown, WV, 26506, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, Morgantown, WV, USA
| | - Quincy A Hathaway
- Heart and Vascular Institute, School of Medicine, West Virginia University, Morgantown, WV, USA
| | - Jonathan Shannahan
- School of Health Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Gangqing Hu
- Department of Microbiology, School of Medicine, West Virginia University, Morgantown, WV, 26506, USA
| | - Timothy R Nurkiewicz
- Department of Physiology, Pharmacology, and Toxicology, Center for Inhalation Toxicology (iTOX), School of Medicine, West Virginia University, Morgantown, WV, 26506, USA
- Center for Inhalation Toxicology (iTOX), School of Medicine, West Virginia University, Morgantown, WV, 26506, USA
| | - Robert M Tighe
- Department of Medicine, Duke University Medical Center, Durham, NC, 2927, USA
| | - Eric E Kelley
- Department of Physiology, Pharmacology, and Toxicology, Center for Inhalation Toxicology (iTOX), School of Medicine, West Virginia University, Morgantown, WV, 26506, USA
- Center for Inhalation Toxicology (iTOX), School of Medicine, West Virginia University, Morgantown, WV, 26506, USA
| | - Salik Hussain
- Department of Physiology, Pharmacology, and Toxicology, Center for Inhalation Toxicology (iTOX), School of Medicine, West Virginia University, Morgantown, WV, 26506, USA.
- Center for Inhalation Toxicology (iTOX), School of Medicine, West Virginia University, Morgantown, WV, 26506, USA.
- Department of Microbiology, School of Medicine, West Virginia University, Morgantown, WV, 26506, USA.
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15
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Mannion JM, McLoughlin RM, Lalor SJ. The Airway Microbiome-IL-17 Axis: a Critical Regulator of Chronic Inflammatory Disease. Clin Rev Allergy Immunol 2023; 64:161-178. [PMID: 35275333 PMCID: PMC10017631 DOI: 10.1007/s12016-022-08928-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2022] [Indexed: 02/07/2023]
Abstract
The respiratory tract is home to a diverse microbial community whose influence on local and systemic immune responses is only beginning to be appreciated. Increasing reports have linked changes in this microbiome to a range of pulmonary and extrapulmonary disorders, including asthma, chronic obstructive pulmonary disease and rheumatoid arthritis. Central to many of these findings is the role of IL-17-type immunity as an important driver of inflammation. Despite the crucial role played by IL-17-mediated immune responses in protection against infection, overt Th17 cell responses have been implicated in the pathogenesis of several chronic inflammatory diseases. However, our knowledge of the influence of bacteria that commonly colonise the respiratory tract on IL-17-driven inflammatory responses remains sparse. In this article, we review the current knowledge on the role of specific members of the airway microbiota in the modulation of IL-17-type immunity and discuss how this line of research may support the testing of susceptible individuals and targeting of inflammation at its earliest stages in the hope of preventing the development of chronic disease.
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Affiliation(s)
- Jenny M Mannion
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Rachel M McLoughlin
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Stephen J Lalor
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
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16
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The Role of the Oral Microbiome in the Development of Diseases. Int J Mol Sci 2023; 24:ijms24065231. [PMID: 36982305 PMCID: PMC10048844 DOI: 10.3390/ijms24065231] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Periodontal disease (PD) is a complex and infectious illness that begins with a disruption of bacterial homeostasis. This disease induces a host inflammatory response, leading to damage of the soft and connective tooth-supporting tissues. Moreover, in advanced cases, it can contribute to tooth loss. The aetiological factors of PDs have been widely researched, but the pathogenesis of PD has still not been totally clarified. There are a number of factors that have an effect on the aetiology and pathogenesis of PD. It is purported that microbiological, genetic susceptibility and lifestyle can determine the development and severity of the disease. The human body’s defence response to the accumulation of plaque and its enzymes is known to be a major factor for PD. The oral cavity is colonised by a characteristic and complex microbiota that grows as diverse biofilms on all mucosal and dental surfaces. The aim of this review was to provide the latest updates in the literature regarding still-existing problems with PD and to highlight the role of the oral microbiome in periodontal health and disease. Better awareness and knowledge of the causes of dysbiosis, environmental risk factors and periodontal therapy can reduce the growing worldwide prevalence of PDs. The promotion of good oral hygiene, limiting smoking, alcohol consumption and exposure to stress and comprehensive treatment to decrease the pathogenicity of oral biofilm can help reduce PD as well as other diseases. Evidence linking disorders of the oral microbiome to various systemic diseases has increased the understanding of the importance of the oral microbiome in regulating many processes in the human body and, thus, its impact on the development of many diseases.
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17
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Alsayed AR, Abed A, Jarrar YB, Alshammari F, Alshammari B, Basheti IA, Zihlif M. Alteration of the Respiratory Microbiome in Hospitalized Patients with Asthma-COPD Overlap during and after an Exacerbation. J Clin Med 2023; 12:jcm12062118. [PMID: 36983122 PMCID: PMC10051973 DOI: 10.3390/jcm12062118] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/02/2023] [Accepted: 03/05/2023] [Indexed: 03/30/2023] Open
Abstract
The immediate aim of this study was to comparatively examine the bacterial respiratory microbiome of patients in a stable state and during an exacerbation of asthma-COPD (chronic obstructive pulmonary disease) overlap (ACO). This prospective observational study took place in Jordan between 1 September 2021 and 30 April 2022. Sputum samples from patients with recognized ACO were acquired within 48 h of the exacerbation onset and again at 3 weeks following the exacerbation. The next-generation sequencing Illumina MiSeq was employed and uncovered significantly high bacterial diversity in the sputa. The results showed a significant decrease in the taxonomic richness in the sputum samples collected during the exacerbation episodes compared with those collected from patients in a stable state (p = 0.008), with an increase in the taxonomic evenness (p < 0.005). This change in the composition of the airway bacterial community suggests that the replacement of a significant portion of the airway microbiome with certain microorganisms may play a role in the decrease in microbial diversity observed during an ACO exacerbation. Greater knowledge of this link could allow for a more focused administration of antibiotics, especially during exacerbations, improving clinical efficacy and patient outcomes.
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Affiliation(s)
- Ahmad R Alsayed
- Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman 11931-166, Jordan
| | - Anas Abed
- Pharmacological and Diagnostic Research Centre, Faculty of Pharmacy, Al-Ahliyya Amman University, Amman 11931-166, Jordan
| | - Yazun Bashir Jarrar
- Department of Basic Medical Sciences, Faculty of Medicine, Al-Balqa Applied University, Al-Salt 19117, Jordan
| | - Farhan Alshammari
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 2440, Saudi Arabia
| | - Bushra Alshammari
- Department of Medical Surgical Nursing, College of Nursing, University of Hail, Hail 2440, Saudi Arabia
| | - Iman A Basheti
- Faculty of Pharmacy, Sydney University, Sydney, NSW 2006, Australia
| | - Malek Zihlif
- Department of Pharmacology, School of Medicine, The University of Jordan, Amman 11942, Jordan
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18
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Plascencia-Cruz M, Plascencia-Hernández A, De Armas-Rodríguez Y, Cervantes-Guevara G, Cervantes-Cardona GA, Ramírez-Ochoa S, González-Ojeda A, Fuentes-Orozco C, Hernández-Mora FJ, González-Valencia CM, Pérez de Acha-Chávez A, Cervantes-Pérez E. Pneumocystis jirovecii Colonization in Mexican Patients with Chronic Obstructive Pulmonary Disease. Trop Med Infect Dis 2023; 8:tropicalmed8030137. [PMID: 36977138 PMCID: PMC10055963 DOI: 10.3390/tropicalmed8030137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 03/02/2023] Open
Abstract
The prevalence of colonization by Pneumocystis jirovecii (P. jirovecii) has not been studied in Mexico. We aimed to determine the prevalence of colonization by P. jirovecii using molecular detection in a population of Mexican patients with chronic obstructive pulmonary disease (COPD) and describe their clinical and sociodemographic profiles. We enrolled patients discharged from our hospital diagnosed with COPD and without pneumonia (n = 15). The primary outcome of this study was P. jirovecii colonization at the time of discharge, as detected by nested polymerase chain reaction (PCR) of oropharyngeal wash samples. The calculated prevalence of colonization for our study group was 26.66%. There were no statistically significant differences between COPD patients with and without colonization in our groups. Colonization of P. jirovecii in patients with COPD is frequent in the Mexican population; the clinical significance, if any, remains to be determined. Oropharyngeal wash and nested PCR are excellent cost-effective options to simplify sample collection and detection in developing countries and can be used for further studies.
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Affiliation(s)
- Marcela Plascencia-Cruz
- Department of Internal Medicine, Hospital Civil de Guadalajara “Fray Antonio Alcalde”, Guadalajara 44280, Jalisco, Mexico
- Health Sciences University Center, Universidad de Guadalajara, Guadalajara 44100, Jalisco, Mexico
| | - Arturo Plascencia-Hernández
- Health Sciences University Center, Universidad de Guadalajara, Guadalajara 44100, Jalisco, Mexico
- Department of Pediatric Infectious Diseases, Hospital Civil de Guadalajara “Fray Antonio Alcalde”, Guadalajara 44280, Jalisco, Mexico
| | | | - Gabino Cervantes-Guevara
- Department of Welfare and Sustainable Development, Centro Universitario del Norte, Universidad de Guadalajara, Colotlán 46200, Jalisco, Mexico
- Department of Gastroenterology, Hospital Civil de Guadalajara “Fray Antonio Alcalde”, Guadalajara 44280, Jalisco, Mexico
| | | | - Sol Ramírez-Ochoa
- Department of Internal Medicine, Hospital Civil de Guadalajara “Fray Antonio Alcalde”, Guadalajara 44280, Jalisco, Mexico
| | - Alejandro González-Ojeda
- Biomedical Research Unit 02, Specialties Hospital of the Western National Medical Center, Mexican Institute of Social Security, Guadalajara 44329, Jalisco, Mexico
| | - Clotilde Fuentes-Orozco
- Biomedical Research Unit 02, Specialties Hospital of the Western National Medical Center, Mexican Institute of Social Security, Guadalajara 44329, Jalisco, Mexico
| | - Francisco Javier Hernández-Mora
- Human Reproduction, Growth and Child Development Clinic, Health Sciences University Center, Universidad de Guadalajara, Guadalajara 44100, Jalisco, Mexico
| | | | - Andrea Pérez de Acha-Chávez
- Department of Geriatrics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico
| | - Enrique Cervantes-Pérez
- Department of Internal Medicine, Hospital Civil de Guadalajara “Fray Antonio Alcalde”, Guadalajara 44280, Jalisco, Mexico
- Health Sciences University Center, Universidad de Guadalajara, Guadalajara 44100, Jalisco, Mexico
- Correspondence:
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19
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Liu S, Xie G, Chen M, He Y, Yu W, Chen X, Mao W, Liu N, Zhang Y, Chang Q, Qiao Y, Ma X, Xue J, Jin M, Guo S, Hou Y, Gao Z. Oral microbial dysbiosis in patients with periodontitis and chronic obstructive pulmonary disease. Front Cell Infect Microbiol 2023; 13:1121399. [PMID: 36844402 PMCID: PMC9948037 DOI: 10.3389/fcimb.2023.1121399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Background Oral microbiota is closely related to the homeostasis of the oral cavity and lungs. To provide potential information for the prediction, screening, and treatment strategies of individuals, this study compared and investigated the bacterial signatures in periodontitis and chronic obstructive pulmonary disease (COPD). Materials and methods We collected subgingival plaque and gingival crevicular fluid samples from 112 individuals (31 healthy controls, 24 patients with periodontitis, 28 patients with COPD, and 29 patients with both periodontitis and COPD). The oral microbiota was analyzed using 16S rRNA gene sequencing and diversity and functional prediction analysis were performed. Results We observed higher bacterial richness in individuals with periodontitis in both types of oral samples. Using LEfSe and DESeq2 analyses, we found differentially abundant genera that may be potential biomarkers for each group. Mogibacterium is the predominant genus in COPD. Ten genera, including Desulfovibrio, Filifactor, Fretibacterium, Moraxella, Odoribacter, Pseudoramibacter Pyramidobacter, Scardovia, Shuttleworthia and Treponema were predominant in periodontitis. Bergeyella, Lautropia, Rothia, Propionibacterium and Cardiobacterium were the signature of the healthy controls. The significantly different pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) between healthy controls and other groups were concentrated in genetic information processing, translation, replication and repair, and metabolism of cofactors and vitamins. Conclusions We found the significant differences in the bacterial community and functional characterization of oral microbiota in periodontitis, COPD and comorbid diseases. Compared to gingival crevicular fluid, subgingival plaque may be more appropriate for reflecting the difference of subgingival microbiota in periodontitis patients with COPD. These results may provide potentials for predicting, screening, and treatment strategies for individuals with periodontitis and COPD.
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Affiliation(s)
- Siqin Liu
- School of Stomatology, Binzhou Medical University, Yantai, China
| | - Guofang Xie
- Department of Stomatology, Linfen Central Hospital, Linfen, China
| | - Meifeng Chen
- Department of Respiratory and Critical Care Medicine, Linfen Central Hospital, Linfen, China
| | - Yukun He
- Department of Respiratory and Critical Care Medicine, Peking University People’s hospital, Beijing, China
| | - Wenyi Yu
- Department of Respiratory and Critical Care Medicine, Peking University People’s hospital, Beijing, China
| | - Xiaobo Chen
- Department of Stomatology, Linfen Central Hospital, Linfen, China
| | - Weigang Mao
- Department of Stomatology, Linfen Central Hospital, Linfen, China
| | - Nanxia Liu
- Department of Stomatology, Linfen Central Hospital, Linfen, China
| | - Yuanjie Zhang
- Department of Stomatology, Linfen Central Hospital, Linfen, China
| | - Qin Chang
- Department of Respiratory and Critical Care Medicine, Linfen Central Hospital, Linfen, China
| | - Yingying Qiao
- Department of Respiratory and Critical Care Medicine, Linfen Central Hospital, Linfen, China
| | - Xinqian Ma
- Department of Respiratory and Critical Care Medicine, Peking University People’s hospital, Beijing, China
| | - Jianbo Xue
- Department of Respiratory and Critical Care Medicine, Peking University People’s hospital, Beijing, China
| | - Mengtong Jin
- Department of Science and Education, Linfen Central Hospital, Linfen, China
| | - Shuming Guo
- Nursing department, Linfen Central Hospital, Linfen, China
| | - Yudong Hou
- School of Stomatology, Binzhou Medical University, Yantai, China
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People’s hospital, Beijing, China
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20
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Kayongo A, Robertson NM, Siddharthan T, Ntayi ML, Ndawula JC, Sande OJ, Bagaya BS, Kirenga B, Mayanja-Kizza H, Joloba ML, Forslund SK. Airway microbiome-immune crosstalk in chronic obstructive pulmonary disease. Front Immunol 2023; 13:1085551. [PMID: 36741369 PMCID: PMC9890194 DOI: 10.3389/fimmu.2022.1085551] [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: 10/31/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
Chronic Obstructive Pulmonary Disease (COPD) has significantly contributed to global mortality, with three million deaths reported annually. This impact is expected to increase over the next 40 years, with approximately 5 million people predicted to succumb to COPD-related deaths annually. Immune mechanisms driving disease progression have not been fully elucidated. Airway microbiota have been implicated. However, it is still unclear how changes in the airway microbiome drive persistent immune activation and consequent lung damage. Mechanisms mediating microbiome-immune crosstalk in the airways remain unclear. In this review, we examine how dysbiosis mediates airway inflammation in COPD. We give a detailed account of how airway commensal bacteria interact with the mucosal innate and adaptive immune system to regulate immune responses in healthy or diseased airways. Immune-phenotyping airway microbiota could advance COPD immunotherapeutics and identify key open questions that future research must address to further such translation.
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Affiliation(s)
- Alex Kayongo
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda,Department of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda,Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda,Department of Medicine, Center for Emerging Pathogens, Rutgers, The State University of New Jersey, New Jersey Medical School, Newark, NJ, United States
| | | | - Trishul Siddharthan
- Division of Pulmonary Medicine, School of Medicine, University of Miami, Miami, FL, United States
| | - Moses Levi Ntayi
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda,Department of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda,Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Josephine Caren Ndawula
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Obondo J. Sande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Bernard S. Bagaya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Bruce Kirenga
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Harriet Mayanja-Kizza
- Department of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses L. Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Sofia K. Forslund
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany,Experimental and Clinical Research Center, a cooperation of Charité - Universitatsmedizin Berlin and Max Delbrück Center for Molecular Medicine, Berlin, Germany,Charité-Universitatsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany,DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany,*Correspondence: Sofia K. Forslund,
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21
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Hamidou Soumana I, Ryu MH, Leitao Filho FS, Yang J, Orach J, Nislow C, Leung JM, Rider CF, Carlsten C. Exposure to diesel exhaust alters the functional metagenomic composition of the airway microbiome in former smokers. ENVIRONMENTAL RESEARCH 2023; 216:114826. [PMID: 36403657 DOI: 10.1016/j.envres.2022.114826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/01/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
The lung microbiome plays a crucial role in airway homeostasis, yet we know little about the effects of exposures such as air pollution therein. We conducted a controlled human exposure study to assess the impact of diesel exhaust (DE) on the human airway microbiome. Twenty-four participants (former smokers with mild to moderate COPD (N = 9), healthy former smokers (N = 7), and control healthy never smokers (N = 8)) were exposed to DE (300 μg/m3 PM2.5) and filtered air (FA) for 2 h in a randomized order, separated by a 4-week washout. Endobronchial brushing samples were collected 24 h post-exposure and sequenced for the 16S microbiome, which was analyzed using QIIME2 and PICRUSt2 to examine diversity and metabolic functions, respectively. DE exposure altered airway microbiome metabolic functions in spite of statistically stable microbiome diversity. Affected functions included increases in: superpathway of purine deoxyribonucleosides degradation (pathway differential abundance 743.9, CI 95% 201.2 to 1286.6), thiazole biosynthesis I (668.5, CI 95% 139.9 to 1197.06), and L-lysine biosynthesis II (666.5, CI 95% 73.3 to 1257.7). There was an exposure-by-age effect, such that menaquinone biosynthesis superpathways were the most enriched function in the microbiome of participants aged >60, irrespective of smoking or health status. Moreover, exposure-by-phenotype analysis showed metabolic alterations in former smokers after DE exposure. These observations suggest that DE exposure induced substantial changes in the metabolic functions of the airway microbiome despite the absence of diversity changes.
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Affiliation(s)
- Illiassou Hamidou Soumana
- Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Min Hyung Ryu
- Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | | | - Julia Yang
- Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Juma Orach
- Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Janice M Leung
- Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Christopher Francis Rider
- Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Christopher Carlsten
- Air Pollution Exposure Laboratory, Vancouver Coastal Health Research Institute, Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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22
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Zhang Z, Yu W, Li G, He Y, Shi Z, Wu J, Ma X, Zhu Y, Zhao L, Liu S, Wei Y, Xue J, Guo S, Gao Z. Characteristics of oral microbiome of healthcare workers in different clinical scenarios: a cross-sectional analysis. BMC Oral Health 2022; 22:481. [PMID: 36357898 PMCID: PMC9648452 DOI: 10.1186/s12903-022-02501-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/12/2022] [Indexed: 11/11/2022] Open
Abstract
The environment of healthcare institutes (HCIs) potentially affects the internal microecology of medical workers, which is reflected not only in the well-studied gut microbiome but also in the more susceptible oral microbiome. We conducted a prospective cross-sectional cohort study in four hospital departments in Central China. Oropharyngeal swabs from 65 healthcare workers were collected and analyzed using 16S rRNA gene amplicon sequencing. The oral microbiome of healthcare workers exhibited prominent deviations in diversity, microbial structure, and predicted function. The coronary care unit (CCU) samples exhibited robust features and stability, with significantly higher abundances of genera such as Haemophilus, Fusobacterium, and Streptococcus, and a lower abundance of Prevotella. Functional prediction analysis showed that vitamin, nucleotide, and amino acid metabolisms were significantly different among the four departments. The CCU group was at a potential risk of developing periodontal disease owing to the increased abundance of F. nucleatum. Additionally, oral microbial diversification of healthcare workers was related to seniority. We described the oral microbiome profile of healthcare workers in different clinical scenarios and demonstrated that community diversity, structure, and potential functions differed markedly among departments. Intense modulation of the oral microbiome of healthcare workers occurs because of their original departments, especially in the CCU.
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Affiliation(s)
- Zhixia Zhang
- Nursing Department, Linfen Central Hospital, 041000 Shanxi, Shanxi China
| | - Wenyi Yu
- grid.411634.50000 0004 0632 4559Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing, China
| | - Guangyao Li
- Science and Education Department, Linfen Central Hospital, Hainan, Shanxi China
| | - Yukun He
- grid.411634.50000 0004 0632 4559Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing, China
| | - Zhiming Shi
- Cardiology Department, Linfen Central Hospital, Hainan, Shanxi China
| | - Jing Wu
- Nursing Department, Linfen Central Hospital, 041000 Shanxi, Shanxi China
| | - Xinqian Ma
- grid.411634.50000 0004 0632 4559Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing, China
| | - Yu Zhu
- Science and Education Department, Linfen Central Hospital, Hainan, Shanxi China
| | - Lili Zhao
- grid.411634.50000 0004 0632 4559Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing, China
| | - Siqin Liu
- grid.440653.00000 0000 9588 091XThe Stomatology College of Binzhou Medical University, Yantai, Shandong China
| | - Yue Wei
- grid.263452.40000 0004 1798 4018Nursing College of Shanxi Medical University, Shanxi, China
| | - Jianbo Xue
- grid.411634.50000 0004 0632 4559Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing, China
| | - Shuming Guo
- Nursing Department, Linfen Central Hospital, 041000 Shanxi, Shanxi China
| | - Zhancheng Gao
- grid.411634.50000 0004 0632 4559Department of Respiratory and Critical Care Medicine, Peking University People’s Hospital, Beijing, China ,grid.411634.50000 0004 0632 4559Department of Pulmonary and Critical Care Medicine, Peking University People’s Hospital, 100044 Beijing, China
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23
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Closing the Loop on the Vicious Circle in Chronic Obstructive Pulmonary Disease. Ann Am Thorac Soc 2022; 19:1803-1805. [PMID: 36318080 PMCID: PMC9667802 DOI: 10.1513/annalsats.202208-697ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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24
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The effect of oral bacterial lysates on the respiratory microbiome in patients with chronic obstructive pulmonary disease exacerbations – A pilot study. MEDICINE IN MICROECOLOGY 2022. [DOI: 10.1016/j.medmic.2022.100067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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25
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Laiman V, Lo YC, Chen HC, Yuan TH, Hsiao TC, Chen JK, Chang CW, Lin TC, Li SJ, Chen YY, Heriyanto DS, Chung KF, Chuang KJ, Ho KF, Chang JH, Chuang HC. Effects of antibiotics and metals on lung and intestinal microbiome dysbiosis after sub-chronic lower-level exposure of air pollution in ageing rats. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 246:114164. [PMID: 36244167 DOI: 10.1016/j.ecoenv.2022.114164] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/05/2022] [Accepted: 10/05/2022] [Indexed: 05/06/2023]
Abstract
We investigated the effects of antibiotics, drugs, and metals on lung and intestinal microbiomes after sub-chronic exposure of low-level air pollution in ageing rats. Male 1.5-year-old Fischer 344 ageing rats were exposed to low-level traffic-related air pollution via whole-body exposure system for 3 months with/without high-efficiency particulate air (HEPA) filtration (gaseous vs. particulate matter with aerodynamic diameter of ≤2.5 µm (PM2.5) pollution). Lung functions, antibiotics, drugs, and metals in lungs were examined and linked to lung and fecal microbiome analyses by high-throughput sequencing analysis of 16 s ribosomal (r)DNA. Rats were exposed to 8.7 μg/m3 PM2.5, 10.1 ppb NO2, 1.6 ppb SO2, and 23.9 ppb O3 in average during the study period. Air pollution exposure decreased forced vital capacity (FVC), peak expiratory flow (PEF), forced expiratory volume in 20 ms (FEV20), and FEF at 25∼75% of FVC (FEF25-75). Air pollution exposure increased antibiotics and drugs (benzotriazole, methamphetamine, methyl-1 H-benzotriazole, ketamine, ampicillin, ciprofloxacin, pentoxifylline, erythromycin, clarithromycin, ceftriaxone, penicillin G, and penicillin V) and altered metals (V, Cr, Cu, Zn, and Ba) levels in lungs. Fusobacteria and Verrucomicrobia at phylum level were increased in lung microbiome by air pollution, whereas increased alpha diversity, Bacteroidetes and Proteobacteria and decreased Firmicutes at phylum level were occurred in intestinal microbiome. Lung function decline was correlated with increasing antibiotics, drugs, and metals in lungs as well as lung and intestinal microbiome dysbiosis. The antibiotics, drugs, and Cr, Co, Ca, and Cu levels in lung were correlated with lung and intestinal microbiome dysbiosis. The lung microbiome was correlated with intestinal microbiome at several phylum and family levels after air pollution exposure. Our results revealed that antibiotics, drugs, and metals in the lung caused lung and intestinal microbiome dysbiosis in ageing rats exposed to air pollution, which may lead to lung function decline.
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Affiliation(s)
- Vincent Laiman
- International Ph.D. Program in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Department of Anatomical Pathology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada - Dr. Sardjito Hospital, Yogyakarta, Indonesia.
| | - Yu-Chun Lo
- Ph.D. Program in Medical Neuroscience, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.
| | - Hsin-Chang Chen
- Department of Chemistry, College of Science, Tunghai University, Taichung, Taiwan.
| | - Tzu-Hsuen Yuan
- Department of Health and Welfare, College of City Management, University of Taipei, Taipei, Taiwan.
| | - Ta-Chih Hsiao
- Graduate Institute of Environmental Engineering, National Taiwan University, Taipei, Taiwan.
| | - Jen-Kun Chen
- Institute of Biomedical Engineering & Nanomedicine, National Health Research Institutes, Miaoli, Taiwan.
| | - Ching-Wen Chang
- Industrial Ph.D. Program of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Ting-Chun Lin
- Department of Biomedical Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Ssu-Ju Li
- Department of Biomedical Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - You-Yin Chen
- Ph.D. Program in Medical Neuroscience, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Industrial Ph.D. Program of Biomedical Science and Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan; Department of Biomedical Engineering, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Didik Setyo Heriyanto
- Department of Anatomical Pathology, Faculty of Medicine, Public Health, and Nursing, Universitas Gadjah Mada - Dr. Sardjito Hospital, Yogyakarta, Indonesia.
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, UK.
| | - Kai-Jen Chuang
- School of Public Health, College of Public Health, Taipei Medical University, Taipei, Taiwan; Department of Public Health, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan.
| | - Kin-Fai Ho
- School of Public Health and Primary Care, the Chinese University of Hong Kong, Hong Kong.
| | - Jer-Hwa Chang
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Pulmonary Medicine, Departments of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
| | - Hsiao-Chi Chuang
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan; Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan; Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan.
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26
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Blackburn JB, Schaff JA, Gutor S, Du RH, Nichols D, Sherrill T, Gutierrez AJ, Xin MK, Wickersham N, Zhang Y, Holtzman MJ, Ware LB, Banovich NE, Kropski JA, Blackwell TS, Richmond BW. Secretory Cells Are the Primary Source of pIgR in Small Airways. Am J Respir Cell Mol Biol 2022; 67:334-345. [PMID: 35687143 PMCID: PMC9447142 DOI: 10.1165/rcmb.2021-0548oc] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 06/13/2022] [Indexed: 11/24/2022] Open
Abstract
Loss of secretory IgA (SIgA) is common in chronic obstructive pulmonary disease (COPD) small airways and likely contributes to disease progression. We hypothesized that loss of SIgA results from reduced expression of pIgR (polymeric immunoglobulin receptor), a chaperone protein needed for SIgA transcytosis, in the COPD small airway epithelium. pIgR-expressing cells were defined and quantified at single-cell resolution in human airways using RNA in situ hybridization, immunostaining, and single-cell RNA sequencing. Complementary studies in mice used immunostaining, primary murine tracheal epithelial cell culture, and transgenic mice with secretory or ciliated cell-specific knockout of pIgR. SIgA degradation by human neutrophil elastase or secreted bacterial proteases from nontypeable Haemophilus influenzae was evaluated in vitro. We found that secretory cells are the predominant cell type responsible for pIgR expression in human and murine airways. Loss of SIgA in small airways was not associated with a reduction in secretory cells but rather a reduction in pIgR protein expression despite intact PIGR mRNA expression. Neutrophil elastase and nontypeable H. influenzae-secreted proteases are both capable of degrading SIgA in vitro and may also contribute to a deficient SIgA immunobarrier in COPD. Loss of the SIgA immunobarrier in small airways of patients with severe COPD is complex and likely results from both pIgR-dependent defects in IgA transcytosis and SIgA degradation.
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Affiliation(s)
- Jessica B. Blackburn
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Jacob A. Schaff
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Sergey Gutor
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Rui-Hong Du
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - David Nichols
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Taylor Sherrill
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | | | - Matthew K. Xin
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Nancy Wickersham
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | - Yong Zhang
- Division of Pulmonary and Critical Care Medicine, Washington University–St. Louis, St. Louis, Missouri
| | - Michael J. Holtzman
- Division of Pulmonary and Critical Care Medicine, Washington University–St. Louis, St. Louis, Missouri
| | - Lorraine B. Ware
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
| | | | - Jonathan A. Kropski
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
| | - Timothy S. Blackwell
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
| | - Bradley W. Richmond
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
- Division of Allergy, Pulmonary, and Critical Care Medicine, School of Medicine, and
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
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27
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Wu Z, Tang J, Zhuang R, Meng D, Zhang L, Gu C, Teng X, Zhu Z, Liu J, Pang J, Hu J, Lv X. The microbiome of lower respiratory tract and tumor tissue in lung cancer manifested as radiological ground-glass opacity. Front Bioeng Biotechnol 2022; 10:892613. [PMID: 36091439 PMCID: PMC9455596 DOI: 10.3389/fbioe.2022.892613] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Recent studies have confirmed the existence of microbiota in the lungs. The relationship between lung ground-glass opacity (GGO) and microbiota in the lung microenvironment is not clear. In this study, we investigated the microbial composition and diversity in bronchoalveolar lavage fluid (BALF) of diseased lung segments and paired contralateral healthy lung segments from 11 GGO patients. Furthermore, lung GGO and paired normal tissues of 26 GGO patients were explored whether there are microbial characteristics related to GGO. Compared with the control group, the community richness of GGO tissue and BALF of GGO lung segment (α-diversity) and overall microbiome difference (β-diversity) had no significant difference. The microbiome composition of BALF of GGO segments is distinct from that of paired healthy lung segments [genus (Rothia), order (Lachnospiraceae), family (Lachnospiraceae), genus (Lachnospiraceae_NK4A136_group, Faecalibacterium), and species (Faecalibacterium prausnitzii, Bacteroides uniforms)]. GGO tissue and adjacent lung tissue had more significant differences at the levels of class, order, family, genus, and species level, and most of them are enriched in normal lung tissue. The area under the curve (AUC) using 10 genera-based biomarkers to predict GGO was 91.05% (95% CI: 81.93–100%). In conclusion, this study demonstrates there are significant differences in the lower respiratory tract and lung microbiome between GGO and the non-malignant control group through the BALF and lung tissues. Furthermore, some potential bacterial biomarkers showed good performance to predict GGO.
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Affiliation(s)
- Zhigang Wu
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jie Tang
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Runzhou Zhuang
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Di Meng
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lichen Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Chen Gu
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiao Teng
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ziyue Zhu
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiacong Liu
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jinghua Pang
- Department of Thoracic Surgery, Fenghua People’s Hospital, Ningbo, China
| | - Jian Hu
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Jian Hu, ; Xiayi Lv,
| | - Xiayi Lv
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Jian Hu, ; Xiayi Lv,
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Cho Y, Kim J, Pai H, Rho M. Deciphering Resistome in Patients With Chronic Obstructive Pulmonary Diseases and Clostridioides difficile Infections. Front Microbiol 2022; 13:919907. [PMID: 35983323 PMCID: PMC9378971 DOI: 10.3389/fmicb.2022.919907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/20/2022] [Indexed: 12/03/2022] Open
Abstract
Antibiotics alter the gut microbiome and cause dysbiosis leading to antibiotic-resistant organisms. Different patterns of antibiotic administration cause a difference in bacterial composition and resistome in the human gut. We comprehensively investigated the association between the distribution of antibiotic resistance genes (ARGs), bacterial composition, and antibiotic treatments in patients with chronic obstructive pulmonary diseases (COPD) and Clostridioides difficile infections (CDI) who had chronic or acute intermittent use of antibiotics and compared them with healthy individuals. We analyzed the gut microbiomes of 61 healthy individuals, 16 patients with COPD, and 26 patients with CDI. The COPD patients were antibiotic-free before stool collection for a median of 40 days (Q1: 9.5; Q3: 60 days), while the CDI patients were antibiotic-free for 0 days (Q1: 0; Q3: 0.3). The intra-group beta diversity measured by the median Bray-Curtis index was the lowest for the healthy individuals (0.55), followed by the COPD (0.69) and CDI groups (0.72). The inter-group beta diversity was the highest among the healthy and CDI groups (median index = 0.89). The abundance of ARGs measured by the number of reads per kilobase per million reads (RPKM) was 684.2; 1,215.2; and 2,025.1 for the healthy, COPD, and CDI groups. It was negatively correlated with the alpha diversity of bacterial composition. For the prevalent ARG classes, healthy individuals had the lowest diversity and abundance of aminoglycoside, β-lactam, and macrolide-lincosamide-streptogramin (MLS) resistance genes, followed by the COPD and CDI groups. The abundances of Enterococcus and Escherichia species were positively correlated with ARG abundance and the days of antibiotic treatment, while Bifidobacterium and Ruminococcus showed negative correlations for the same. In addition, we analyzed the mobilome patterns of aminoglycoside and β-lactam resistance gene carriers using metagenomic sequencing data. In conclusion, the ARGs were significantly enhanced in the CDI and COPD groups than in healthy individuals. In particular, aminoglycoside and β-lactam resistance genes were more abundant in the CDI and COPD groups, but the dominant mobile genetic elements that enable the transfer of such genes showed similar prevalence patterns among the groups.
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Affiliation(s)
- Youna Cho
- Department of Computer Science, Hanyang University, Seoul, South Korea
| | - Jieun Kim
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, South Korea
| | - Hyunjoo Pai
- Department of Internal Medicine, College of Medicine, Hanyang University, Seoul, South Korea
- Hyunjoo Pai,
| | - Mina Rho
- Department of Computer Science, Hanyang University, Seoul, South Korea
- Department of Biomedical Informatics, Hanyang University, Seoul, South Korea
- *Correspondence: Mina Rho,
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29
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Park SS, Perez Perez JL, Perez Gandara B, Agudelo CW, Rodriguez Ortega R, Ahmed H, Garcia-Arcos I, McCarthy C, Geraghty P. Mechanisms Linking COPD to Type 1 and 2 Diabetes Mellitus: Is There a Relationship between Diabetes and COPD? Medicina (B Aires) 2022; 58:medicina58081030. [PMID: 36013497 PMCID: PMC9415273 DOI: 10.3390/medicina58081030] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 01/09/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) patients frequently suffer from multiple comorbidities, resulting in poor outcomes for these patients. Diabetes is observed at a higher frequency in COPD patients than in the general population. Both type 1 and 2 diabetes mellitus are associated with pulmonary complications, and similar therapeutic strategies are proposed to treat these conditions. Epidemiological studies and disease models have increased our knowledge of these clinical associations. Several recent genome-wide association studies have identified positive genetic correlations between lung function and obesity, possibly due to alterations in genes linked to cell proliferation; embryo, skeletal, and tissue development; and regulation of gene expression. These studies suggest that genetic predisposition, in addition to weight gain, can influence lung function. Cigarette smoke exposure can also influence the differential methylation of CpG sites in genes linked to diabetes and COPD, and smoke-related single nucleotide polymorphisms are associated with resting heart rate and coronary artery disease. Despite the vast literature on clinical disease association, little direct mechanistic evidence is currently available demonstrating that either disease influences the progression of the other, but common pharmacological approaches could slow the progression of these diseases. Here, we review the clinical and scientific literature to discuss whether mechanisms beyond preexisting conditions, lifestyle, and weight gain contribute to the development of COPD associated with diabetes. Specifically, we outline environmental and genetic confounders linked with these diseases.
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Affiliation(s)
- Sangmi S. Park
- Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA; (S.S.P.); (J.L.P.P.); (B.P.G.); (C.W.A.); (R.R.O.); (H.A.); (I.G.-A.)
| | - Jessica L. Perez Perez
- Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA; (S.S.P.); (J.L.P.P.); (B.P.G.); (C.W.A.); (R.R.O.); (H.A.); (I.G.-A.)
| | - Brais Perez Gandara
- Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA; (S.S.P.); (J.L.P.P.); (B.P.G.); (C.W.A.); (R.R.O.); (H.A.); (I.G.-A.)
| | - Christina W. Agudelo
- Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA; (S.S.P.); (J.L.P.P.); (B.P.G.); (C.W.A.); (R.R.O.); (H.A.); (I.G.-A.)
| | - Romy Rodriguez Ortega
- Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA; (S.S.P.); (J.L.P.P.); (B.P.G.); (C.W.A.); (R.R.O.); (H.A.); (I.G.-A.)
| | - Huma Ahmed
- Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA; (S.S.P.); (J.L.P.P.); (B.P.G.); (C.W.A.); (R.R.O.); (H.A.); (I.G.-A.)
| | - Itsaso Garcia-Arcos
- Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA; (S.S.P.); (J.L.P.P.); (B.P.G.); (C.W.A.); (R.R.O.); (H.A.); (I.G.-A.)
| | - Cormac McCarthy
- University College Dublin School of Medicine, Education and Research Centre, St. Vincent’s University Hospital, D04 T6F4 Dublin, Ireland;
| | - Patrick Geraghty
- Department of Medicine, State University of New York Downstate Health Sciences University, Brooklyn, NY 11203, USA; (S.S.P.); (J.L.P.P.); (B.P.G.); (C.W.A.); (R.R.O.); (H.A.); (I.G.-A.)
- Correspondence: ; Tel.: +1-718-270-3141
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30
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Malvisi L, Yarraguntla A, Mortier MC, Osman K, Cleary DW, Sente B, Pascal TG, Weynants V, Clarke SC, Taddei L, Wilkinson TMA, Devaster JM, Devos N. Impact of bacterial strain acquisition in the lung of patients with COPD: the AERIS study. Infect Dis (Lond) 2022; 54:784-793. [PMID: 35794793 DOI: 10.1080/23744235.2022.2092648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Bacterial infections are associated with acute exacerbations of chronic obstructive pulmonary disease (AECOPD), but the mechanism is incompletely understood. METHOD In a COPD observational study (NCT01360398), sputum samples were collected monthly at the stable state and exacerbation. Post-hoc analyses of 1307 non-typeable Haemophilus influenzae (NTHi) isolates from 20 patients and 756 Moraxella catarrhalis isolates from 38 patients in one year of follow-up were conducted by multilocus sequence typing (MLST). All isolates came from cultured sputum samples that were analyzed for bacterial species presence, apparition (infection not detected at the preceding visit), or acquisition (first-time infection), with the first study visit as a baseline. Strain apparition or new strain acquisition was analyzed by MLST. The odds ratio (OR) of experiencing an exacerbation vs. stable state was estimated by conditional logistic regression modelling, stratified by patient. RESULTS The culture results confirmed a significant association with exacerbation only for NTHi species presence (OR 2.28; 95% confidence interval [CI]: 1.12-4.64) and strain apparition (OR 2.38; 95% CI: 1.08-5.27). For M. catarrhalis, although confidence intervals overlapped, the association with exacerbation for first-time species acquisition (OR 5.99; 2.75-13.02) appeared stronger than species presence (OR 3.67; 2.10-6.40), new strain acquisition (OR 2.94; 1.43-6.04), species apparition (OR 4.18; 2.29-7.63), and strain apparition (OR 2.78; 1.42-5.42). This may suggest that previous M. catarrhalis colonization may modify the risk of exacerbation associated with M. catarrhalis infection. CONCLUSIONS The results confirm that NTHi and M. catarrhalis infections are associated with AECOPD but suggest different dynamic mechanisms in triggering exacerbations.
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Affiliation(s)
| | | | | | - Karen Osman
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK
| | - David W Cleary
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.,Southampton NIHR Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK
| | | | | | | | - Stuart C Clarke
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.,Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK
| | | | - Tom M A Wilkinson
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton, UK.,Southampton NIHR Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK.,Wessex Investigational Sciences Hub, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK
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31
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Wu Y, Meng H, Qiao B, Li N, Zhang Q, Jia W, Xing H, Li Y, Yuan J, Yang Z. Yifei Sanjie Formula Treats Chronic Obstructive Pulmonary Disease by Remodeling Pulmonary Microbiota. Front Med (Lausanne) 2022; 9:927607. [PMID: 35847812 PMCID: PMC9277004 DOI: 10.3389/fmed.2022.927607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is one of the most common pulmonary diseases. Evidence suggests that dysbiosis of pulmonary microbiota leads to the COPD pathological process. Yifei Sanjie Formula (YS) is widely used to treat diseases in respiratory systems, yet little is known about its mechanisms. In the present study, we first established the fingerprint of YS as the background for UHPLC-QTOF-MS. Components were detected, including alkaloids, amino acid derivatives, phenylpropanoids, flavonoids, terpenoids, organic acids, phenols, and the like. The therapeutic effect of YS on COPD was evaluated, and the pulmonary function and ventilatory dysfunction (EF50, TV, and MV) were improved after the administration of YS. Further, the influx of lymphocytes was inhibited in pulmonary parenchyma, accompanied by down-regulation of inflammation cytokines via the NLRP3/caspase-1/IL-1β signaling pathway. The severity of pulmonary pathological damage was reversed. Disturbed pulmonary microbiota was discovered to involve an increased relative abundance of Ralstonia and Mycoplasma and a decreased relative abundance of Lactobacillus and Bacteroides in COPD animals. However, the subversive effect was shown. The abundance and diversity of pulmonary microflora were remodeled, especially increasing beneficial genua Lactobacillus and Bacteroides, as well as downregulating pathogenic genua Ralstonia and Mycoplasma in the YS group. Environmental factor correlation analysis showed that growing pulmonary microbiota was positively correlated with the inflammatory factor, referring to Ralstonia and Mycoplasma, as well as negatively correlated with the inflammatory factor, referring to Lactobacillus and Bacteroides. These results suggest that the effects of YS involved remodeling lung microbes and anti-inflammatory signal pathways, revealing that intervention microbiota and an anti-inflammatory may be a potential therapeutic strategy for COPD.
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Affiliation(s)
- Yueying Wu
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Kunming, China
- First Clinical School of Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Hui Meng
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Kunming, China
| | - Bo Qiao
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Kunming, China
| | - Ning Li
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Kunming, China
- First Clinical School of Medicine, Yunnan University of Chinese Medicine, Kunming, China
| | - Qiang Zhang
- Basic Medical School, Shanghai University of Chinese Medicine, Shanghai, China
| | - Wenqing Jia
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Kunming, China
| | - Haijing Xing
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Kunming, China
| | - Yuqing Li
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Kunming, China
| | - Jiali Yuan
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Kunming, China
- Jiali Yuan
| | - Zhongshan Yang
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Kunming, China
- *Correspondence: Zhongshan Yang
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32
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Stankovic M, Veljovic K, Popovic N, Kojic S, Dunjic Manevski S, Radojkovic D, Golic N. Lactobacillus brevis BGZLS10-17 and Lb. plantarum BGPKM22 Exhibit Anti-Inflammatory Effect by Attenuation of NF-κB and MAPK Signaling in Human Bronchial Epithelial Cells. Int J Mol Sci 2022; 23:ijms23105547. [PMID: 35628361 PMCID: PMC9146699 DOI: 10.3390/ijms23105547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 12/28/2022] Open
Abstract
Bronchial epithelial cells are exposed to environmental influences, microbiota, and pathogens and also serve as a powerful effector that initiate and propagate inflammation by the release of pro-inflammatory mediators. Recent studies suggested that lung microbiota differ between inflammatory lung diseases and healthy lungs implicating their contribution in the modulation of lung immunity. Lactic acid bacteria (LAB) are natural inhabitants of healthy human lungs and also possess immunomodulatory effects, but so far, there are no studies investigating their anti-inflammatory potential in respiratory cells. In this study, we investigated immunomodulatory features of 21 natural LAB strains in lipopolysaccharide (LPS)-stimulated human bronchial epithelial cells (BEAS-2B). Our results show that several LAB strains reduced the expression of pro-inflammatory cytokine and chemokine genes. We also demonstrated that two LAB strains, Lactobacillus brevis BGZLS10-17 and Lb. plantarum BGPKM22, effectively attenuated LPS-induced nuclear factor-κB (NF-κB) nuclear translocation. Moreover, BGZLS10-17 and BGPKM22 reduced the activation of p38, extracellular signal-related kinase (ERK), and c-Jun amino-terminal kinase (JNK) signaling cascade resulting in a reduction of pro-inflammatory mediator expressions in BEAS-2B cells. Collectively, the LAB strains BGZLS10-17 and BGPKM22 exhibited anti-inflammatory effects in BEAS-2B cells and could be employed to balance immune response in lungs and replenish diminished lung microbiota in chronic lung diseases.
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Affiliation(s)
- Marija Stankovic
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (S.K.); (S.D.M.); (D.R.)
- Correspondence:
| | - Katarina Veljovic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (K.V.); (N.P.); (N.G.)
| | - Nikola Popovic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (K.V.); (N.P.); (N.G.)
| | - Snezana Kojic
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (S.K.); (S.D.M.); (D.R.)
| | - Sofija Dunjic Manevski
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (S.K.); (S.D.M.); (D.R.)
| | - Dragica Radojkovic
- Laboratory for Molecular Biology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (S.K.); (S.D.M.); (D.R.)
| | - Natasa Golic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, 11042 Belgrade, Serbia; (K.V.); (N.P.); (N.G.)
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33
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Mammen MJ, Tu C, Morris MC, Richman S, Mangione W, Falls Z, Qu J, Broderick G, Sethi S, Samudrala R. Proteomic Network Analysis of Bronchoalveolar Lavage Fluid in Ex-Smokers to Discover Implicated Protein Targets and Novel Drug Treatments for Chronic Obstructive Pulmonary Disease. Pharmaceuticals (Basel) 2022; 15:566. [PMID: 35631392 PMCID: PMC9147475 DOI: 10.3390/ph15050566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/23/2022] Open
Abstract
Bronchoalveolar lavage of the epithelial lining fluid (BALF) can sample the profound changes in the airway lumen milieu prevalent in chronic obstructive pulmonary disease (COPD). We compared the BALF proteome of ex-smokers with moderate COPD who are not in exacerbation status to non-smoking healthy control subjects and applied proteome-scale translational bioinformatics approaches to identify potential therapeutic protein targets and drugs that modulate these proteins for the treatment of COPD. Proteomic profiles of BALF were obtained from (1) never-smoker control subjects with normal lung function (n = 10) or (2) individuals with stable moderate (GOLD stage 2, FEV1 50−80% predicted, FEV1/FVC < 0.70) COPD who were ex-smokers for at least 1 year (n = 10). After identifying potential crucial hub proteins, drug−proteome interaction signatures were ranked by the computational analysis of novel drug opportunities (CANDO) platform for multiscale therapeutic discovery to identify potentially repurposable drugs. Subsequently, a literature-based knowledge graph was utilized to rank combinations of drugs that most likely ameliorate inflammatory processes. Proteomic network analysis demonstrated that 233 of the >1800 proteins identified in the BALF were significantly differentially expressed in COPD versus control. Functional annotation of the differentially expressed proteins was used to detail canonical pathways containing the differential expressed proteins. Topological network analysis demonstrated that four putative proteins act as central node proteins in COPD. The drugs with the most similar interaction signatures to approved COPD drugs were extracted with the CANDO platform. The drugs identified using CANDO were subsequently analyzed using a knowledge-based technique to determine an optimal two-drug combination that had the most appropriate effect on the central node proteins. Network analysis of the BALF proteome identified critical targets that have critical roles in modulating COPD pathogenesis, for which we identified several drugs that could be repurposed to treat COPD using a multiscale shotgun drug discovery approach.
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Affiliation(s)
- Manoj J. Mammen
- Department of Medicine, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
- Department of Biomedical Informatics, Jacobs School of Medicine and Biological Sciences, State University of New York, Buffalo, NY 14214, USA; (W.M.); (Z.F.)
| | - Chengjian Tu
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA; (C.T.); (J.Q.)
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203, USA
| | - Matthew C. Morris
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY 14621, USA; (M.C.M.); (S.R.); (G.B.)
| | - Spencer Richman
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY 14621, USA; (M.C.M.); (S.R.); (G.B.)
| | - William Mangione
- Department of Biomedical Informatics, Jacobs School of Medicine and Biological Sciences, State University of New York, Buffalo, NY 14214, USA; (W.M.); (Z.F.)
| | - Zackary Falls
- Department of Biomedical Informatics, Jacobs School of Medicine and Biological Sciences, State University of New York, Buffalo, NY 14214, USA; (W.M.); (Z.F.)
| | - Jun Qu
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, NY 14260, USA; (C.T.); (J.Q.)
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203, USA
| | - Gordon Broderick
- Center for Clinical Systems Biology, Rochester General Hospital, Rochester, NY 14621, USA; (M.C.M.); (S.R.); (G.B.)
| | - Sanjay Sethi
- WNY VA Healthcare System, Buffalo, NY 14215, USA;
- Department of Medicine, Jacobs School of Medicine and Biological Sciences, State University of New York at Buffalo, Buffalo, NY 14214, USA
| | - Ram Samudrala
- Department of Biomedical Informatics, Jacobs School of Medicine and Biological Sciences, State University of New York, Buffalo, NY 14214, USA; (W.M.); (Z.F.)
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Bourdiol A, Roquilly A. New Insights in the Pathophysiology of Hospital- and Ventilator-Acquired Pneumonia: A Complex Interplay between Dysbiosis and Critical-Illness-Related Immunosuppression. Semin Respir Crit Care Med 2022; 43:271-279. [PMID: 35100649 DOI: 10.1055/s-0041-1740606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Both hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP) have long been considered as diseases resulting from the invasion by pathogens of a previously sterile lung environment. Based on this historical understanding of their pathophysiology, our approaches for the prevention and treatment have significantly improved the outcomes of patients, but treatment failures remain frequent. Recent studies have suggested that the all-antimicrobial therapy-based treatment of pneumonia has reached a glass ceiling. The demonstration that the constant interactions between the respiratory microbiome and mucosal immunity are required to tune homeostasis in a state of symbiosis has changed our comprehension of pneumonia. We proposed that HAP and VAP should be considered as a state of dysbiosis, defined as the emergence of a dominant pathogen thriving at the same time from the catastrophic collapse of the fragile ecosystem of the lower respiratory tract and from the development of critical-illness-related immunosuppression. This multidimensional approach to the pathophysiology of HAP and VAP holds the potential to achieve future successes in research and critical care. Microbiome and mucosal immunity can indeed be manipulated and used as adjunctive therapies or targets to prevent or treat pneumonia.
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Affiliation(s)
- A Bourdiol
- Université de Nantes, CHU Nantes, Pôle Anesthésie Réanimations, Service d'Anesthésie Réanimation Chirurgicale, Hôtel Dieu, Nantes, France
| | - A Roquilly
- Université de Nantes, CHU Nantes, Pôle Anesthésie Réanimations, Service d'Anesthésie Réanimation Chirurgicale, Hôtel Dieu, Nantes, France
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35
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Chiu YC, Lee SW, Liu CW, Lan TY, Wu LSH. Relationship between gut microbiota and lung function decline in patients with chronic obstructive pulmonary disease: a 1-year follow-up study. Respir Res 2022; 23:10. [PMID: 35033061 PMCID: PMC8760664 DOI: 10.1186/s12931-022-01928-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/05/2022] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVE Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory lung disease characterized by a persistent limitation in airflow. Gut microbiota is closely correlated with lung inflammation. However, gut microbiota has not been studied in patients with declining lung function, due to chronic lung disease progression. SUBJECTS AND METHODS Stool samples were obtained from 55 patients with COPD that were in stable condition at enrolment (stage 1) and at a 1-year follow-up (stage 2). After extracting stool DNA, we performed next generation sequencing to analyse the distribution of gut microbiota. RESULTS Patients were divided to control and declining lung function groups, based on whether the rate of forced expiratory volume in 1 s (FEV1) had declined over time. An alpha diversity analysis of initial and follow-up stool samples showed a significant difference in the community richness of microbiota in the declining function group, but not in the control group. At the phylum level, Bacteroidetes was more abundant in the control group and Firmicutes was more abundant in the declining function group. The Alloprevotella genus was more abundant in the control group than in the declining function group. At 1-year follow-up, the mean proportions of Acinetobacter and Stenotrophomonas significantly increased in the control and declining function groups, respectively. CONCLUSION Some community shifts in gut microbiota were associated with lung function decline in COPD patients under regular treatment. Future studies should investigate the mechanism underlying alterations in lung function, due to changes in gut bacterial communities, in COPD.
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Affiliation(s)
- Yu-Chi Chiu
- Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan.,Institute of Hospital and Health Care Administration, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Department of Nursing, Yuanpei University of Medical Technology, Hsinchu, Taiwan
| | - Shih-Wei Lee
- Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
| | - Chi-Wei Liu
- Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
| | - Tzuo-Yun Lan
- Institute of Hospital and Health Care Administration, National Yang Ming Chiao Tung University, Taipei, Taiwan.
| | - Lawrence Shih-Hsin Wu
- Graduate Institute of Biomedical Sciences, China Medical University, No. 91 Hsueh-Shih Road, Taichung, 404, Taiwan. .,Center of Allergy, Immunology, and Microbiome (A.I.M.), China Medical University Children's Hospital, Taichung, Taiwan.
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36
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Schoonbroodt S, Ichanté JL, Boffé S, Devos N, Devaster JM, Taddei L, Rondini S, Arora AK, Pascal T, Malvaux L. Real-time PCR has advantages over culture-based methods in identifying major airway bacterial pathogens in chronic obstructive pulmonary disease: Results from three clinical studies in Europe and North America. Front Microbiol 2022; 13:1098133. [PMID: 36909845 PMCID: PMC10000296 DOI: 10.3389/fmicb.2022.1098133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/29/2022] [Indexed: 03/14/2023] Open
Abstract
Introduction We compared the performance of real-time PCR with culture-based methods for identifying bacteria in sputum samples from patients with chronic obstructive pulmonary disease (COPD) in three studies. Methods This was an exploratory analysis of sputum samples collected during an observational study of 127 patients (AERIS; NCT01360398), phase 2 study of 145 patients (NTHI-004; NCT02075541), and phase 2b study of 606 patients (NTHI-MCAT-002; NCT03281876). Bacteria were identified by culture-based microbiological methods in local laboratories using fresh samples or by real-time PCR in a central laboratory using frozen samples. Haemophilus influenzae positivity with culture was differentiated from H. haemolyticus positivity by microarray analysis or PCR. The feasibility of bacterial detection by culture-based methods on previously frozen samples was also examined in the NTHI-004 study. Results Bacterial detection results from both culture-based and PCR assays were available from 2,293 samples from AERIS, 974 from the NTHI-004 study, and 1736 from the NTHI-MCAT-002 study. Quantitative real-time PCR (qPCR) showed higher positivity rates than culture for H. influenzae (percentages for each study: 43.4% versus 26.2%, 47.1% versus 23.6%, 32.7% versus 10.4%) and Moraxella catarrhalis (12.9% versus 6.3%, 19.0% versus 6.0%, 15.5% versus 4.1%). In the NTHI-004 and NTHI-MCAT-002 studies, positivity rates were higher with qPCR for Streptococcus pneumoniae (15.6% versus 6.1%, 15.5% versus 3.8%); in AERIS, a lower rate with qPCR than with culture (11.0% versus 17.4%) was explained by misidentification of S. pseudopneumoniae/mitis isolates via conventional microbiological methods. Concordance analysis showed lowest overall agreement for H. influenzae (82.0%, 75.6%, 77.6%), due mainly to culture-negative/qPCR-positive samples, indicating lower sensitivity of the culture-based methods. The lowest positive agreement (culture-positive/qPCR-positive samples) was observed for S. pneumoniae (35.1%, 71.2%, 71.2%). Bacterial load values for each species showed a proportion of culture-negative samples with a load detected by qPCR; for some samples, the loads were in line with those observed in culture-positive samples. In the NTHI-004 study, of fresh samples that tested culture-positive, less than 50% remained culture-positive when tested from freeze/thawed samples. In the NTHI-004 study, of fresh samples that tested culture-positive, less than 50% remained culture-positive when tested from freeze/thawed samples. Discussion Real-time PCR on frozen sputum samples has enhanced sensitivity and specificity over culture-based methods, supporting its use for the identification of common respiratory bacterial species in patients with COPD.
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Fedotov VD, Zhestkov A, Lyamin AV, Zaslavskaya M, Dobrotina I, Tulichev A. Microbiota in the pathogenesis of COPD and its impact on the course of the disease. CLINICAL MICROBIOLOGY AND ANTIMICROBIAL CHEMOTHERAPY 2022. [DOI: 10.36488/cmac.2022.3.202-212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a serious problem for global health. Infectious agents play a main role in the development of COPD exacerbations. Bacterial colonization of the lower respiratory tract is common in patients with stable COPD. The role of microbiota and host immune response to potential pathogens is not well studied. Microbiota composition disorders in respiratory tract are found in patients with COPD and associated with maladaptive changes in the immune system of the lungs and increased level of inflammation. This review investigates role of microbiota in the pathogenesis of COPD and its impact on the course of the disease. Some important issues such as pneumococcal vaccination and antimicrobial resistance of respiratory pathogens are also discussed.
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Affiliation(s)
| | | | | | - M.I. Zaslavskaya
- Privolzhskiy Research Medical University (Nizhny Novgorod, Russia)
| | - I.S. Dobrotina
- Privolzhskiy Research Medical University (Nizhny Novgorod, Russia)
| | - A.A. Tulichev
- Privolzhskiy Research Medical University (Nizhny Novgorod, Russia)
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Mei X, Lu R, Cui L, Tian Y, Zhao P, Li J. Poly I:C Exacerbates Airway Inflammation and Remodeling in Cigarette Smoke-Exposed Mice. Lung 2022; 200:677-686. [PMID: 36269393 PMCID: PMC9675662 DOI: 10.1007/s00408-022-00574-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 09/22/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is a chronic respiratory disorder characterized by chronic inflammation and airway remodeling. Cigarette smoke (CS) and respiratory viruses are major causes of COPD development and exacerbation, but the mechanisms of these compounding factors on inflammation and pathological changes in airway structure still need further investigation. PURPOSE This work aimed to investigate the effects and mechanisms of Poly I:C on pathological changes in CS-induced COPD mice, such as airway inflammation and remodeling. METHODS From 1 to 8 weeks, the mice were exposed to CS, Poly I:C, or a combination of both. To compare the pathological changes among different groups over time, the mice were sacrificed at week 4, 8, 16, and 24, then the lungs were harvested to measure pulmonary pathology, inflammatory cytokines, and airway remodeling. RESULTS Our data revealed that the fundamental characteristics of COPD, such as pulmonary pathological damage, the release of inflammatory mediators, and the remodeling of airway walls, were observed at week 8 in CS-exposed mice and these pathological changes persisted to week 16. Compared with the CS group, the pathological changes, including decreased lung function, inflammatory cell infiltration, alveolar destruction, and airway wall thickening, were weaker in the Poly I:C group. These pathological changes were observed at week 8 and persisted to week 16 in Poly I:C-induced mice. Furthermore, Poly I:C exacerbated lung tissue damage in CS-induced COPD mice. The decreased lung function, airway inflammation and remodeling were observed in the combined group at week 4, and these pathological changes persisted to week 24. Our research indicated that Poly I:C enhanced the expression of p-P38, p-JNK and p-NF-κB in CS-exposed mice. CONCLUSION Poly I:C could promote airway inflammation and remodeling in CS-induced COPD mice probably by NF-κB and MAPK signaling.
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Affiliation(s)
- Xiaofeng Mei
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, 450046 Henan Province China ,Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province & Education Ministry of P.R. China, Zhengzhou, 450046 Henan Province China
| | - Ruilong Lu
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, 450046 Henan Province China ,Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province & Education Ministry of P.R. China, Zhengzhou, 450046 Henan Province China
| | - Lili Cui
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, 450046 Henan Province China ,Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province & Education Ministry of P.R. China, Zhengzhou, 450046 Henan Province China
| | - Yange Tian
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, 450046 Henan Province China ,Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province & Education Ministry of P.R. China, Zhengzhou, 450046 Henan Province China ,Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, 450000 China
| | - Peng Zhao
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, 450046 Henan Province China ,Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province & Education Ministry of P.R. China, Zhengzhou, 450046 Henan Province China ,Department of Respiratory Diseases, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450000 China ,Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, 450000 China
| | - Jiansheng Li
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, 450046 Henan Province China ,Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases Co-constructed by Henan Province & Education Ministry of P.R. China, Zhengzhou, 450046 Henan Province China ,Department of Respiratory Diseases, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450000 China
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Ding K, Chen J, Zhan W, Zhang S, Chen Y, Long S, Lei M. Microbiome Links Cigarette Smoke-Induced Chronic Obstructive Pulmonary Disease and Dietary Fiber via the Gut-Lung Axis: A Narrative Review. COPD 2021; 19:10-17. [PMID: 34963421 DOI: 10.1080/15412555.2021.2019208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Existing comprehensive management strategies for COPD effectively relieve the symptoms of patients, delay the deterioration of lung function, and prevent the progression of COPD through various means and multidisciplinary interventions. However, there has been limited progress in therapies that address the underlying causes of COPD pathogenesis. Recent studies have identified specific changes in the gut and pulmonary microbiota in response to exposure to smoke that can cause or exacerbate CS-COPD by regulating the inflammatory immune response in the lungs through the gut-lung axis. As a convenient and controllable intervention, modifying the diet to include more dietary fiber can effectively improve the prognosis of CS-COPD. Gut microbiota ferment dietary fiber to produce short-chain fatty acids, which connect the microbial communities in the lung and gut mucosa across the gut-lung axis, playing an anti-inflammatory and immunosuppressive role in the lungs. Given that the effect of dietary fiber on gut microbiota was highly similar to that of quitting smoking on gut microbiota, we assume that microbiota might be a potential therapeutic target for dietary fiber to alleviate and prevent CS-COPD. This study examines the similarities between pulmonary and gut microbiota changes in the presence of smoking and dietary fiber. It also highlights the mechanism by which SCFAs link pulmonary and gut microbiota in CS-COPD and analyzes the anti-inflammatory and immunomodulatory effects of short-chain fatty acids on CS-COPD via the gut-lung axis.
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Affiliation(s)
- Kaixi Ding
- Department of Geriatrics, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jieling Chen
- Department of Respiration, Shehong Hospital of Traditional Chinese Medicine, Shehong, China
| | - Wenling Zhan
- Department of Geriatrics, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shipeng Zhang
- Department of Geriatrics, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yi Chen
- Department of Geriatrics, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Sipei Long
- Department of Geriatrics, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ming Lei
- Department of Geriatrics, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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D’Anna SE, Maniscalco M, Cappello F, Carone M, Motta A, Balbi B, Ricciardolo FLM, Caramori G, Di Stefano A. Bacterial and viral infections and related inflammatory responses in chronic obstructive pulmonary disease. Ann Med 2021; 53:135-150. [PMID: 32997525 PMCID: PMC7877965 DOI: 10.1080/07853890.2020.1831050] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/25/2020] [Indexed: 12/24/2022] Open
Abstract
In chronic obstructive pulmonary disease (COPD) patients, bacterial and viral infections play a relevant role in worsening lung function and, therefore, favour disease progression. The inflammatory response to lung infections may become a specific indication of the bacterial and viral infections. We here review data on the bacterial-viral infections and related airways and lung parenchyma inflammation in stable and exacerbated COPD, focussing our attention on the prevalent molecular pathways in these different clinical conditions. The roles of macrophages, autophagy and NETosis are also briefly discussed in the context of lung infections in COPD. Controlling their combined response may restore a balanced lung homeostasis, reducing the risk of lung function decline. KEY MESSAGE Bacteria and viruses can influence the responses of the innate and adaptive immune system in the lung of chronic obstructive pulmonary disease (COPD) patients. The relationship between viruses and bacterial colonization, and the consequences of the imbalance of these components can modulate the inflammatory state of the COPD lung. The complex actions involving immune trigger cells, which activate innate and cell-mediated inflammatory responses, could be responsible for the clinical consequences of irreversible airflow limitation, lung remodelling and emphysema in COPD patients.
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Affiliation(s)
| | - Mauro Maniscalco
- Divisione di Pneumologia, Istituti Clinici Scientifici Maugeri, IRCCS, Telese, Italy
| | - Francesco Cappello
- Dipartimento di Biomedicina, Neuroscienze e Diagnostica avanzata (BIND), Istituto di Anatomia Umana e Istologia Università degli Studi di Palermo, Palermo, Italy
- Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Mauro Carone
- UOC Pulmonology and Pulmonary Rehabilitation, Istituti Clinici Scientifici Maugeri, IRCCS di Bari, Bari, Italy
| | - Andrea Motta
- Institute of Biomolecular Chemistry, National Research Council, Pozzuoli, Italy
| | - Bruno Balbi
- Divisione di Pneumologia e Laboratorio di Citoimmunopatologia dell’Apparato Cardio Respiratorio, Istituti Clinici Scientifici Maugeri, IRCCS, Veruno, Italy
| | - Fabio L. M. Ricciardolo
- Dipartimento di Scienze Cliniche e Biologiche, Università di Torino, AOU San Luigi Gonzaga, Torino, Italy
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini morfologiche e funzionali (BIOMORF), Università degli studi di Messina, Italy
| | - Antonino Di Stefano
- Divisione di Pneumologia e Laboratorio di Citoimmunopatologia dell’Apparato Cardio Respiratorio, Istituti Clinici Scientifici Maugeri, IRCCS, Veruno, Italy
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Cardoso J, Ferreira AJ, Guimarães M, Oliveira AS, Simão P, Sucena M. Treatable Traits in COPD - A Proposed Approach. Int J Chron Obstruct Pulmon Dis 2021; 16:3167-3182. [PMID: 34824530 PMCID: PMC8609199 DOI: 10.2147/copd.s330817] [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: 07/29/2021] [Accepted: 11/03/2021] [Indexed: 12/20/2022] Open
Abstract
The well-recognized individual heterogeneity within COPD patients has led to a growing interest in greater personalization in the approach of these patients. Thus, the treatable traits strategy has been proposed as a further step towards precision medicine in the management of chronic airway disease, both in stable phase and acute exacerbations. The aim of this paper is to perform a critical review on the treatable traits strategy and propose a guide to approach COPD patients in the light of this new concept. An innovative stepwise approach is proposed - a multidisciplinary model based on two distinct phases, with the potential to be implemented in both primary care and hospital settings. The first phase is the initial and focused assessment of a selected subset of treatable traits, which should be addressed in all COPD patients in both settings (primary care and hospital). As some patients may present with advanced disease at diagnosis or may progress despite this initial treatment requiring a more specialized assessment, they should progress to a second phase, in which a broader approach is recommended. Beyond stable COPD, we explore how the treatable traits strategy may be applied to reduce the risk of future exacerbations and improve the management of COPD exacerbations. Since many treatable traits have already been related to exacerbation risk, the strategy proposed here represents an opportunity to be proactive. Although it still lacks prospective validation, we believe this is the way forward for the future of the COPD approach.
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Affiliation(s)
- João Cardoso
- Pulmonology Department, Centro Hospitalar Universitário de Lisboa Central, Lisboa, Portugal
- NOVA Medical School, Nova University Lisbon, Lisboa, Portugal
| | - António Jorge Ferreira
- Pulmonology Department, Centro Hospitalar Universitário de Coimbra, Coimbra, Portugal
- Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Miguel Guimarães
- Pulmonology Department, Centro Hospitalar Vila Nova de Gaia/Espinho EPE, Vila Nova de Gaia, Portugal
| | - Ana Sofia Oliveira
- Pulmonology Department, Centro Hospitalar Universitário de Lisboa Norte EPE, Lisboa, Portugal
| | - Paula Simão
- Pulmonology Department, Unidade Local de Saúde de Matosinhos EPE, Matosinhos, Portugal
| | - Maria Sucena
- Pulmonology Department, Centro Hospitalar Universitário do Porto EPE, Porto, Portugal
- Lung Function and Ventilation Unit, Centro Hospitalar Universitário do Porto EPE, Porto, Portugal
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Therapeutic approaches targeting molecular signaling pathways common to diabetes, lung diseases and cancer. Adv Drug Deliv Rev 2021; 178:113918. [PMID: 34375681 DOI: 10.1016/j.addr.2021.113918] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 07/23/2021] [Accepted: 08/05/2021] [Indexed: 12/12/2022]
Abstract
Diabetes mellitus (DM), is the most common metabolic disease and is characterized by sustained hyperglycemia. Accumulating evidences supports a strong association between DM and numerous lung diseases including chronic obstructive pulmonary disease (COPD), fibrosis, and lung cancer (LC). The global incidence of DM-associated lung disorders is rising and several ongoing studies, including clinical trials, aim to elucidate the molecular mechanisms linking DM with lung disorders, in particular LC. Several potential mechanisms, including hyperglycemia, hyperinsulinemia, glycation, inflammation, and hypoxia, are cited as plausible links between DM and LC. In addition, studies also propose a connection between the use of anti-diabetic medications and reduction in the incidence of LC. However, the exact cause for DM associated lung diseases especially LC is not clear and is an area under intense investigation. Herein, we review the biological links reported between DM and lung disorders with an emphasis on LC. Furthermore, we report common signaling pathways (eg: TGF-β, IL-6, HIF-1, PDGF) and miRNAs that are dysregulated in DM and LC and serve as molecular targets for therapy. Finally, we propose a nanomedicine based approach for delivering therapeutics (eg: IL-24 plasmid DNA, HuR siRNA) to disrupt signaling pathways common to DM and LC and thus potentially treat DM-associated LC. Finally, we conclude that the effective modulation of commonly regulated signaling pathways would help design novel therapeutic protocols for treating DM patients diagnosed with LC.
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Inhaled Corticosteroids and the Lung Microbiome in COPD. Biomedicines 2021; 9:biomedicines9101312. [PMID: 34680429 PMCID: PMC8533282 DOI: 10.3390/biomedicines9101312] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/17/2021] [Accepted: 09/22/2021] [Indexed: 12/16/2022] Open
Abstract
The Global Initiative for Chronic Obstructive Lung Disease 2021 Report recommends inhaled corticosteroid (ICS)-containing regimens as part of pharmacological treatment in patients with chronic obstructive lung disease (COPD) and frequent exacerbations, particularly with eosinophilic inflammation. However, real-world studies reveal overprescription of ICS in COPD, irrespective of disease presentation and inflammatory endotype, leading to increased risk of side effects, mainly respiratory infections. The optimal use of ICS in COPD therefore remains an area of intensive research, and additional biomarkers of benefit and risk are needed. Although the interplay between inflammation and infection in COPD is widely acknowledged, the role of the microbiome in shaping lower airway inflammation has only recently been explored. Next-generation sequencing has revealed that COPD disease progression and exacerbation frequency are associated with changes in the composition of the lung microbiome, and that the immunosuppressive effects of ICS can contribute to potentially deleterious airway microbiota changes by increasing bacterial load and the abundance of potentially pathogenic taxa such as Streptococcus and Haemophilus. Here, we explore the relationship between microbiome, inflammation, ICS use and disease phenotype. This relationship may inform the benefit:risk assessment of ICS use in patients with COPD and lead to more personalised pharmacological management.
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Links between Infections, Lung Cancer, and the Immune System. Int J Mol Sci 2021; 22:ijms22179394. [PMID: 34502312 PMCID: PMC8431665 DOI: 10.3390/ijms22179394] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/25/2021] [Accepted: 08/25/2021] [Indexed: 12/25/2022] Open
Abstract
Lung cancer is the leading disease of cancer-related deaths worldwide. Since the beginning of the 20th century, various infectious agents associated with lung cancer have been identified. The mechanisms that include systemic inflammatory pathways as effect of microbial persistence in the lung can secondarily promote the development of lung carcinogenesis. Chronic inflammation associated with lung-cancer infections is known to precede tumor development, and it has a strong effect on the response(s) to therapy. In fact, both viral and bacterial infections can activate inflammatory cells and inflammatory signaling pathways. In this review, an overview of critical findings of recent studies investigating associations between each of viral and bacterial pathogens and lung carcinoma is provided, with particular emphasis on how infectious organisms can interfere with oncogenic processes and all the way through immunity. Moreover, a discussion of the direct crosstalk between lung tumor development and inflammatory processes is also presented.
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Goolam Mahomed T, Peters R, Pretorius G, Goolam Mahomed A, Ueckermann V, Kock MM, Ehlers MM. Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome. BMC Microbiol 2021; 21:228. [PMID: 34407769 PMCID: PMC8371770 DOI: 10.1186/s12866-021-02288-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 07/29/2021] [Indexed: 12/23/2022] Open
Abstract
Background Targeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagenomics and IS-Pro methods for the ability to discern the microbial composition of the lung microbiome of COPD patients. Methods Spontaneously expectorated sputum specimens were collected from COPD patients. Bacterial DNA was extracted and used for targeted metagenomics and IS-Pro method. The analysis was performed using QIIME2 (targeted metagenomics) and IS-Pro software (IS-Pro method). Additionally, a laboratory cost per isolate and time analysis was performed for each method. Results Statistically significant differences were observed in alpha diversity when targeted metagenomics and IS-Pro methods’ data were compared using the Shannon diversity measure (p-value = 0.0006) but not with the Simpson diversity measure (p-value = 0.84). Distinct clusters with no overlap between the two technologies were observed for beta diversity. Targeted metagenomics had a lower relative abundance of phyla, such as the Proteobacteria, and higher relative abundance of phyla, such as Firmicutes when compared to the IS-Pro method. Haemophilus, Prevotella and Streptococcus were most prevalent genera across both methods. Targeted metagenomics classified 23 % (144/631) of OTUs to a species level, whereas IS-Pro method classified 86 % (55/64) of OTUs to a species level. However, unclassified OTUs accounted for a higher relative abundance when using the IS-Pro method (35 %) compared to targeted metagenomics (5 %). The two methods performed comparably in terms of cost and time; however, the IS-Pro method was more user-friendly. Conclusions It is essential to understand the value of different methods for characterisation of the microbiome. Targeted metagenomics and IS-Pro methods showed differences in ability in identifying and characterising OTUs, diversity and microbial composition of the lung microbiome. The IS-Pro method might miss relevant species and could inflate the abundance of Proteobacteria. However, the IS-Pro kit identified most of the important lung pathogens, such as Burkholderia and Pseudomonas and may work in a more diagnostics-orientated setting. Both methods were comparable in terms of cost and time; however, the IS-Pro method was easier to use. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02288-x.
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Affiliation(s)
- T Goolam Mahomed
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Rph Peters
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.,CAPHRI School for Public Health & Primary Care, Department of Medical Microbiology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | | | | | - V Ueckermann
- Department of Internal Medicine, University of Pretoria, Pretoria, South Africa
| | - M M Kock
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.,Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Tshwane, South Africa
| | - M M Ehlers
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa. .,Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service, Tshwane, South Africa.
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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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Segal LN, Huang YJ. Crossing Kingdoms: Host-Microbial Endotyping and the Quest to Understand Treatable Traits in Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2021; 203:1447-1448. [PMID: 33651664 PMCID: PMC8483227 DOI: 10.1164/rccm.202101-0169ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine New York University School of Medicine, New York New York
| | - Yvonne J Huang
- Division of Pulmonary and Critical Care Medicine University of Michigan Ann Arbor, Michigan
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48
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Szalontai K, Gémes N, Furák J, Varga T, Neuperger P, Balog JÁ, Puskás LG, Szebeni GJ. Chronic Obstructive Pulmonary Disease: Epidemiology, Biomarkers, and Paving the Way to Lung Cancer. J Clin Med 2021; 10:jcm10132889. [PMID: 34209651 PMCID: PMC8268950 DOI: 10.3390/jcm10132889] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/24/2021] [Accepted: 06/24/2021] [Indexed: 12/16/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD), the frequently fatal pathology of the respiratory tract, accounts for half a billion cases globally. COPD manifests via chronic inflammatory response to irritants, frequently to tobacco smoke. The progression of COPD from early onset to advanced disease leads to the loss of the alveolar wall, pulmonary hypertension, and fibrosis of the respiratory epithelium. Here, we focus on the epidemiology, progression, and biomarkers of COPD with a particular connection to lung cancer. Dissecting the cellular and molecular players in the progression of the disease, we aim to shed light on the role of smoking, which is responsible for the disease, or at least for the more severe symptoms and worse patient outcomes. We summarize the inflammatory conditions, as well as the role of EMT and fibroblasts in establishing a cancer-prone microenvironment, i.e., the soil for ‘COPD-derived’ lung cancer. We highlight that the major health problem of COPD can be alleviated via smoking cessation, early diagnosis, and abandonment of the usage of biomass fuels on a global basis.
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Affiliation(s)
- Klára Szalontai
- Csongrád County Hospital of Chest Diseases, Alkotmány u. 36., H6772 Deszk, Hungary;
| | - Nikolett Gémes
- Laboratory of Functional Genomics, Biological Research Centre, Temesvári krt. 62., H6726 Szeged, Hungary; (N.G.); (T.V.); (P.N.); (J.Á.B.); (L.G.P.)
- PhD School in Biology, University of Szeged, H6726 Szeged, Hungary
| | - József Furák
- Department of Surgery, University of Szeged, Semmelweis u. 8., H6725 Szeged, Hungary;
| | - Tünde Varga
- Laboratory of Functional Genomics, Biological Research Centre, Temesvári krt. 62., H6726 Szeged, Hungary; (N.G.); (T.V.); (P.N.); (J.Á.B.); (L.G.P.)
| | - Patrícia Neuperger
- Laboratory of Functional Genomics, Biological Research Centre, Temesvári krt. 62., H6726 Szeged, Hungary; (N.G.); (T.V.); (P.N.); (J.Á.B.); (L.G.P.)
- PhD School in Biology, University of Szeged, H6726 Szeged, Hungary
| | - József Á. Balog
- Laboratory of Functional Genomics, Biological Research Centre, Temesvári krt. 62., H6726 Szeged, Hungary; (N.G.); (T.V.); (P.N.); (J.Á.B.); (L.G.P.)
- PhD School in Biology, University of Szeged, H6726 Szeged, Hungary
| | - László G. Puskás
- Laboratory of Functional Genomics, Biological Research Centre, Temesvári krt. 62., H6726 Szeged, Hungary; (N.G.); (T.V.); (P.N.); (J.Á.B.); (L.G.P.)
- Avicor Ltd. Alsó Kikötő sor 11/D, H6726 Szeged, Hungary
| | - Gábor J. Szebeni
- Laboratory of Functional Genomics, Biological Research Centre, Temesvári krt. 62., H6726 Szeged, Hungary; (N.G.); (T.V.); (P.N.); (J.Á.B.); (L.G.P.)
- Department of Physiology, Anatomy and Neuroscience, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H6726 Szeged, Hungary
- CS-Smartlab Devices Ltd., Ady E. u. 14., H7761 Kozármisleny, Hungary
- Correspondence:
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49
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Linfield DT, Gao N, Raduka A, Harford TJ, Piedimonte G, Rezaee F. RSV attenuates epithelial cell restitution by inhibiting actin cytoskeleton-dependent cell migration. Am J Physiol Lung Cell Mol Physiol 2021; 321:L189-L203. [PMID: 34010080 DOI: 10.1152/ajplung.00118.2021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The airway epithelium's ability to repair itself after injury, known as epithelial restitution, is an essential mechanism enabling the respiratory tract's normal functions. Respiratory Syncytial Virus (RSV) is the leading cause of lower respiratory tract infections worldwide. We sought to determine whether RSV delays the airway epithelium wound repair process both in vitro and in vivo. We found that RSV infection attenuated epithelial cell migration, a step in wound repair, promoted stress fiber formation, and mediated assembly of large focal adhesions (FA). Inhibition of Rho kinase (ROCK), a master regulator of actin function, reversed these effects. There was increased RhoA and phospho-myosin light chain (pMLC2) following RSV infection. In vivo, mice were intraperitoneally inoculated with naphthalene to induce lung injury, followed by RSV infection. RSV infection delayed re-epithelialization. There were increased concentrations of pMLC2 in day 7 naphthalene plus RSV animals which normalized by day 14. This study suggests a key mechanism by which RSV infection delays wound healing.
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Affiliation(s)
| | - Nannan Gao
- Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, United States
| | - Andjela Raduka
- Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, United States
| | - Terri J Harford
- Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, United States
| | | | - Fariba Rezaee
- Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, United States.,Center for Pediatric Pulmonology, Cleveland Clinic Children's, Cleveland, Ohio, United States
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50
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Chiu YC, Lee SW, Liu CW, Lin RCJ, Huang YC, Lan TY, Wu LSH. Comprehensive profiling of the gut microbiota in patients with chronic obstructive pulmonary disease of varying severity. PLoS One 2021; 16:e0249944. [PMID: 33836012 PMCID: PMC8034725 DOI: 10.1371/journal.pone.0249944] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 03/27/2021] [Indexed: 12/23/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a chronic respiratory disease that reduces lung and respiratory function, with a high mortality rate. Severe and acute deterioration of COPD can easily lead to respiratory failure, resulting in personal, social, and medical burden. Recent studies have shown a high correlation between the gut microbiota and lung inflammation. In this study, we investigated the relationship between gut microbiota and COPD severity. A total of 60 COPD patients with varying severity according to GOLD guidelines were enrolled in this study. DNA was extracted from patients' stool and 16S rRNA data analysis conducted using high-throughput sequencing followed by bioinformatics analysis. The richness of the gut microbiota was not associated with COPD severity. The gut microbiome is more similar in stage 1 and 2 COPD than stage 3+4 COPD. Fusobacterium and Aerococcus were more abundant in stage 3+4 COPD. Ruminococcaceae NK4A214 group and Lachnoclostridium were less abundant in stage 2-4, and Tyzzerella 4 and Dialister were less abundant in stage 1. However, the abundance of a Bacteroides was associated with blood eosinophils and lung function. This study suggests that no distinctive gut microbiota pattern is associated with the severity of COPD. The gut microbiome could affect COPD by gut inflammation shaping the host immune system.
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Affiliation(s)
- Yu-Chi Chiu
- Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
- Institute of Hospital & Health Care Administration, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shih-Wei Lee
- Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
| | - Chi-Wei Liu
- Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
| | - Rebecca Chou-Jui Lin
- Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
| | - Yung-Chia Huang
- Department of Internal Medicine, Taoyuan General Hospital, Ministry of Health and Welfare, Taoyuan, Taiwan
| | - Tzuo-Yun Lan
- Institute of Hospital & Health Care Administration, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Lawrence Shih-Hsin Wu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan
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