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Nickerson R, Thornton CS, Johnston B, Lee AHY, Cheng Z. Pseudomonas aeruginosa in chronic lung disease: untangling the dysregulated host immune response. Front Immunol 2024; 15:1405376. [PMID: 39015565 PMCID: PMC11250099 DOI: 10.3389/fimmu.2024.1405376] [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: 03/22/2024] [Accepted: 06/14/2024] [Indexed: 07/18/2024] Open
Abstract
Pseudomonas aeruginosa is a highly adaptable opportunistic pathogen capable of exploiting barriers and immune defects to cause chronic lung infections in conditions such as cystic fibrosis. In these contexts, host immune responses are ineffective at clearing persistent bacterial infection, instead driving a cycle of inflammatory lung damage. This review outlines key components of the host immune response to chronic P. aeruginosa infection within the lung, beginning with initial pathogen recognition, followed by a robust yet maladaptive innate immune response, and an ineffective adaptive immune response that propagates lung damage while permitting bacterial persistence. Untangling the interplay between host immunity and chronic P. aeruginosa infection will allow for the development and refinement of strategies to modulate immune-associated lung damage and potentiate the immune system to combat chronic infection more effectively.
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Affiliation(s)
- Rhea Nickerson
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Christina S. Thornton
- Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Brent Johnston
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Amy H. Y. Lee
- Department of Molecular Biology and Biochemistry, Faculty of Science, Simon Fraser University, Burnaby, BC, Canada
| | - Zhenyu Cheng
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
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2
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Siegel NA, Jimenez MT, Rocha CS, Rolston M, Dandekar S, Solnick JV, Miller LA. Helicobacter pylori infection in infant rhesus macaque monkeys is associated with an altered lung and oral microbiome. Sci Rep 2024; 14:9998. [PMID: 38693196 PMCID: PMC11063185 DOI: 10.1038/s41598-024-59514-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 04/11/2024] [Indexed: 05/03/2024] Open
Abstract
It is estimated that more than half of the world population has been infected with Helicobacter pylori. Most newly acquired H. pylori infections occur in children before 10 years of age. We hypothesized that early life H. pylori infection could influence the composition of the microbiome at mucosal sites distant to the stomach. To test this hypothesis, we utilized the infant rhesus macaque monkey as an animal model of natural H. pylori colonization to determine the impact of infection on the lung and oral microbiome during a window of postnatal development. From a cohort of 4-7 month-old monkeys, gastric biopsy cultures identified 44% of animals infected by H. pylori. 16S ribosomal RNA gene sequencing of lung washes and buccal swabs from animals showed distinct profiles for the lung and oral microbiome, independent of H. pylori infection. In order of relative abundance, the lung microbiome was dominated by the phyla Proteobacteria, Firmicutes, Bacteroidota, Fusobacteriota, Campilobacterota and Actinobacteriota while the oral microbiome was dominated by Proteobacteria, Firmicutes, Bacteroidota, and Fusobacteriota. In comparison to the oral cavity, the lung was composed of more genera and species that significantly differed by H. pylori status, with a total of 6 genera and species that were increased in H. pylori negative infant monkey lungs. Lung, but not plasma IL-8 concentration was also associated with gastric H. pylori load and lung microbial composition. We found the infant rhesus macaque monkey lung harbors a microbiome signature that is distinct from that of the oral cavity during postnatal development. Gastric H. pylori colonization and IL-8 protein were linked to the composition of microbial communities in the lung and oral cavity. Collectively, these findings provide insight into how H. pylori infection might contribute to the gut-lung axis during early childhood and modulate future respiratory health.
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Affiliation(s)
- Noah A Siegel
- California National Primate Research Center, University of California Davis, Davis, CA, USA
| | - Monica T Jimenez
- California National Primate Research Center, University of California Davis, Davis, CA, USA
| | - Clarissa Santos Rocha
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, USA
| | - Matthew Rolston
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, USA
| | - Satya Dandekar
- California National Primate Research Center, University of California Davis, Davis, CA, USA
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, USA
| | - Jay V Solnick
- California National Primate Research Center, University of California Davis, Davis, CA, USA
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, Davis, CA, USA
| | - Lisa A Miller
- California National Primate Research Center, University of California Davis, Davis, CA, USA.
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California Davis, Davis, CA, USA.
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3
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O’Toole GA. We have a community problem. J Bacteriol 2024; 206:e0007324. [PMID: 38529952 PMCID: PMC11025320 DOI: 10.1128/jb.00073-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Affiliation(s)
- George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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4
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McDermott G, Walsh A, Crispie F, Frost S, Greally P, Cotter PD, O’Sullivan O, Renwick J. Insights into the Adolescent Cystic Fibrosis Airway Microbiome Using Shotgun Metagenomics. Int J Mol Sci 2024; 25:3893. [PMID: 38612702 PMCID: PMC11011389 DOI: 10.3390/ijms25073893] [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: 03/01/2024] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
Cystic fibrosis (CF) is an inherited genetic disorder which manifests primarily in airway disease. Recent advances in molecular technologies have unearthed the diverse polymicrobial nature of the CF airway. Numerous studies have characterised the genus-level composition of this airway community using targeted 16S rDNA sequencing. Here, we employed whole-genome shotgun metagenomics to provide a more comprehensive understanding of the early CF airway microbiome. We collected 48 sputum samples from 11 adolescents and children with CF over a 12-month period and performed shotgun metagenomics on the Illumina NextSeq platform. We carried out functional and taxonomic analysis of the lung microbiome at the species and strain levels. Correlations between microbial diversity measures and independent demographic and clinical variables were performed. Shotgun metagenomics detected a greater diversity of bacteria than culture-based methods. A large proportion of the top 25 most-dominant species were anaerobes. Samples dominated by Staphylococcus aureus and Prevotella melaninogenica had significantly higher microbiome diversity, while no CF pathogen was associated with reduced microbial diversity. There was a diverse resistome present in all samples in this study, with 57.8% agreement between shotgun metagenomics and culture-based methods for detection of resistance. Pathogenic sequence types (STs) of S. aureus, Pseudomonas aeruginosa, Haemophilus influenzae and Stenotrophomonas maltophilia were observed to persist in young CF patients, while STs of S. aureus were both persistent and shared between patients. This study provides new insight into the temporal changes in strain level composition of the microbiome and the landscape of the resistome in young people with CF. Shotgun metagenomics could provide a very useful one-stop assay for detecting pathogens, emergence of resistance and conversion to persistent colonisation in early CF disease.
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Affiliation(s)
- Gillian McDermott
- Trinity Centre for Health Science, Clinical Microbiology Department, School of Medicine, Faculty of Health Science, Trinity College Dublin, Tallaght University Hospital, D24 NR0A Dublin, Ireland;
| | - Aaron Walsh
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Co Cork, Ireland; (A.W.); (F.C.); (P.D.C.); (O.O.)
- APC Microbiome Ireland, University College Cork, T12 R229 Co Cork, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Co Cork, Ireland; (A.W.); (F.C.); (P.D.C.); (O.O.)
- APC Microbiome Ireland, University College Cork, T12 R229 Co Cork, Ireland
| | - Susanna Frost
- Tallaght University Hospital, Tallaght, D24 NR0 Dublin, Ireland (P.G.)
| | - Peter Greally
- Tallaght University Hospital, Tallaght, D24 NR0 Dublin, Ireland (P.G.)
- Hermitage Medical Clinic, Lucan, D20 W722 Dublin, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Co Cork, Ireland; (A.W.); (F.C.); (P.D.C.); (O.O.)
- APC Microbiome Ireland, University College Cork, T12 R229 Co Cork, Ireland
| | - Orla O’Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, P61 C996 Co Cork, Ireland; (A.W.); (F.C.); (P.D.C.); (O.O.)
- APC Microbiome Ireland, University College Cork, T12 R229 Co Cork, Ireland
| | - Julie Renwick
- Trinity Centre for Health Science, Clinical Microbiology Department, School of Medicine, Faculty of Health Science, Trinity College Dublin, Tallaght University Hospital, D24 NR0A Dublin, Ireland;
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5
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Rosenboom I, Thavarasa A, Richardson H, Long MB, Wiehlmann L, Davenport CF, Shoemark A, Chalmers JD, Tümmler B. Sputum metagenomics of people with bronchiectasis. ERJ Open Res 2024; 10:01008-2023. [PMID: 38444657 PMCID: PMC10910388 DOI: 10.1183/23120541.01008-2023] [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: 12/13/2023] [Accepted: 01/08/2024] [Indexed: 03/07/2024] Open
Abstract
Background The microbiota in the sputum of people with bronchiectasis has repeatedly been investigated in cohorts of different geographic origin, but so far has not been studied to the species level in comparison to control populations including healthy adults and smokers without lung disease. Methods The microbial metagenome from sputa of 101 European Bronchiectasis Registry (EMBARC) study participants was examined by using whole-genome shotgun sequencing. Results Our analysis of the metagenome of people with bronchiectasis revealed four clusters characterised by a predominance of Haemophilus influenzae, Pseudomonas aeruginosa or polymicrobial communities with varying compositions of nonpathogenic commensals and opportunistic pathogens. The metagenomes of the severely affected patients showed individual profiles characterised by low alpha diversity. Importantly, nearly 50% of patients with severe disease were grouped in a cluster characterised by commensals. Comparisons with the sputum metagenomes of healthy smokers and healthy nonsmokers revealed a gradient of depletion of taxa in bronchiectasis, most often Neisseria subflava, Fusobacterium periodonticum and Eubacterium sulci. Conclusion The gradient of depletion of commensal taxa found in healthy airways is a key feature of bronchiectasis associated with disease severity.
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Affiliation(s)
- Ilona Rosenboom
- Department of Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Ajith Thavarasa
- Department of Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Hollian Richardson
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - Merete B. Long
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, Hannover, Germany
| | | | - Amelia Shoemark
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - James D. Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Dundee, UK
| | - Burkhard Tümmler
- Department of Paediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), German Centre for Lung Research, Hannover, Germany
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6
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Cauwenberghs E, De Boeck I, Spacova I, Van Tente I, Bastiaenssen J, Lammertyn E, Verhulst S, Van Hoorenbeeck K, Lebeer S. Positioning the preventive potential of microbiome treatments for cystic fibrosis in the context of current therapies. Cell Rep Med 2024; 5:101371. [PMID: 38232705 PMCID: PMC10829789 DOI: 10.1016/j.xcrm.2023.101371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/24/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
Antibiotics and cystic fibrosis transmembrane conductance regulator (CFTR) modulators play a pivotal role in cystic fibrosis (CF) treatment, but both have limitations. Antibiotics are linked to antibiotic resistance and disruption of the airway microbiome, while CFTR modulators are not widely accessible, and structural lung damage and pathogen overgrowth still occur. Complementary strategies that can beneficially modulate the airway microbiome in a preventive way are highly needed. This could be mediated via oral probiotics, which have shown some improvement of lung function and reduction of airway infections and exacerbations, as a cost-effective approach. However, recent data suggest that specific and locally administered probiotics in the respiratory tract might be a more targeted approach to prevent pathogen outgrowth in the lower airways. This review aims to summarize the current knowledge on the CF airway microbiome and possibilities of microbiome treatments to prevent bacterial and/or viral infections and position them in the context of current CF therapies.
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Affiliation(s)
- Eline Cauwenberghs
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Ilke De Boeck
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Irina Spacova
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Ilke Van Tente
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Joke Bastiaenssen
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Elise Lammertyn
- Belgian CF Association, Driebruggenstraat 124, 1160 Brussels, Belgium; Cystic Fibrosis Europe, Driebruggenstraat 124, 1160 Brussels, Belgium
| | - Stijn Verhulst
- University of Antwerp, Laboratory of Experimental Medicine and Pediatrics, Universiteitsplein 1, 2610 Wilrijk, Belgium; Antwerp University Hospital, Department of Pediatric Pulmonology, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Kim Van Hoorenbeeck
- University of Antwerp, Laboratory of Experimental Medicine and Pediatrics, Universiteitsplein 1, 2610 Wilrijk, Belgium; Antwerp University Hospital, Department of Pediatric Pulmonology, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Sarah Lebeer
- University of Antwerp, Department of Bioscience Engineering, Groenenborgerlaan 171, 2020 Antwerp, Belgium.
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7
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Martin C, Guzior DV, Gonzalez CT, Okros M, Mielke J, Padillo L, Querido G, Gil M, Thomas R, McClelland M, Conrad D, Widder S, Quinn RA. Longitudinal microbial and molecular dynamics in the cystic fibrosis lung after Elexacaftor-Tezacaftor-Ivacaftor therapy. Respir Res 2023; 24:317. [PMID: 38104128 PMCID: PMC10725582 DOI: 10.1186/s12931-023-02630-z] [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: 10/18/2023] [Accepted: 12/04/2023] [Indexed: 12/19/2023] Open
Abstract
BACKGROUND Cystic fibrosis (CF) is a genetic disorder causing poor mucociliary clearance in the airways and subsequent respiratory infection. The recently approved triple therapy Elexacaftor-Tezacaftor-Ivacaftor (ETI) has significantly improved lung function and decreased airway infection in persons with CF (pwCF). This improvement has been shown to occur rapidly, within the first few weeks of treatment. The effects of longer term ETI therapy on lung infection dynamics, however, remain mostly unknown. RESULTS Here, we applied 16S rRNA gene amplicon sequencing, untargeted metabolomics, and neutral models to high-resolution, longitudinally collected sputum samples from pwCF on ETI therapy (162 samples, 7 patients) and compared to similarly collected data set from pwCF not taking ETI (630 samples, 9 patients). Because ETI reduces sputum production, samples were collected in freezers provided in the subject's homes at least 3 months after first taking ETI, with those on ETI collecting a sample approximately weekly. The lung function (%ppFEV1) of those in our longitudinal cohort significantly improved after ETI (6.91, SD = 7.74), indicating our study cohort was responsive to ETI. The daily variation of alpha- and beta-diversity of both the microbiome and metabolome was higher for those on ETI, reflecting a more dynamic microbial community and chemical environment during treatment. Four of the seven subjects on ETI were persistently infected with Pseudomonas or Burkholderia in their sputum throughout the sampling period while the total bacterial load significantly decreased with time (R = - 0.42, p = 0.01) in only one subject. The microbiome and metabolome dynamics on ETI were personalized, where some subjects had a progressive change with time on therapy, whereas others had no association with time on treatment. To further classify the augmented variance of the CF microbiome under therapy, we fit the microbiome data to a Hubbell neutral dynamics model in a patient-stratified manner and found that the subjects on ETI had better fit to a neutral model. CONCLUSION This study shows that the longitudinal microbiology and chemistry in airway secretions from subjects on ETI has become more dynamic and neutral and that after the initial improvement in lung function, many are still persistently infected with CF pathogens.
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Affiliation(s)
- Christian Martin
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Douglas V Guzior
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Cely T Gonzalez
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Maxwell Okros
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Jenna Mielke
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lienwil Padillo
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gabriel Querido
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Marissa Gil
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ryan Thomas
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI, USA
| | | | - Doug Conrad
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Stefanie Widder
- Department of Medicine, Research Division Infection Biology, Medical University of Vienna, Vienna, Austria
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
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Czarnecka-Chrebelska KH, Kordiak J, Brzeziańska-Lasota E, Pastuszak-Lewandoska D. Respiratory Tract Oncobiome in Lung Carcinogenesis: Where Are We Now? Cancers (Basel) 2023; 15:4935. [PMID: 37894302 PMCID: PMC10605430 DOI: 10.3390/cancers15204935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/02/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
The importance of microbiota in developing and treating diseases, including lung cancer (LC), is becoming increasingly recognized. Studies have shown differences in microorganism populations in the upper and lower respiratory tracts of patients with lung cancer compared to healthy individuals, indicating a link between dysbiosis and lung cancer. However, it is not only important to identify "which bacteria are present" but also to understand "how" they affect lung carcinogenesis. The interactions between the host and lung microbiota are complex, and our knowledge of this relationship is limited. This review presents research findings on the bacterial lung microbiota and discusses the mechanisms by which lung-dwelling microorganisms may directly or indirectly contribute to the development of lung cancer. These mechanisms include influences on the host immune system regulation and the local immune microenvironment, the regulation of oncogenic signaling pathways in epithelial cells (causing cell cycle disorders, mutagenesis, and DNA damage), and lastly, the MAMPs-mediated path involving the effects of bacteriocins, TLRs signaling induction, and TNF release. A better understanding of lung microbiota's role in lung tumor pathology could lead to identifying new diagnostic and therapeutic biomarkers and developing personalized therapeutic management for lung cancer patients.
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Affiliation(s)
| | - Jacek Kordiak
- Department of Thoracic, General and Oncological Surgery, Medical University of Lodz, 90-151 Lodz, Poland
| | - Ewa Brzeziańska-Lasota
- Department of Biomedicine and Genetics, Medical University of Lodz, Mazowiecka 5, 92-215 Lodz, Poland
| | - Dorota Pastuszak-Lewandoska
- Department of Microbiology and Laboratory Medical Immunology, Medical University of Lodz, Pomorska 251, 90-151 Lodz, Poland;
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9
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Martin C, Guzior DV, Gonzalez CT, Okros M, Mielke J, Padillo L, Querido G, Gil M, Thomas R, McClelland M, Conrad D, Widder S, Quinn RA. Longitudinal Microbial and Molecular Dynamics in the Cystic Fibrosis Lung after Elexacaftor-Tezacaftor-Ivacaftor therapy. RESEARCH SQUARE 2023:rs.3.rs-3356170. [PMID: 37841851 PMCID: PMC10571617 DOI: 10.21203/rs.3.rs-3356170/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Background Cystic fibrosis (CF) is a genetic disorder causing poor mucociliary clearance in the airways and subsequent respiratory infection. The recently approved triple therapy Elexacaftor-Tezacaftor-Ivacaftor (ETI) has significantly improved the lung function and decreased airway infection of persons with CF (pwCF). This improvement has been shown to occur rapidly, within the first few weeks of treatment. The effects of longer term ETI therapy on lung infection dynamics, however, remains mostly unknown. Results Here, we applied 16S rRNA gene amplicon sequencing, untargeted metabolomics, and neutral models to high-resolution, longitudinally collected sputum samples from pwCF on ETI therapy (162 samples, 7 patients) and compared to similarly collected data set of CF subjects not taking ETI (630 samples, 9 patients). Because ETI reduces sputum production, samples were collected in freezers provided in the subject's homes at least 3 months after first taking ETI, with those on ETI collecting a sample approximately weekly. The lung function (%ppFEV1) of those in our longitudinal cohort significantly improved after ETI (6.91, SD = 7.74), indicating our study cohort was responsive to ETI. The daily variation of alpha- and beta-diversity of both the microbiome and metabolome was higher for those on ETI, reflecting a more dynamic microbial community and chemical environment during treatment. Four of the seven subjects on ETI were persistently infected with Pseudomonas or Burkholderia in their sputum throughout the sampling period. The microbiome and metabolome dynamics on ETI were personalized, where some subjects had a progressive change with time on therapy, whereas others had no association with time on treatment. To further classify the augmented variance of the CF microbiome under therapy, we fit the microbiome data to a Hubbell neutral dynamics model in a patient-stratified manner and found that the subjects on ETI had better fit to a neutral model. Conclusion This study shows that the longitudinal microbiology and chemistry in airway secretions from subjects on ETI has become more dynamic and neutral, and that after the initial improvement in lung function, many are still persistently infected with CF pathogens.
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10
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Siegel NA, Jimenez MT, Rocha CS, Rolston M, Dandekar S, Solnick JV, Miller LA. Helicobacter pylori Infection in Infant Rhesus Macaque Monkeys is Associated with an Altered Lung and Oral Microbiome. RESEARCH SQUARE 2023:rs.3.rs-3225953. [PMID: 37609264 PMCID: PMC10441512 DOI: 10.21203/rs.3.rs-3225953/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Background It is estimated that more than half of the world population has been infected with Helicobacter pylori. Most newly acquired H. pylori infections occur in children before 10 years of age. We hypothesized that early life H. pylori infection could influence the composition of the microbiome at mucosal sites distant to the stomach. To test this hypothesis, we utilized the infant rhesus macaque monkey as an animal model of natural H. pylori colonization to determine the impact of infection on the lung and oral microbiome during a window of postnatal development. Results From a cohort of 4-7-month-old monkeys, gastric biopsy cultures identified 44% of animals infected by H. pylori. 16S ribosomal RNA gene sequencing of lung washes and buccal swabs from animals showed distinct profiles for the lung and oral microbiome, independent of H. pylori infection. In relative order of abundance, the lung microbiome was dominated by the phyla Proteobacteria, Firmicutes, Bacteroidota, Fusobacteriota, Campilobacterota and Actinobacteriota while the oral microbiome was dominated by Proteobacteria, Firmicutes, Bacteroidota, and Fusobacteriota. Relative to the oral cavity, the lung was composed of more genera and species that significantly differed by H. pylori status, with a total of 6 genera and species that were increased in H. pylori negative infant monkey lungs. Lung, but not plasma IL-8 concentration was also associated with gastric H. pylori load and lung microbial composition. Conclusions We found the infant rhesus macaque monkey lung harbors a microbiome signature that is distinct from that of the oral cavity during postnatal development. Gastric H. pylori colonization and IL-8 protein were linked to the composition of microbial communities in the lung and oral cavity. Collectively, these findings provide insight into how H. pylori infection might contribute to the gut-lung axis during early childhood and modulate future respiratory health.
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