51
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The Airway Microbiome: Present and Future Applications. Arch Bronconeumol 2022; 58:8-10. [DOI: 10.1016/j.arbres.2021.08.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 08/03/2021] [Indexed: 01/07/2023]
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52
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Pantaleón García J, Hinkle KJ, Falkowski NR, Evans SE, Dickson RP. Response to "Response of Lung Microbiota to Changes of Pulmonary Innate Immunity Under Healthy Conditions". Am J Respir Crit Care Med 2021; 205:477-479. [PMID: 34797744 PMCID: PMC8886949 DOI: 10.1164/rccm.202110-2257le] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Jezreel Pantaleón García
- The University of Texas MD Anderson Cancer Center, 4002, Pulmonary Medicine, Houston, Texas, United States
| | - Kevin J Hinkle
- University of Michigan Health System, Internal Medicine, Ann Arbor, Michigan, United States
| | - Nicole R Falkowski
- University of Michigan Health System, Internal Medicine, Ann Arbor, Michigan, United States
| | - Scott E Evans
- University of Texas-M.D. Anderson Cancer Center, Pulmonary Medicine, Houston, Texas, United States
| | - Robert P Dickson
- University of Michigan Health System, Internal Medicine, Ann Arbor, Michigan, United States;
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53
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The Lung Microbiome during Health and Disease. Int J Mol Sci 2021; 22:ijms221910872. [PMID: 34639212 PMCID: PMC8509400 DOI: 10.3390/ijms221910872] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 12/24/2022] Open
Abstract
Healthy human lungs have traditionally been considered to be a sterile organ. However, culture-independent molecular techniques have reported that large numbers of microbes coexist in the lung and airways. The lungs harbor diverse microbial composition that are undetected by previous approaches. Many studies have found significant differences in microbial composition between during health and respiratory disease. The lung microbiome is likely to not only influence susceptibility or causes of diseases but be affected by disease activities or responses to treatment. Although lung microbiome research has some limitations from study design to reporting, it can add further dimensionality to host-microbe interactions. Moreover, there is a possibility that extending understanding to the lung microbiome with new multiple omics approaches would be useful for developing both diagnostic and prognostic biomarkers for respiratory diseases in clinical settings.
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54
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Rigauts C, Aizawa J, Taylor S, Rogers GB, Govaerts M, Cos P, Ostyn L, Sims S, Vandeplassche E, Sze M, Dondelinger Y, Vereecke L, Van Acker H, Simpson JL, Burr L, Willems A, Tunney MM, Cigana C, Bragonzi A, Coenye T, Crabbé A. Rothia mucilaginosa is an anti-inflammatory bacterium in the respiratory tract of patients with chronic lung disease. Eur Respir J 2021; 59:13993003.01293-2021. [PMID: 34588194 PMCID: PMC9068977 DOI: 10.1183/13993003.01293-2021] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/10/2021] [Indexed: 11/24/2022]
Abstract
Background Chronic airway inflammation is the main driver of pathogenesis in respiratory diseases such as severe asthma, chronic obstructive pulmonary disease, cystic fibrosis (CF) and bronchiectasis. While the role of common pathogens in airway inflammation is widely recognised, the influence of other microbiota members is still poorly understood. Methods We hypothesised that the lung microbiota contains bacteria with immunomodulatory activity which modulate net levels of immune activation by key respiratory pathogens. Therefore, we assessed the immunomodulatory effect of several members of the lung microbiota frequently reported as present in CF lower respiratory tract samples. Results We show that Rothia mucilaginosa, a common resident of the oral cavity that is also often detectable in the lower airways in chronic disease, has an inhibitory effect on pathogen- or lipopolysaccharide-induced pro-inflammatory responses, in vitro (three-dimensional cell culture model) and in vivo (mouse model). Furthermore, in a cohort of adults with bronchiectasis, the abundance of Rothia species was negatively correlated with pro-inflammatory markers (interleukin (IL)-8 and IL-1β) and matrix metalloproteinase (MMP)-1, MMP-8 and MMP-9 in sputum. Mechanistic studies revealed that R. mucilaginosa inhibits NF-κB pathway activation by reducing the phosphorylation of IκBα and consequently the expression of NF-κB target genes. Conclusions These findings indicate that the presence of R. mucilaginosa in the lower airways potentially mitigates inflammation, which could in turn influence the severity and progression of chronic respiratory disorders. A commensal bacterium of the lower airways, Rothia mucilaginosa, inhibits inflammation by NF-κB pathway inactivation. R. mucilaginosa abundance inversely correlates with sputum pro-inflammatory markers in chronic lung disease, indicating a beneficial role.https://bit.ly/3lNT9th
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Affiliation(s)
- Charlotte Rigauts
- Laboratory of Pharmaceutical Microbiology, Ghent University, Gent, Belgium
| | - Juliana Aizawa
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Wilrijk, Belgium
| | - Steven Taylor
- Microbiome and Host Health Programme, the South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia.,The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Geraint B Rogers
- Microbiome and Host Health Programme, the South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia.,The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Matthias Govaerts
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Wilrijk, Belgium
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene, University of Antwerp, Wilrijk, Belgium
| | - Lisa Ostyn
- Laboratory of Pharmaceutical Microbiology, Ghent University, Gent, Belgium
| | - Sarah Sims
- Microbiome and Host Health Programme, the South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia.,The SAHMRI Microbiome Research Laboratory, School of Medicine, Flinders University, Adelaide, South Australia, Australia
| | - Eva Vandeplassche
- Laboratory of Pharmaceutical Microbiology, Ghent University, Gent, Belgium
| | - Mozes Sze
- VIB Center for Inflammation Research, Ghent, Belgium
| | - Yves Dondelinger
- VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Gent, Belgium
| | - Lars Vereecke
- VIB Center for Inflammation Research, Ghent, Belgium.,Department of Rheumatology, Ghent University, Gent, Belgium
| | - Heleen Van Acker
- Laboratory of Pharmaceutical Microbiology, Ghent University, Gent, Belgium
| | - Jodie L Simpson
- Faculty of Health and Medicine, Priority Research Centre for Healthy Lungs, University of Newcastle, Callaghan, New South Wales, Australia
| | - Lucy Burr
- Department of Respiratory Medicine, Mater Health Services, South Brisbane, QLD, Australia.,Mater Research - University of Queensland, Aubigny Place, South Brisbane, QLD, Australia
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Michael M Tunney
- School of Pharmacy, Queen's University Belfast, Belfast, United Kingdom
| | - Cristina Cigana
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandra Bragonzi
- Infections and Cystic Fibrosis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Gent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Gent, Belgium
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Abstract
The healthy lung was long thought of as sterile, but recent advances using molecular sequencing approaches have detected bacteria at low levels. Healthy lung bacteria largely reflect communities present in the upper respiratory tract that enter the lung via microaspiration, which is balanced by mechanical and immune clearance and likely involves limited local replication. The nature and dynamics of the lung microbiome, therefore, differ from those of ecological niches with robust self-sustaining microbial communities. Aberrant populations (dysbiosis) have been demonstrated in many pulmonary diseases not traditionally considered microbial in origin, and potential pathways of microbe-host crosstalk are emerging. The question now is whether and how dysbiotic microbiota contribute to initiation or perpetuation of injury. The fungal microbiome and virome are less well studied. This Review highlights features of the lung microbiome, unique considerations in studying it, examples of dysbiosis in selected disease, emerging concepts in lung microbiome-host interactions, and critical areas for investigation.
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56
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Baker JM, Dickson RP. Is the lung microbiome alive? Lessons from Antarctic soil. Eur Respir J 2021; 58:58/1/2100321. [PMID: 34326174 DOI: 10.1183/13993003.00321-2021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 01/22/2023]
Affiliation(s)
- Jennifer M Baker
- Division of Pulmonary and Critical Care Medicine, Dept of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.,Dept of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, Dept of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA .,Dept of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA.,Michigan Center for Integrative Research in Critical Care, Ann Arbor, MI, USA
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57
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Sulaiman I, Wu BG, Li Y, Tsay JC, Sauthoff M, Scott AS, Ji K, Koralov SB, Weiden M, Clemente JC, Jones D, Huang YJ, Stringer KA, Zhang L, Geber A, Banakis S, Tipton L, Ghedin E, Segal LN. Functional lower airways genomic profiling of the microbiome to capture active microbial metabolism. Eur Respir J 2021; 58:13993003.03434-2020. [PMID: 33446604 DOI: 10.1183/13993003.03434-2020] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/19/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND Microbiome studies of the lower airways based on bacterial 16S rRNA gene sequencing assess microbial community structure but can only infer functional characteristics. Microbial products, such as short-chain fatty acids (SCFAs), in the lower airways have significant impact on the host's immune tone. Thus, functional approaches to the analyses of the microbiome are necessary. METHODS Here we used upper and lower airway samples from a research bronchoscopy smoker cohort. In addition, we validated our results in an experimental mouse model. We extended our microbiota characterisation beyond 16S rRNA gene sequencing with the use of whole-genome shotgun (WGS) and RNA metatranscriptome sequencing. SCFAs were also measured in lower airway samples and correlated with each of the sequencing datasets. In the mouse model, 16S rRNA gene and RNA metatranscriptome sequencing were performed. RESULTS Functional evaluations of the lower airway microbiota using inferred metagenome, WGS and metatranscriptome data were dissimilar. Comparison with measured levels of SCFAs shows that the inferred metagenome from the 16S rRNA gene sequencing data was poorly correlated, while better correlations were noted when SCFA levels were compared with WGS and metatranscriptome data. Modelling lower airway aspiration with oral commensals in a mouse model showed that the metatranscriptome most efficiently captures transient active microbial metabolism, which was overestimated by 16S rRNA gene sequencing. CONCLUSIONS Functional characterisation of the lower airway microbiota through metatranscriptome data identifies metabolically active organisms capable of producing metabolites with immunomodulatory capacity, such as SCFAs.
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Affiliation(s)
- Imran Sulaiman
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Benjamin G Wu
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Yonghua Li
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Jun-Chieh Tsay
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Maya Sauthoff
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Adrienne S Scott
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Kun Ji
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Sergei B Koralov
- Dept of Pathology, New York University School of Medicine, New York, NY, USA
| | - Michael Weiden
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
| | - Jose C Clemente
- Dept of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Drew Jones
- Dept of Biochemistry and Molecular Pharmacology and Dept of Radiation Oncology, New York University School of Medicine, New York, NY, USA
| | - Yvonne J Huang
- Division of Pulmonary and Critical Care Medicine, Dept of Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kathleen A Stringer
- Dept of Clinical Pharmacy, College of Pharmacy, and Division of Pulmonary and Critical Care Medicine, Dept of Medicine, School of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Lingdi Zhang
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA
| | - Adam Geber
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA
| | - Stephanie Banakis
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA
| | - Laura Tipton
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA
| | - Elodie Ghedin
- Center for Genomics and Systems Biology, Dept of Biology, New York University, New York, NY, USA.,Dept of Epidemiology, School of Global Public Health, New York University, New York, NY, USA
| | - Leopoldo N Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, Dept of Medicine, New York University School of Medicine, New York, NY, USA
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58
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Slimmen LJM, Janssens HM, van Rossum AMC, Unger WWJ. Antigen-Presenting Cells in the Airways: Moderating Asymptomatic Bacterial Carriage. Pathogens 2021; 10:pathogens10080945. [PMID: 34451409 PMCID: PMC8400527 DOI: 10.3390/pathogens10080945] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/16/2021] [Accepted: 07/22/2021] [Indexed: 12/18/2022] Open
Abstract
Bacterial respiratory tract infections (RTIs) are a major global health burden, and the role of antigen-presenting cells (APCs) in mounting an immune response to contain and clear invading pathogens is well-described. However, most encounters between a host and a bacterial pathogen do not result in symptomatic infection, but in asymptomatic carriage instead. The fact that a pathogen will cause infection in one individual, but not in another does not appear to be directly related to bacterial density, but rather depend on qualitative differences in the host response. Understanding the interactions between respiratory pathogens and airway APCs that result in asymptomatic carriage, will provide better insight into the factors that can skew this interaction towards infection. This review will discuss the currently available knowledge on airway APCs in the context of asymptomatic bacterial carriage along the entire respiratory tract. Furthermore, in order to interpret past and futures studies into this topic, we propose a standardized nomenclature of the different stages of carriage and infection, based on the pathogen’s position with regard to the epithelium and the amount of inflammation present.
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Affiliation(s)
- Lisa J. M. Slimmen
- Laboratory of Pediatrics, Department of Pediatrics, Erasmus MC-Sophia Children’s Hospital, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands;
- Division of Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus MC-Sophia Children’s Hospital, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands;
| | - Hettie M. Janssens
- Division of Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus MC-Sophia Children’s Hospital, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands;
| | - Annemarie M. C. van Rossum
- Division of Infectious Diseases and Immunology, Department of Pediatrics, Erasmus MC-Sophia Children’s Hospital, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands;
| | - Wendy W. J. Unger
- Laboratory of Pediatrics, Department of Pediatrics, Erasmus MC-Sophia Children’s Hospital, University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands;
- Correspondence:
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59
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Mac Aogáin M, Baker JM, Dickson RP. On Bugs and Blowholes: Why Is Aspiration the Rule, Not the Exception? Am J Respir Crit Care Med 2021; 203:1049-1051. [PMID: 33596387 PMCID: PMC8314891 DOI: 10.1164/rccm.202011-4257ed] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Micheál Mac Aogáin
- Department of Biochemistry St. James's Hospital Dublin, Ireland.,School of Medicine Trinity College Dublin Dublin, Ireland
| | - Jennifer M Baker
- Department of Internal Medicine University of Michigan Medical School Ann Arbor, Michigan.,Department of Microbiology and Immunology University of Michigan Medical School Ann Arbor, Michigan and
| | - Robert P Dickson
- Department of Internal Medicine University of Michigan Medical School Ann Arbor, Michigan.,Department of Microbiology and Immunology University of Michigan Medical School Ann Arbor, Michigan and.,Michigan Center for Integrative Research in Critical Care Ann Arbor, Michigan
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60
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Systems Biology and Bile Acid Signalling in Microbiome-Host Interactions in the Cystic Fibrosis Lung. Antibiotics (Basel) 2021; 10:antibiotics10070766. [PMID: 34202495 PMCID: PMC8300688 DOI: 10.3390/antibiotics10070766] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/14/2021] [Accepted: 06/21/2021] [Indexed: 12/16/2022] Open
Abstract
The study of the respiratory microbiota has revealed that the lungs of healthy and diseased individuals harbour distinct microbial communities. Imbalances in these communities can contribute to the pathogenesis of lung disease. How these imbalances occur and establish is largely unknown. This review is focused on the genetically inherited condition of Cystic Fibrosis (CF). Understanding the microbial and host-related factors that govern the establishment of chronic CF lung inflammation and pathogen colonisation is essential. Specifically, dissecting the interplay in the inflammation–pathogen–host axis. Bile acids are important host derived and microbially modified signal molecules that have been detected in CF lungs. These bile acids are associated with inflammation and restructuring of the lung microbiota linked to chronicity. This community remodelling involves a switch in the lung microbiota from a high biodiversity/low pathogen state to a low biodiversity/pathogen-dominated state. Bile acids are particularly associated with the dominance of Proteobacterial pathogens. The ability of bile acids to impact directly on both the lung microbiota and the host response offers a unifying principle underpinning the pathogenesis of CF. The modulating role of bile acids in lung microbiota dysbiosis and inflammation could offer new potential targets for designing innovative therapeutic approaches for respiratory disease.
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61
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Lipinski JH, Falkowski NR, Huffnagle GB, Erb-Downward JR, Dickson RP, Moore BB, O'Dwyer DN. Toll-like receptors, environmental caging, and lung dysbiosis. Am J Physiol Lung Cell Mol Physiol 2021; 321:L404-L415. [PMID: 34159791 DOI: 10.1152/ajplung.00002.2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Recent studies have implicated lung microbiota in shaping local alveolar immune responses. Toll-like receptors are major sensors of microbiota and determinants of local epithelial homeostasis. The impact of toll-like receptor deficiency on lung microbiota is unknown. To determine whether the absence of toll-like receptors results in altered lung microbiota or dysbiosis, we compared lung microbiota in wild-type and toll-like receptor-deficient experimental mice using 16S ribosomal RNA gene quantification and sequencing. We used a randomized environmental caging strategy to determine the impact of toll-like receptors on lung microbiota. Lung microbiota are detectable in toll-like receptor-deficient experimental mice and exhibit considerable variability. The lung microbiota of toll-like receptor-deficient mice are altered in community composition (PERMANOVA P < 0.001), display reduced diversity (t test P = 0.0075), and bacterial burden (t test P = 0.016) compared with wild-type mice with intact toll-like receptors and associated signaling pathways. The lung microbiota of wild-type mice when randomized to cages with toll-like receptor-deficient mice converged with no significant difference in community composition (PERMANOVA P > 0.05) after 3 wk of cohousing. The lung microbiome of toll-like receptor-deficient mice is distinct from wild-type mice and may be less susceptible to the effects of caging as an environmental variable. Our observations support a role for toll-like receptor signaling in the shaping of lung microbiota.
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Affiliation(s)
- Jay H Lipinski
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Nicole R Falkowski
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Gary B Huffnagle
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Michigan.,Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - John R Erb-Downward
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Robert P Dickson
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Michigan.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Beth B Moore
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Michigan.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan
| | - David N O'Dwyer
- Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Michigan
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62
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Pantaleón García J, Hinkle KJ, Falkowski NR, Evans SE, Dickson RP. Selective Modulation of the Pulmonary Innate Immune Response Does not Change Lung Microbiota in Healthy Mice. Am J Respir Crit Care Med 2021; 204:734-736. [PMID: 34153197 DOI: 10.1164/rccm.202104-0836le] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Jezreel Pantaleón García
- The University of Texas MD Anderson Cancer Center, 4002, Pulmonary Medicine, Houston, Texas, United States
| | - Kevin J Hinkle
- University of Michigan Health System, 21707, Internal Medicine, Ann Arbor, Michigan, United States
| | - Nicole R Falkowski
- University of Michigan Health System, 21707, Internal Medicine, Ann Arbor, Michigan, United States
| | - Scott E Evans
- University of Texas-M.D. Anderson Cancer Center, Pulmonary Medicine, Houston, Texas, United States
| | - Robert P Dickson
- University of Michigan Health System, 21707, Internal Medicine, Ann Arbor, Michigan, United States;
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63
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Baker JM, Hinkle KJ, McDonald RA, Brown CA, Falkowski NR, Huffnagle GB, Dickson RP. Whole lung tissue is the preferred sampling method for amplicon-based characterization of murine lung microbiota. MICROBIOME 2021; 9:99. [PMID: 33952355 PMCID: PMC8101028 DOI: 10.1186/s40168-021-01055-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/22/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Low-biomass microbiome studies (such as those of the lungs, placenta, and skin) are vulnerable to contamination and sequencing stochasticity, which obscure legitimate microbial signal. While human lung microbiome studies have rigorously identified sampling strategies that reliably capture microbial signal from these low-biomass microbial communities, the optimal sampling strategy for characterizing murine lung microbiota has not been empirically determined. Performing accurate, reliable characterization of murine lung microbiota and distinguishing true microbial signal from noise in these samples will be critical for further mechanistic microbiome studies in mice. RESULTS Using an analytic approach grounded in microbial ecology, we compared bacterial DNA from the lungs of healthy adult mice collected via two common sampling approaches: homogenized whole lung tissue and bronchoalveolar lavage (BAL) fluid. We quantified bacterial DNA using droplet digital PCR, characterized bacterial communities using 16S rRNA gene sequencing, and systematically assessed the quantity and identity of bacterial DNA in both specimen types. We compared bacteria detected in lung specimens to each other and to potential source communities: negative (background) control specimens and paired oral samples. By all measures, whole lung tissue in mice contained greater bacterial signal and less evidence of contamination than did BAL fluid. Relative to BAL fluid, whole lung tissue exhibited a greater quantity of bacterial DNA, distinct community composition, decreased sample-to-sample variation, and greater biological plausibility when compared to potential source communities. In contrast, bacteria detected in BAL fluid were minimally different from those of procedural, reagent, and sequencing controls. CONCLUSIONS An ecology-based analytical approach discriminates signal from noise in this low-biomass microbiome study and identifies whole lung tissue as the preferred specimen type for murine lung microbiome studies. Sequencing, analysis, and reporting of potential source communities, including negative control specimens and contiguous biological sites, are crucial for biological interpretation of low-biomass microbiome studies, independent of specimen type. Video abstract.
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Affiliation(s)
- Jennifer M Baker
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, 6220 MSRB III/SPC 5642, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109-5642, USA
| | - Kevin J Hinkle
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, 6220 MSRB III/SPC 5642, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109-5642, USA
| | - Roderick A McDonald
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, 6220 MSRB III/SPC 5642, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109-5642, USA
| | - Christopher A Brown
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, 6220 MSRB III/SPC 5642, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109-5642, USA
| | - Nicole R Falkowski
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, 6220 MSRB III/SPC 5642, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109-5642, USA
| | - Gary B Huffnagle
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, 6220 MSRB III/SPC 5642, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109-5642, USA
- Department of Molecular, Cellular, & Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Mary H. Weiser Food Allergy Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Robert P Dickson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Health System, 6220 MSRB III/SPC 5642, 1150 W. Medical Center Dr, Ann Arbor, MI, 48109-5642, USA.
- Michigan Center for Integrative Research in Critical Care, Ann Arbor, MI, USA.
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