The Cystic Fibrosis Upper and Lower Airway Metagenome

Pienkowska, Katarzyna; Pust, Marie-Madlen; Gessner, Margaux; Gaedcke, Svenja; Thavarasa, Ajith; Rosenboom, Ilona; Losada, Patricia Morán; Minso, Rebecca; Arnold, Christin; Hedtfeld, Silke; Dorda, Marie; Wiehlmann, Lutz; Mainz, J.G.; Klockgether, Jens; Tümmler, Burkhard

doi:10.1128/spectrum.03633-22

Cited by 14 publications

(15 citation statements)

References 88 publications

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“…Moreover, the healthy control group was on average younger than the people with BE. However, as the gradient of depletion noted in patients with BE matches with that observed in patients with cystic fibrosis seen at the Hannover clinic [ 12 ], the divergent geographic origin of samples from Scotland and Northern Germany should not have substantially influenced the outcome of our study.…”

Section: Discussionmentioning

confidence: 60%

“…The strongest depletion was seen for the phylogenetically unrelated species F. periodonticum , E. sulci and N. subflava. We have observed the same pattern of depletion in sputa collected from individuals with cystic fibrosis [ 12 ]. F. periodonticum and E. sulci have so far not been investigated in the context of respiratory health and disease.…”

Section: Discussionmentioning

confidence: 67%

“…The heat trees additionally resolved that cluster DMM1 contained infrequently occurring, personalised pathogens such as Serratia liquefaciens , Neisseria meningitidis and Elizabethkingia miricola . To resolve the different abundances in more detail, figures 5a and 5b compare the quantitative abundances of randomly selected pairs of the four age quartiles in the four clusters with that of the average metagenome of healthy nonsmokers aged 20–59 years [ 12 ]. Each BE sample demonstrated a substantial and individual depletion of the taxa present in healthy airways, whereby more taxa were absent in specimens of DMM3 and DMM4 ( figure 5b ).…”

Section: Resultsmentioning

confidence: 99%

“…For this analysis, all participants were enrolled from Ninewells Hospital, Dundee, UK. To compare the airway metagenome profiles in non-cystic fibrosis BE with lung health, control groups of healthy smokers (n=8) and healthy nonsmokers (n=88) were recruited [ 12 ]. Clinical metadata are available from the Supplementary Material ( Tables S1, S2, S3 ).…”

Section: Methodsmentioning

confidence: 99%

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Sputum metagenomics of people with bronchiectasis

Rosenboom,

Thavarasa,

Richardson

et al. 2024

ERJ Open Res

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BackgroundThe 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.MethodsThe microbial metagenome from sputa of 101 EMBARC study participants was examined by using whole genome shotgun sequencing.ResultsOur analysis of the metagenome of people with bronchiectasis revealed four clusters characterised by predominance ofHaemophilus influenzae, Pseudomonas aeruginosaor polymicrobial communities with a differential composition of non-pathogenic commensals and opportunistic pathogens. The metagenomes of the severely affected patients showed individual profiles of low alpha diversity. Importantly, nearly 50% of patients with severe disease was in a cluster characterised by commensals. Comparison with the sputum metagenome of healthy smokers and healthy non-smokers revealed a gradient of depletion of taxa in bronchiectasis, most oftenNeisseria subflava, Fusobacterium periodonticumandEubacterium sulci.ConclusionThe gradient of depletion of commensal taxa found in healthy airways is a key feature of bronchiectasis associated with disease severity.

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Section: Discussionmentioning

confidence: 60%

Section: Discussionmentioning

confidence: 67%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Sputum metagenomics of people with bronchiectasis

Rosenboom,

Thavarasa,

Richardson

et al. 2024

ERJ Open Res

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“…In comparison for the oral cavity, there was a significant positive correlation between plasma IL-8 and the genera Porphyromonas and Alysiella . Given that Staphylococcus aureus and Stenotrophomonas maltophilia are opportunistic pathogens in the respiratory tract and frequently detected in cystic fibrosis patients, it may be speculated that innate immune function in the lung mucosa could contribute to shifts in these genera [ 54 ]. The pathogenicity of Alysiella is unknown but it is commonly found in the oral cavity of mammals, whereas Porphyromonas gingivalis is associated with periodontal disease [ 55 , 56 ].…”

Section: Discussionmentioning

confidence: 99%

Helicobacter pylori Infection in Infant Rhesus Macaque Monkeys is Associated with an Altered Lung and Oral Microbiome

Siegel

Jimenez

Rocha

et al. 2023

Preprint

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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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Metagenomics Applied to the Respiratory Mycobiome in Cystic Fibrosis

Angebault,

Botterel

2024

Mycopathologia

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The Cystic Fibrosis Upper and Lower Airway Metagenome

Cited by 14 publications

References 88 publications

Sputum metagenomics of people with bronchiectasis

Sputum metagenomics of people with bronchiectasis

Helicobacter pylori Infection in Infant Rhesus Macaque Monkeys is Associated with an Altered Lung and Oral Microbiome

Metagenomics Applied to the Respiratory Mycobiome in Cystic Fibrosis

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