Microbial communities in the respiratory tract of patients with interstitial lung disease

Abstract

BackgroundMolecular methods based on phylogenetic differences in the 16S rRNA gene are able to characterise the microbiota of the respiratory tract in health and disease.ObjectivesOur goals were (1) to characterise bacterial communities in lower and upper airways of patients with interstitial lung disease (ILD) and (2) to compare the results with the microbiota of patients with Pneumocystis pneumonia (PCP) and normal controls.MethodsWe examined the upper and lower respiratory tract of 18 patients with ILD of whom 5, 6, and 7 had idiopathic interstitial pneumonia (IIP), non-IIP and sarcoidosis, respectively. In addition, six immune-compromised patients with PCP and nine healthy subjects were included as controls. Exclusion criteria were recent bacterial/viral respiratory tract infection, HIV-positivity and subjects receiving antibiotic therapy. Bronchoalveolar lavage fluid and oropharyngeal swabs were simultaneously collected, and microbiota was characterised by ultra-deep 16S rRNA gene sequencing.ResultsThe microbiota in lower airways of the majority of patients (30; 90%) primarily consisted of Prevotellaceae, Streptococcaceae and Acidaminococcaceae. α and β diversity measurements revealed no significant differences in airway microbiota composition between the five different groups of patients. Comparison of bacterial populations in upper and lower respiratory tract showed significant topographical discontinuities for 7 (23%) individuals.ConclusionsIIP, non-IIP and sarcoidosis are not associated with disordered airway microbiota and a pathogenic role of commensals in the disease process is therefore unlikely. Nevertheless, molecular analysis of the topographical microbiota continuity along the respiratory tract may provide additional information to assist management of individual patients.

The role of the local microbial ecosystem in respiratory health and disease

“…Metagenomic sequencing has demonstrated that the healthy adult oropharynx is colonized with pathobionts such as Streptococcus, Haemophilus and Neisseria spp. and the Gramnegative, anaerobic putative commensal genera Veillonella, Prevotella, Leptotrichia and Fusobacterium [3,[70][71][72][73][74]. A recent study in children showed a similar oropharyngeal microbiome composition to that observed in adults, with enrichment of, most notably, Neisseria, Granulicatella, Prevotella, Porphyromonas, Fusobacteriaceae and certain Prevotella spp.…”

Respiratory microbiota and lower respiratory tract disease

“…78 On the other hand, Garzoni et al compared the microbiota composition and diversity in upper and lower respiratory tract samples from 24 patients with interstitial lung disease or Pneumocystis jirovecii pneumonia and 9 healthy controls, and found no differences in richness, diversity and presence of commensals such as Prevotella or Acidaminococcaceae suggesting no effect of respiratory microbiota in the disease process. 49 The small sample size and the variety of diagnoses in the disease group could arise concerns about the internal validity of this study, but if confirmed, these negative results could help researchers in narrowing the pathophysiology of hostmicrobe interactions in lung disease.…”

“…48,49,53,54 Three studies assessed the association between respiratory microbiota and lung function, measured by spirometry, and found a correlation between microbiota diversity and forced expiratory volume in 1 second (FEV1). 48,53,54 In one of these studies, however, the lung function deterioration seemed to be driven more by bacterial abundance than microbiota diversity or composition.…”

Lung Microbiome for Clinicians. New Discoveries about Bugs in Healthy and Diseased Lungs

“…In interstitial lung diseases such as idiopathic pulmonary fibrosis and sarcoidosis, there are few data about the composition of the airway microbiome (90). The common use of immunosuppressing drugs in the setting of chronic inflammation due to the disease process likely represents a major confounder in the study of the lung microbiome in these diseases.…”