Profiling bacterial community in upper respiratory tracts

Abstract

BackgroundInfection by pathogenic viruses results in rapid epithelial damage and significantly impacts on the condition of the upper respiratory tract, thus the effects of viral infection may induce changes in microbiota. Thus, we aimed to define the healthy microbiota and the viral pathogen-affected microbiota in the upper respiratory tract. In addition, any association between the type of viral agent and the resultant microbiota profile was assessed.MethodsWe analyzed the upper respiratory tract bacterial content of 57 healthy asymptomatic people (17 health-care workers and 40 community people) and 59 patients acutely infected with influenza, parainfluenza, rhino, respiratory syncytial, corona, adeno, or metapneumo viruses using culture-independent pyrosequencing.ResultsThe healthy subjects harbored primarily Streptococcus, whereas the patients showed an enrichment of Haemophilus or Moraxella. Quantifying the similarities between bacterial populations by using Fast UniFrac analysis indicated that bacterial profiles were apparently divisible into 6 oropharyngeal types in the tested subjects. The oropharyngeal types were not associated with the type of viruses, but were rather linked to the age of the subjects. Moraxella nonliquefaciens exhibited unprecedentedly high abundance in young subjects aged <6 years. The genome of M. nonliquefaciens was found to encode various proteins that may play roles in pathogenesis.ConclusionsThis study identified 6 oropharyngeal microbiome types. No virus-specific bacterial profile was discovered, but comparative analysis of healthy adults and patients identified a bacterium specific to young patients, M. nonliquefaciens.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-014-0583-3) contains supplementary material, which is available to authorized users.

Interactions of Respiratory Viruses and the Nasal Microbiota during the First Year of Life in Healthy Infants

“…As reported before from adult studies, we found a lower diversity and a higher density during symptomatic HRV colonization (20,25,26). The rather high intra-and interindividual heterogeneity is also in line with previous data (10,25) and supports the hypothesis of a different composition of the microbiota during viral infection (27), possibly explained by an outgrowth of potential pathogens triggered through HRV.…”

“…Studies in adults reported no sustained changes in healthy subjects (20), whereas in chronic obstructive pulmonary disease (COPD) patients, a higher abundance of Haemophilus influenzae and an increase in 16S rRNA gene copy number could be seen up to 42 days after infection (20). Our finding of a higher abundance of Moraxellaceae and a lower abundance of Staphylococcaceae after HRV infection was not reported before, but other studies described an association of a higher abundance of Moraxellaceae with acute respiratory infections (ARIs) (23) and viral colonization (26). These results support the hypothesis of persistent bacterial outgrowth after viral infection, especially as Moraxella catarrhalis is a potential pathogen in respiratory disease (1).…”

Dynamics of the upper airway microbiome in the pathogenesis of asthma-associated persistent wheeze in preschool children

“…The relative abundances of these OTUs were significantly correlated with one another (Figure 4A); we hypothesise this is related to the protection provided by the Moraxella biofilm (Tan et al, 2007), which can release outer membrane surface proteins that protect other bacteria from complement-dependent killing. Other groups have previously reported reduced upper airway microbial diversity during or prior to ARIs (Frank et al, 2010;Santee et al, 2016;Yi et al, 2014); our data supports this, both in terms of enrichment of a small number of community profiles (MPGs) during ARI, and a higher abundance of ARI-associated OTUs and lower alpha diversity within these MPGs compared to that observed in the absence of ARI symptoms (Figures 2B, S3; Tables S1, S3). We therefore propose that overgrowth of these particular taxa may tip the balance towards respiratory symptomatology, either by direct action as invasive pathogens or via indirect dysregulation of the local immunological milieu.…”

16S Metagenomic Comparison of Plasmodium falciparum–Infected and Noninfected Anopheles gambiae and Anopheles funestus Microbiota from Senegal

“…This observation contrasts with previous metagenomic-based studies of vertebrates (mostly humans) showing a lower microbial diversity and/or richness among the patient group versus the control group for certain respiratory pathologies for instance. 40,41 This could be related to the carriage of some bacterial genera such as Burkholderia, which was well represented in Pf-free specimens of both species. Moreover, patients often present an increasing proportion of pathogenic bacteria.…”