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. 2014 Nov 13:14:583.
doi: 10.1186/s12879-014-0583-3.

Profiling bacterial community in upper respiratory tracts

Hana Yi  1   2   3 , Dongeun Yong  4 , Kyungwon Lee  5 , Yong-Joon Cho  6 , Jongsik Chun  7   8
Affiliations

Profiling bacterial community in upper respiratory tracts

Hana Yi et al. BMC Infect Dis. .

Abstract

Background: Infection 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.

Methods: We 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.

Results: The 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.

Conclusions: This 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.

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Figures

Figure 1
Figure 1
Bacterial diversity observed in healthy-adult and patient groups represented by Shannon index and number of phylotypes (97% clustering). Healthy people contained more diverse bacterial communities in their upper respiratory tract than did patients.
Figure 2
Figure 2
Distinct populations of multiple genera observed in healthy-adult and patient groups. The 7-most dominant genera observed in the samples were selected and are depicted in the radiation diagram. The height of each peak represents the percent ratio of the corresponding genus in a sample. Streptococcus and Gemella dominated in the healthy-adult group, whereas the genera Haemophilus and Moraxella dominated in the patient group.
Figure 3
Figure 3
Dependence of microbiome structure on several key genera. Principal coordinate analysis (PCoA) of the bacterial communities isolated from 57 healthy-adult and 59 patient samples was performed using the weighted pairwise UniFrac distance matrix. The UniFrac distance represents the distance between 2 samples in terms of the microbial community structure. Samples are color-coded according to the 7 clustering groups.
Figure 4
Figure 4
Phylogenetic tree based on 16S rRNA gene sequences showing the relationship of the newly discoveredMoraxellasequences with publically available sequences of otherMoraxellastrains. Representatives of 3M. catarrhalis type strains were included together with the type strains of Moraxella species. Red text and blue test indicate M. nonliquefaciens contigs and M. catarrhalis contigs recovered from patient samples, respectively. The neighbor-joining tree was evaluated using 1,000 bootstrap pseudoreplicates. Only bootstrap values over 70% are shown at branch nodes. The scale bar represents the genetic distance.
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