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. 2017 Dec 7;12(12):e0188461.
doi: 10.1371/journal.pone.0188461. eCollection 2017.

Composition and Variation of Respiratory Microbiota in Healthy Military Personnel

Free PMC article

Composition and Variation of Respiratory Microbiota in Healthy Military Personnel

Jun Hang et al. PLoS One. .
Free PMC article


Certain occupational and geographical exposures have been associated with an increased risk of lung disease. As a baseline for future studies, we sought to characterize the upper respiratory microbiomes of healthy military personnel in a garrison environment. Nasal, oropharyngeal, and nasopharyngeal swabs were collected from 50 healthy active duty volunteers eight times over the course of one year (1107 swabs, completion rate = 92.25%) and subjected to pyrosequencing of the V1-V3 region of 16S rDNA. Respiratory bacterial taxa were characterized at the genus level, using QIIME 1.8 and the Ribosomal Database Project classifier. High levels of Staphylococcus, Corynebacterium, and Propionibacterium were observed among both nasal and nasopharyngeal microbiota, comprising more than 75% of all operational taxonomical units (OTUs). In contrast, Streptococcus was the sole dominant bacterial genus (approximately 50% of all OTUs) in the oropharynx. The average bacterial diversity was greater in the oropharynx than in the nasal or nasopharyngeal region at all time points. Diversity analysis indicated a significant overlap between nasal and nasopharyngeal samples, whereas oropharyngeal samples formed a cluster distinct from these two regions. The study produced a large set of pyrosequencing data on the V1-V3 region of bacterial 16S rDNA for the respiratory microbiomes of healthy active duty Service Members. Pre-processing of sequencing reads showed good data quality. The derived microbiome profiles were consistent both internally and with previous reports, suggesting their utility for further analyses and association studies based on sequence and demographic data.

Conflict of interest statement

Competing Interests: The views expressed in this article are those of the authors and do not necessarily reflect the official policy or position of the Department of the Army, DoD, or US government. JH, RCR, LRM, RGJ, JR, RAK and PBK are military service members (or employees of the U.S. Government). This work was prepared as part of their official duties. Title 17 U.S.C. §105 provides that “Copyright protection under this title is not available for any work of the United States Government.” Title 17 U.S.C. §101 defines a US Government work as a work prepared by a military Service Member or employee of the US Government as part of that person’s official duties.


Fig 1
Fig 1. Sample collection from 50 human subjects.
Three swabs (nasal, oropharyngeal, and nasopharyngeal) were collected from each volunteer (subject numbers 14–63) during each of two visits (1/2) in every quarter (i.e., S1–S4). Green diamond symbols show swab collection dates. Red bars denote flu shot vaccination dates (26 subjects). Black bars denote Flu Mist vaccination dates (19 subjects). The dots on the X-axis filled in with color show musician types: Empty, non-musician (11); Green, pianist or conductor (2); Purple, percussionist (5); Cyan, vocalist (4); Yellow, violinist (3); Gray, wind instrumentalist (25).
Fig 2
Fig 2. Bacterial community composition of respiratory microbiota in 36 human subjects.
Bacterial genera with an average relative abundance of ≥0.5% across the 36 samples are shown. Reads that were classified at the higher taxonomic levels other than genus are denoted as “other”. Each sample name includes the quarter number S1–S4 (first digit), visit 1 or 2 (second digit), subject number (last three digits), and type of swab (A, anterior nares [top panel]; N, nasopharynx [middle panel]; T, oropharynx [bottom panel]).
Fig 3
Fig 3. Variation in average α-diversity as a function of upper respiratory region and time.
Within-subject α-diversity values for 30 subjects that had a complete set of 24 swabs and at least 3000 reads per sample were computed by using the Shannon entropy and averaged over each region and time point. Samples from the anterior nares (A) are red, samples from the nasopharynx (N) are blue, and samples from the oropharynx samples (T) are green. Plotting is performed using the ‘boxplot’ function with the standard (default) parameters. The filled bars (boxes) represent the 25th (top) and 75th (bottom) percentiles of the samples. The error bars cover the samples to the furthest distance within the error range. By default, an outlier is a value that is more than 1.5 times the interquartile range away from the top or bottom of the box. The diamond symbol represents the median of the samples.
Fig 4
Fig 4. Variation in β-diversity as a function of upper respiratory regions.
Between-subject β-diversity values were computed for 30 subjects that had a complete set of 24 swabs and at least 3000 reads per sample. The weighted UniFrac distance was used in the principal coordinate analysis of the distance matrices between the respiratory regions.

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Grant support

This work was supported by the Immunizations Healthcare Branch, the Military Infectious Diseases Research Program (MIDRP)/Defense Health Program enhancement (DHPe)/Defense Medical Research and Development Program (DMRDP) of the Department of Defense (DoD) and the Global Emerging Infections Surveillance and Response System (GEIS), a Division of the Armed Forces Health Surveillance Center.