Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children.
BACKGROUND
The nasopharynx is a reservoir for pathogens associated with respiratory illnesses, such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome during health and disease. Most studies so far have surveyed the nasopharynx as a whole; however, less is known about spatial variation (biogeography) in nasal microenvironments and how sampling techniques may capture that microbial diversity.


RESULTS
We used targeted 16S rRNA MiSeq sequencing and two different sampling strategies [nasal washes (NW) and nasal brushes (NB)] to characterize the nasopharyngeal microbiota in 30 asthmatic children. Nasal brushing is more abrasive than nasal washing and targeted the inner portion of the inferior turbinate. This region is expected to be different from other nasal microenvironments. Nasal washing is not spatially specific. Our 30 × 2 nasal microbiomes generated 1,474,497 sequences, from which we identified an average of 157 and 186 OTUs per sample in the NW and NB groups, respectively. Microbiotas from NB showed significantly higher alpha-diversity than microbiotas from NW. Similarly, both nasal microbiotas were distinct from each other (PCoA) and significantly differed in their community composition and abundance in at least 9 genera (effective size ≥1 %).


CONCLUSIONS
Nasopharyngeal microenvironments in asthmatic children contain microbiotas with different diversity and structure. Nasal washes and brushes capture that diversity differently. Future microbial studies of the nasopharynx need to be aware of potential spatial variation (biogeography).
Computational Biology Institute, George Washington University, Innovation Hall, Suite 305, 45085 University Drive, Ashburn, VA, 20147, USA. mlosada323@gmail.com.|Division of Emergency Medicine, Children's National Medical Center, Washington, DC, 20010, USA. mlosada323@gmail.com.|CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, 4485-661, Portugal. mlosada323@gmail.com.
Marcos
M
Pérez-Losada
Computational Biology Institute, George Washington University, Innovation Hall, Suite 305, 45085 University Drive, Ashburn, VA, 20147, USA.
Keith A
KA
Crandall
Division of Emergency Medicine, Children's National Medical Center, Washington, DC, 20010, USA.
Robert J
RJ
Freishtat
D000293:Adolescent; D001249:Asthma / Q000382:microbiology*; D001419:Bacteria / Q000145:classification* / Q000302:isolation & purification; D002648:Child; D004269:DNA, Bacterial / Q000032:analysis; D004275:DNA, Ribosomal / Q000032:analysis; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D064307:Microbiota; D009305:Nasopharynx / Q000382:microbiology*; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D017422:Sequence Analysis, DNA; D013048:Specimen Handling / Q000379:methods*
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
16S rRNA; Asthma; Microbiome; Microenvironment; Nasopharynx