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Front. Genet. | doi: 10.3389/fgene.2019.01176

Comparative Analysis of Microbiome in Nasopharynx and Middle Ear in Young Children with Acute Otitis Media

  • 1Other, United States
  • 2University of Rochester, United States
  • 3Rochester Regional Health, United States

Acute otitis media (AOM) is the most common pediatric infection for which antibiotics are prescribed in the United States. The role of the respiratory tract microbiome in pathogenesis and immune modulation of AOM remains unexplored. We sought to compare the nasopharyngeal (NP) microbiome of children 1-3 weeks prior to onset of AOM vs. at onset of AOM, and the NP microbiome with the microbiome in middle ear (ME). Six children age 6-24 months old were studied. Nasal washes (NW) were collected at healthy visits 1-3 weeks prior to AOM and at onset of AOM. The middle ear fluids (MEF) were collected by tympanocentesis at onset of AOM. Samples were stored in Trizol reagents or PBS at -80oC till use. The microbiome was characterized by 16S rRNA gene sequencing. Taxonomic designations and relative abundance of bacteria were determined using the RDP classifier tool through Quantitative Insights Into Microbial Ecology (QIIME). Cumulative sum scaling (CSS) normalization was applied before determining bacterial diversity and abundance. Shannon diversity index was calculated in Microsoft excel. The relative abundance of each bacteria species was compared via Mann Whitney U test. We found that the NW microbiome of children during healthy state or at baseline was more diverse than microbiome during AOM. At AOM, no significant difference in microbiome diversity was found between NW and MEF, although some bacteria species appear to differ in MEF than in NW. The microbiome of samples stored in PBS had significant greater diversity than samples stored in Trizol reagent.

Keywords: 16S rRNA, sample preparation for microbiome, nasopharyngeal microbiome, middle ear microbiome, acute otitis media

Received: 16 Jul 2019; Accepted: 24 Oct 2019.

Copyright: © 2019 Xu, Gill, Xu, Gonzalez and Pichichero. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dr. Steven Gill, University of Rochester, Rochester, 14627, New York, United States,
Mx. Lei Xu, Rochester Regional Health, Rochester, 14617, New York, United States,
Mx. Eduardo Gonzalez, Rochester Regional Health, Rochester, 14617, New York, United States,
Mx. Michael Pichichero, Rochester Regional Health, Rochester, 14617, New York, United States,