Examining the Evidence for an Adult Healthy Middle Ear Microbiome

ABSTRACT Otitis media (OM) is a cluster of diseases of the middle ear that commonly result from bacterial infection. OM subtypes in which the tympanic membrane is intact (acute otitis media and otitis media with effusion) are presumed to result from pathogen translocation through the eustachian tube...

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Autores principales:	Jake Jervis-Bardy, Lex E. X. Leong, Lito E. Papanicolas, Kerry L. Ivey, Sharad Chawla, Charmaine M. Woods, Claire Frauenfelder, Eng H. Ooi, Geraint B. Rogers
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2019
Materias:	microbiome middle ear otitis media Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/321201cd51334655af1305cad469127f
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spelling	oai:doaj.org-article:321201cd51334655af1305cad469127f2021-11-15T15:27:33ZExamining the Evidence for an Adult Healthy Middle Ear Microbiome10.1128/mSphere.00456-192379-5042https://doaj.org/article/321201cd51334655af1305cad469127f2019-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00456-19https://doaj.org/toc/2379-5042ABSTRACT Otitis media (OM) is a cluster of diseases of the middle ear that commonly result from bacterial infection. OM subtypes in which the tympanic membrane is intact (acute otitis media and otitis media with effusion) are presumed to result from pathogen translocation through the eustachian tube. Recent molecular-based studies have suggested that a diverse middle ear microbiome exists in the absence of disease. These have been largely unsupported by culture and feature species that commonly contaminate low-biomass sequencing data. Combining culture-based and molecular techniques, we undertook a detailed investigation of the evidence for bacterial colonization of the healthy middle ear. Middle ear (ME), nasopharynx (NP), and external ear canal (EC) swabs were collected from a total of 25 adult patients undergoing cochlear implant, stapedotomy, or translabyrinthine vestibular schwannoma resection. Diagnostic culture, microscopy, quantitative PCR, and 16S rRNA gene amplicon sequencing were used to assess sample bacterial content. EC and NP microbiota were consistent with previous reports. In contrast, bacterial levels in ME samples were not significantly above those in unused control swabs. Commonly detected taxa were among recognized sequencing contaminants (Methylobacterium, Pseudomonas, and Acinetobacter). Linear regression of dominant ME taxa confirmed a negative relationship between relative abundance and bacterial load, consistent with contamination. No bacteria were detected by microscopy or diagnostic culture in any middle ear sample. Our findings cast substantial doubt on previous reports identifying a healthy middle ear microbiome using 16S amplicon sequencing. IMPORTANCE Recent molecular-based studies have suggested that a diverse middle ear microbiome in adults and children can exist in the absence of disease. These studies have been largely unsupported by culture and feature species that commonly contaminate low-biomass sequencing data. While 16S rRNA gene amplicon sequencing has proven to be a highly informative technique in many clinical contexts, it is susceptible to spurious signal arising from sequencing reagent contaminants where sample biomass is low. Combining culture-based and molecular techniques, we undertook a detailed investigation of the evidence for bacterial colonization of the healthy middle ear. In finding no evidence of viable bacterial cells in middle ear samples, our study further underlines the importance of careful consideration of amplicon sequence data derived from very-low-biomass contexts and the value of analytical approaches that combine culture and molecular techniques.Jake Jervis-BardyLex E. X. LeongLito E. PapanicolasKerry L. IveySharad ChawlaCharmaine M. WoodsClaire FrauenfelderEng H. OoiGeraint B. RogersAmerican Society for Microbiologyarticlemicrobiomemiddle earotitis mediaMicrobiologyQR1-502ENmSphere, Vol 4, Iss 5 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	microbiome middle ear otitis media Microbiology QR1-502
spellingShingle	microbiome middle ear otitis media Microbiology QR1-502 Jake Jervis-Bardy Lex E. X. Leong Lito E. Papanicolas Kerry L. Ivey Sharad Chawla Charmaine M. Woods Claire Frauenfelder Eng H. Ooi Geraint B. Rogers Examining the Evidence for an Adult Healthy Middle Ear Microbiome
description	ABSTRACT Otitis media (OM) is a cluster of diseases of the middle ear that commonly result from bacterial infection. OM subtypes in which the tympanic membrane is intact (acute otitis media and otitis media with effusion) are presumed to result from pathogen translocation through the eustachian tube. Recent molecular-based studies have suggested that a diverse middle ear microbiome exists in the absence of disease. These have been largely unsupported by culture and feature species that commonly contaminate low-biomass sequencing data. Combining culture-based and molecular techniques, we undertook a detailed investigation of the evidence for bacterial colonization of the healthy middle ear. Middle ear (ME), nasopharynx (NP), and external ear canal (EC) swabs were collected from a total of 25 adult patients undergoing cochlear implant, stapedotomy, or translabyrinthine vestibular schwannoma resection. Diagnostic culture, microscopy, quantitative PCR, and 16S rRNA gene amplicon sequencing were used to assess sample bacterial content. EC and NP microbiota were consistent with previous reports. In contrast, bacterial levels in ME samples were not significantly above those in unused control swabs. Commonly detected taxa were among recognized sequencing contaminants (Methylobacterium, Pseudomonas, and Acinetobacter). Linear regression of dominant ME taxa confirmed a negative relationship between relative abundance and bacterial load, consistent with contamination. No bacteria were detected by microscopy or diagnostic culture in any middle ear sample. Our findings cast substantial doubt on previous reports identifying a healthy middle ear microbiome using 16S amplicon sequencing. IMPORTANCE Recent molecular-based studies have suggested that a diverse middle ear microbiome in adults and children can exist in the absence of disease. These studies have been largely unsupported by culture and feature species that commonly contaminate low-biomass sequencing data. While 16S rRNA gene amplicon sequencing has proven to be a highly informative technique in many clinical contexts, it is susceptible to spurious signal arising from sequencing reagent contaminants where sample biomass is low. Combining culture-based and molecular techniques, we undertook a detailed investigation of the evidence for bacterial colonization of the healthy middle ear. In finding no evidence of viable bacterial cells in middle ear samples, our study further underlines the importance of careful consideration of amplicon sequence data derived from very-low-biomass contexts and the value of analytical approaches that combine culture and molecular techniques.
format	article
author	Jake Jervis-Bardy Lex E. X. Leong Lito E. Papanicolas Kerry L. Ivey Sharad Chawla Charmaine M. Woods Claire Frauenfelder Eng H. Ooi Geraint B. Rogers
author_facet	Jake Jervis-Bardy Lex E. X. Leong Lito E. Papanicolas Kerry L. Ivey Sharad Chawla Charmaine M. Woods Claire Frauenfelder Eng H. Ooi Geraint B. Rogers
author_sort	Jake Jervis-Bardy
title	Examining the Evidence for an Adult Healthy Middle Ear Microbiome
title_short	Examining the Evidence for an Adult Healthy Middle Ear Microbiome
title_full	Examining the Evidence for an Adult Healthy Middle Ear Microbiome
title_fullStr	Examining the Evidence for an Adult Healthy Middle Ear Microbiome
title_full_unstemmed	Examining the Evidence for an Adult Healthy Middle Ear Microbiome
title_sort	examining the evidence for an adult healthy middle ear microbiome
publisher	American Society for Microbiology
publishDate	2019
url	https://doaj.org/article/321201cd51334655af1305cad469127f
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Examining the Evidence for an Adult Healthy Middle Ear Microbiome

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