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...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2019-10-01
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| Series: | mSphere |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mSphere.00456-19 |
| _version_ | 1818427839590957056 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-14T14:52:06Z |
| format | Article |
| id | doaj.art-321201cd51334655af1305cad469127f |
| institution | Directory Open Access Journal |
| issn | 2379-5042 |
| language | English |
| last_indexed | 2024-12-14T14:52:06Z |
| publishDate | 2019-10-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSphere |
| spelling | doaj.art-321201cd51334655af1305cad469127f2022-12-21T22:57:06ZengAmerican Society for MicrobiologymSphere2379-50422019-10-014510.1128/mSphere.00456-19Examining the Evidence for an Adult Healthy Middle Ear MicrobiomeJake Jervis-Bardy0Lex E. X. Leong1Lito E. Papanicolas2Kerry L. Ivey3Sharad Chawla4Charmaine M. Woods5Claire Frauenfelder6Eng H. Ooi7Geraint B. Rogers8Department of Otolaryngology—Head & Neck Surgery, Flinders Medical Centre, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, AustraliaInfection and Immunity Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, AustraliaInfection and Immunity Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, AustraliaSAHMRI Microbiome Research Laboratory, Flinders University School of Medicine, Adelaide, South Australia, AustraliaDepartment of Otolaryngology—Head & Neck Surgery, Flinders Medical Centre, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, AustraliaDepartment of Otolaryngology—Head & Neck Surgery, Flinders Medical Centre, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, AustraliaDepartment of Otolaryngology—Head & Neck Surgery, Flinders Medical Centre, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, AustraliaDepartment of Otolaryngology—Head & Neck Surgery, Flinders Medical Centre, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, AustraliaInfection and Immunity Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia, AustraliaABSTRACT 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.https://journals.asm.org/doi/10.1128/mSphere.00456-19microbiomemiddle earotitis media |
| spellingShingle | 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 mSphere microbiome middle ear otitis media |
| title | 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_short | Examining the Evidence for an Adult Healthy Middle Ear Microbiome |
| title_sort | examining the evidence for an adult healthy middle ear microbiome |
| topic | microbiome middle ear otitis media |
| url | https://journals.asm.org/doi/10.1128/mSphere.00456-19 |
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