Microbiome of the Paranasal Sinuses: Update and Literature Review

Lee, Jivianne T.; Frank, Daniel N.; Ramakrishnan, Vijay R.

doi:10.2500/ajra.2016.30.4255

Cited by 78 publications

(83 citation statements)

References 92 publications

(244 reference statements)

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“…At this point, analyses of sinus microbiota have been challenging and difficult to replicate due to concerns about inclusion of control subjects, optimal sampling technique, sampling site, laboratory protocols, and data analysis pipelines [51]. One major advantage in CRS over microbiome study of other diseases is that patients are seen regularly over time and providers have ready access to the site of disease with nasal endoscopy.…”

Section: Discussionmentioning

confidence: 99%

Investigation of sinonasal microbiome spatial organization in chronic rhinosinusitis

Ramakrishnan

Gitomer

Kofonow

et al. 2016

Int Forum Allergy Rhinol

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Background Chronic rhinosinusitis (CRS) is a multifactorial inflammatory airway disorder in which bacteria are implicated in the initiation and/or sustenance of disease in some patients. The sinuses are colonized by bacteria even in health, and the potential for sinus-specific niches harboring unique microbial consortia raises questions for clinical and research investigation. Objective To determine the degree to which resident upper airways microbiota differ between individuals and anatomic sites, in order to determine the optimal site of microbial sampling for study in CRS. Methods 8 CRS patients undergoing primary surgery were sampled bilaterally at the anterior nares, middle meatus, nasopharynx, maxillary, frontal, and sphenoid sinuses, for investigation using broad-range bacterial 16S rRNA sequencing. Results Between-subject variability in bacterial microbiota was substantially greater than within-subject variability. The middle meatus was fairly representative of the underlying sinuses, although corynebacteria were detected at higher abundances in the middle meatus, relative to the maxillary (P<0.1), frontal (P<0.05), or sphenoid (P<0.1) sinuses. Conclusion Interpersonal variation of the upper airway microbiome greatly outweighs niche-specific differences. The middle meatus is a fair representation of the underlying sinuses and may be considered for use as a simple single site for sampling in longitudinal studies or in subjects who have not undergone sinus surgery.

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Section: Discussionmentioning

confidence: 99%

Investigation of sinonasal microbiome spatial organization in chronic rhinosinusitis

Ramakrishnan

Gitomer

Kofonow

et al. 2016

Int Forum Allergy Rhinol

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“…Recent review articles have thoroughly summarized the literature on microbial communities present in healthy and chronically diseased sinuses [31, 32]. There is no current consensus on the most common bacteria present in the healthy or diseased state, and there is no clear ‘causative’ or ‘protective’ single organism.…”

Section: Current Sinus Microbiome Literature Reviewmentioning

confidence: 99%

The sinonasal bacterial microbiome in health and disease

Ramakrishnan¹,

Hauser²,

Frank³

2016

Current Opinion in Otolaryngology & Head and Neck Surgery

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Purpose of review The development of culture-independent bacterial DNA sequencing techniques and integration into research practice has led to a burgeoning interest in the microbiome and its relevance to human health and disease. Introduction into the study of chronic rhinosinusitis in the past few years has shaped current thinking on the role of bacteria in the disease process. Recent findings Rich and diverse populations of bacteria inhabit the sinonasal cavity at all times. Decreased bacterial richness and diversity may be associated with disease state and outcomes. Summary Although there is much to be explored, the sinus microbiome appears to have potentially promising roles in many aspects of sinus health and disease.

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“…The composition of the human sinonasal microbiome and how it changes in health and disease remains poorly understood, largely due to differences in methodology among studies resulting in large variations in reported bacterial profiles [27][28][29][30][31][32]. Culture-based approaches capture <15% of resident bacterial taxa when compared to nucleic acidbased techniques, since fast-growing bacteria like staphylococci tend to predominate in culture specimens, and recovery of anaerobes and slow-growing bacteria is limited [29,33,34].…”

Section: Introductionmentioning

confidence: 99%

Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes

Earl

Adappa

Król

et al. 2018

Preprint

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Background: Pan-bacterial 16S rRNA microbiome surveys performed with massively parallel DNA sequencing technologies have transformed community microbiological studies. Current 16S profiling methods, however, fail to provide sufficient taxonomic resolution and accuracy to adequately perform species-level associative studies for specific conditions. This is due to the amplification and sequencing of only short 16S rRNA gene regions, typically providing for only family-or genus-level taxonomy.Moreover, sequencing errors often inflate the number of taxa present. PacificBiosciences' (PacBio's) long-read technology in particular suffers from high error rates per base. Herein we present a microbiome analysis pipeline that takes advantage of PacBio circular consensus sequencing (CCS) technology to sequence and error correct full-length bacterial 16S rRNA genes, which provides high-fidelity species-level microbiome dataResults: Analysis of a mock community with 20 bacterial species demonstrated 100% specificity and sensitivity. Examination of a 250-plus species mock community demonstrated correct species-level classification of >90% of taxa and relative abundances were accurately captured. The majority of the remaining taxa were demonstrated to be multiply, incorrectly, or incompletely classified. Using this methodology, we examined the microgeographic variation present among the microbiomes of six sinonasal sites, by both swab and biopsy, from the anterior nasal cavity to the sphenoid sinus from 12 subjects undergoing trans-sphenoidal hypophysectomy. We found greater variation among subjects than among sites within a subject, although significant within-individual differences were also observed.Propiniobacterium acnes (recently renamed Cutibacterium acnes [1]) was the predominant species throughout, but was found at distinct relative abundances by site. Conclusions:Our microbial composition analysis pipeline for single-molecule real-time 16S rRNA gene sequencing (MCSMRT, https://github.com/jpearl01/mcsmrt) overcomes deficits of standard marker gene based microbiome analyses by using CCS of entire 16S rRNA genes to provide increased taxonomic and phylogenetic resolution.Extensions of this approach to other marker genes could help refine taxonomic assignments of microbial species and improve reference databases, as well as strengthen the specificity of associations between microbial communities and dysbiotic states.

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Microbiome of the Paranasal Sinuses: Update and Literature Review

Cited by 78 publications

References 92 publications

Investigation of sinonasal microbiome spatial organization in chronic rhinosinusitis

Investigation of sinonasal microbiome spatial organization in chronic rhinosinusitis

The sinonasal bacterial microbiome in health and disease

Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes

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