Next Generation Sequencing and the Microbiome of Chronic Rhinosinusitis: A Primer for Clinicians and Review of Current Research, Its Limitations, and Future Directions

Bacterial and fungal communities in chronic rhinosinusitis with nasal polyps

OBJECTIVE

Multiple inflammatory mechanisms dynamically interact in the development of chronic rhinosinusitis with nasal polyps (CRSwNP). Disruption of the relationship between host and environmental factors on the mucosal surface leads to the development of inflammation. Microorganisms constitute the most important part of environmental factors.

METHODS

28 volunteers (18 CRSwNP patients and 10 healthy individuals) were included in the study. Eight patients were recurrent nasal polyposis cases, and the remaining were primary cases. Swab samples were taken from the middle meatus under endoscopic examination from all participants. After DNA extraction, a library was created with the Swift Amplicon 16S + ITS kit and sequenced with Illumina Miseq. Sequence analysis was performed using QIIME, UNITE v8.2 database for ITS and Silva v138 for 16S rRNA.

RESULTS

The predominant bacteria in all groups were Firmicutes, Proteobacteria, Actinobacteria as phyla and Staphylococcus, Corynebacterium, Sphingomonas as genera. Comparison of bacterial communities of CRSwNP patients and control group highlighted Corynebacterium, as the differentiating taxa for control group and Streptococcus, Moraxella, Rothia, Micrococcus, Gemella, and Prevotella for CRSwNP patients. The predominant fungal genus in all groups was Malassezia. Staphylococcus; showed a statistically significant negative correlation with Dolosigranulum. Corynebacterium had a positive correlation with Anaerococcus, and a negative correlation with Neisseria, Prevotella, Fusobacterium and Peptostreptococcus.

CONCLUSION

Nasal microbiome of CRSwNP patients shows greater inter-individual variation than the control group. Corynebacterium is less abundant in patients with CRSwNP compared to the control group. Malassezia is the predominant fungus in the nasal cavity and paranasal sinuses and correlates positively with the abundance of Corynebacterium.

Effect of Antibiotic Eye Drops on the Nasal Microbiome in Healthy Subjects—A Pilot Study

Background: Antibiotic eye drops are frequently used in clinical practice. Due to the anatomical connection via the nasolacrimal duct, it seems possible that they have an influence on the nasal/pharyngeal microbiome. This was investigated by using two different commonly used antibiotic eye drops. Methods: 20 subjects were randomized to four groups of five subjects receiving eye drops containing gentamicin, ciprofloxacin, or, as controls, unpreserved povidone or benzalkonium chloride-preserved povidone. Nasal and pharyngeal swabs were performed before and after the instillation period. Swabs were analyzed by Illumina next-generation sequencing (NGS)-based 16S rRNA analysis. Bacterial culture was performed on solid media, and bacterial isolates were identified to the species level by MALDI-TOF MS. Species-dependent antimicrobial susceptibility testing was performed using single isolates and pools of isolates. Results: Bacterial richness in the nose increased numerically from 163 ± 30 to 243 ± 100 OTUs (gentamicin) and from 114 ± 17 to 144 ± 45 OTUs (ciprofloxacin). Phylogenetic diversity index (pd) of different bacterial strains in the nasal microbiome increased from 12.4 ± 1.0 to 16.9 ± 5.6 pd (gentamicin) and from 10.2 ± 1.4 to 11.8 ± 3.1 pd (ciprofloxacin). Unpreserved povidone eye drops resulted in minimal changes in bacterial counts. Preservative-containing povidone eye drops resulted in no change. A minor increase (1–2-fold) in the minimal inhibitory concentration (MIC) was observed in single streptococcal isolates. Conclusions: Antibiotic eye drops could affect the nasal microbiome. After an instillation period of seven days, an increase in the diversity and richness of bacterial strains in the nasal microbiome was observed.

Microbiome of Unilateral Chronic Rhinosinusitis: A Controlled Paired Analysis

The sinonasal microbiota in human upper airway may play an important role in chronic rhinosinusitis (CRS). Thus, this study aimed to investigate the human upper airway microbiome in patients with unilateral CRS, and compare the sinonasal microbiome of the unilateral diseased site with that of a contralateral healthy site. Thirty samples, 15 each from the diseased and healthy sites, were collected from the middle meatus and/or anterior ethmoid region of 15 patients with unilateral CRS during endoscopic sinus surgery. DNA extraction and bacterial microbiome analysis via 16S rRNA gene sequencing were then performed. Corynebacterium showed the highest relative abundance, followed by Staphylococcus in samples from both the diseased and healthy sites. Further, the relative abundances of Staphylococcus and Pseudomonas were significantly lower in samples from diseased sites than in those from healthy sites. Conversely, anaerobes, including Fusobacterium, Bacteroides, and Propionibacterium, were abundantly present in samples from both sites, more so in samples from diseased sites. However, the sites showed no significant difference with respect to richness or diversity (p > 0.05). Our results indicate that CRS might be a polymicrobial infection, and also suggest that Corynebacterium and Staphylococcus may exist as commensals on the sinus mucosal surface in the upper respiratory tract.

Association Between Microbiota and Nasal Mucosal Diseases in terms of Immunity

The pathogenesis of nasal inflammatory diseases is related to various factors such as anatomical structure, heredity, and environment. The nasal microbiota play a key role in coordinating immune system functions. Dysfunction of the microbiota has a significant impact on the occurrence and development of nasal inflammation. This review will introduce the positive and negative roles of microbiota involved in immunity surrounding nasal mucosal diseases such as chronic sinusitis and allergic rhinitis. In addition, we will also introduce recent developments in DNA sequencing, metabolomics, and proteomics combined with computation-based bioinformatics.

The Microbiome of the Nasolacrimal System and Its Role in Nasolacrimal Duct Obstruction

PURPOSE

Acquired nasolacrimal duct obstruction (NLDO) is a common problem leading to epiphora, the pathophysiology of which remains unclear. Culture-based studies have found Staphylococcal species to be the most prevalent organisms, reported in 47% to 73% of patients with NLDO. Recently, culture-independent molecular methods of have allowed more comprehensive detailing of local microbiota. This study aims to evaluate the sinonasal and lacrimal microbiome of patients undergoing dacryocystorhinostomy for NLDO using 16S-amplicon sequencing.

METHODS

Guarded intraoperative swabs were taken from the middle meatus (MM), inferior meatus, and the opened lacrimal sac of 14 NLDO patients undergoing dacryocystorhinostomy and from the inferior meatus and MM on the contralateral unaffected side. MM swabs from 12 control patients were compared with NLDO patients.

RESULTS

Comparing microbiota at lacrimal sac to MM and inferior meatus sites reveals that the lacrimal sac microbiome is dominated by Staphylococci (36.3%) and Corynebacterium (35.8%). No significant genus differential abundance between the 3 sites, and between the ipsilateral and contralateral sinonasal swabs, and no convincing evidence of reduced alpha diversity in all comparisons. There was a statistically significant lower relative abundance of Corynebacterium (37.6% vs. 65.1%; p = 0.035) in the MM of NLDO patients compared with controls.

CONCLUSIONS

The lacrimal sac microbiome in acquired NLDO is similar to the sinonasal microbiome. The relative abundance of Corynebacterium was reduced compared with controls. These findings suggest that an altered sinonasal microbiome may be associated with NLDO, either as a consequence or a risk factor, and merits future research.The authors have demonstrated a decreased relative abundance of Corynebacterium at the middle meatus of patients with ipsilateral nasolacrimal duct obstruction (NLDO), compared with controls, and that the lacrimal sac microbiome is similar to the sinonasal microbiome. An altered microbial state may, therefore, be associated with NLDO, either as a consequence or a risk factor, and merits future research.

Temporal Characteristics of the Oropharyngeal and Nasal Microbiota Structure in Crewmembers Stayed 180 Days in the Controlled Ecological Life Support System

Confined experiments are carried out to simulate the closed environment of space capsule on the ground. The Chinese Controlled Ecological Life Support System (CELSS) is designed including a closed-loop system supporting 4 healthy volunteers surviving for 180 days, and we aim to reveal the temporal characteristics of the oropharyngeal and nasal microbiota structure in crewmembers stayed 180 days in the CELSS, so as to accumulate the information about microbiota balance associated with respiratory health for estimating health risk in future spaceflight. We investigated the distribution of microorganisms and their dynamic characteristics in the nasal cavity and oropharynx of occupants with prolonged confinement. Based on the 16S rDNA v3–v4 regions using Illumina high-throughput sequencing technology, the oropharyngeal and nasal microbiota were monitored at eight time points during confinement. There were significant differences between oropharyngeal and nasal microbiota, and there were also individual differences among the same site of different volunteers. Analysis on the structure of the microbiota showed that, in the phylum taxon, the nasal bacteria mainly belonged to Actinobacteria, Firmicutes, Proteobacteria, Bacteroidetes, etc. In addition to the above phyla, in oropharyngeal bacteria Fusobacterial accounted for a relatively high proportion. In the genus taxon, the nasal and oropharyngeal bacteria were independent. Corynebacterium and Staphylococcus were dominant in nasal cavity, and Corynebacterium, Streptococcus, and Neisseria were dominant in oropharynx. With the extension of the confinement time, the abundance of Staphylococcus in the nasal cavity and Neisseria in the oropharynx increased, and the index Chao fluctuated greatly from 30 to 90 days after the volunteers entered the CELSS.

Conclusion: The structure and diversity of the nasal and oropharyngeal microbiota changed in the CELSS, and there was the phenomenon of migration between occupants, suggesting that the microbiota structure and health of the respiratory tract could be affected by living in a closed environment for a long time.

Microbiomics of irrigation with xylitol or Lactococcus lactis in chronic rhinosinusitis

OBJECTIVE

Topical sinonasal rinse therapies may alter the local microbiome and improve disease control in chronic rhinosinusitis (CRS). The objective of this study was to examine microbiome changes in post-surgical CRS patients when rinsing with commercially available products containing xylitol or Lactococcus lactis.

METHODS

A crossover-type protocol with a washout period was designed. Swab samples from anterior ethmoid cavities of CRS patients were collected prospectively at baseline. Subjects were provided packets containing either L. lactis W136 or xylitol in non-blinded fashion and instructed to add it to their rinse bottles daily for 28 days, after which another swab was taken. A saline wash-out period was completed and a third swab taken. A final 28-day regimen of the opposite product was followed by a final swab. DNA extraction and sequencing of the 16S rRNA gene allowed for global microbiome analysis.

RESULTS

We enrolled 25 subjects with CRS and 10 controls resulting in 70 adequate samples. Increased detection of Lactococcus was observed after use of L. lactis. No significant trends in alpha or beta diversity as a result of treatment were observed. SNOT-22 score did not change significantly following treatment with xylitol, L. lactis, or saline.

CONCLUSION

We did not detect any major clinical or microbiome-level effect due to treatment with two topical rinse products. Further research is needed to elucidate their clinical utility and possible probiotic effect.

LEVEL OF EVIDENCE

3.

Clinical Detection of Chronic Rhinosinusitis through Next-Generation Sequencing of the Oral Microbiota

Chronic rhinosinusitis (CRS) is the chronic inflammation of the sinus cavities of the upper respiratory tract, which can be caused by a disrupted microbiome. However, the role of the oral microbiome in CRS is not well understood. Polymicrobial and anaerobic infections of CRS frequently increased the difficulty of cultured and antibiotic therapy. This study aimed to elucidate the patterns and clinical feasibility of the oral microbiome in CRS diagnosis. Matched saliva and nasal swabs were collected from 18 CRS patients and 37 saliva specimens from normal volunteers were collected for 16S rRNA sequencing. The α-diversity of the saliva displayed no significant difference between control and CRS patients, whereas the β-diversity was significantly different (p = 0.004). Taxonomic indices demonstrated that Veillonella dispar, Rothia mucilaginosa, and Porphyromonas endodontalis were enriched, while Campylobacter and Cardiobacterium were reduced in the saliva of CRS patients. These microbial markers could significantly distinguish CRS patients from control (AUC = 0.939). It is noted that the 16S rRNA results of the nasal swab were consistent with the nasopharynx aerobic culture, and additionally detected multiple pathogens in CRS patients. In summary, these results indicated these oral microbiomes may provide a novel signal for CRS detection and that NGS may be an alternative approach for CRS diagnosis.

Bacterial Community Interactions During Chronic Respiratory Disease

Chronic respiratory diseases including chronic rhinosinusitis, otitis media, asthma, cystic fibrosis, non-CF bronchiectasis, and chronic obstructive pulmonary disease are a major public health burden. Patients suffering from chronic respiratory disease are prone to persistent, debilitating respiratory infections due to the decreased ability to clear pathogens from the respiratory tract. Such infections often develop into chronic, life-long complications that are difficult to treat with antibiotics due to the formation of recalcitrant biofilms. The microbial communities present in the upper and lower respiratory tracts change as these respiratory diseases progress, often becoming less diverse and dysbiotic, correlating with worsening patient morbidity. Those with chronic respiratory disease are commonly infected with a shared group of respiratory pathogens including Haemophilus influenzae, Streptococcus pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, and Moraxella catarrhalis, among others. In order to understand the microbial landscape of the respiratory tract during chronic disease, we review the known inter-species interactions among these organisms and other common respiratory flora. We consider both the balance between cooperative and competitive interactions in relation to microbial community structure. By reviewing the major causes of chronic respiratory disease, we identify common features across disease states and signals that might contribute to community shifts. As microbiome shifts have been associated with respiratory disease progression, worsening morbidity, and increased mortality, these underlying community interactions likely have an impact on respiratory disease state.

Association of the sinonasal bacterial microbiome with clinical outcomes in chronic rhinosinusitis: a systematic review

Background

The association between sinonasal microbiome and clinical outcomes of patients with chronic rhinosinusitis (CRS) is unclear. We performed a systematic review of prior studies evaluating the CRS microbiome in relation to clinical outcomes.

Methods

Computerized searches of PubMed/Medline, Cochrane, and EMBASE were updated through October 2019 revealing a total of 9 studies including 244 CRS patients. A systematic review of the literature was performed, including data extraction focusing on sample region, sequencing platforms, predominant organisms, and outcomes measures.

Results

Nine criterion‐meeting studies included 244 CRS patients, with varied results. Eight studies used 16s–ribosomal RNA (16s‐rRNA) gene sequencing to assess the sinonasal microbiome and 1 used 16s‐rRNA PhyloChip analysis. Seven studies used Sino‐Nasal Outcome Test scores, 1 applied another CRS symptom metric, and 1 used need for additional procedures/antibiotics as the primary clinical outcome. Three studies suggest that baseline abundance of phylum Actinobacteria (specifically genus Corynebacterium) was predictive of better surgical outcome. One study found C. tuberculostearicum was positively correlated with symptom severity. Another study revealed genus Escherichia was overrepresented in CRS and had positive correlation with increased symptom scores. In addition, 1 study identified Acinetobacter johnsonii to be associated with improvement in symptom scores while supporting Pseudomonas aeruginosa as having a negative impact on quality of life.

Conclusion

Microbiome data are varied in their association with clinical outcomes of CRS patients. Further research is required to identify if predominance of certain microbes within the microbiome is predictive of CRS patients’ outcomes.

Predictors of nasal bacterial culture rates in patients with chronic rhinosinusitis

All nontechnical factors were analyzed to predict nasal bacterial culture results in patients with chronic rhinosinusitis (CRS). Four hundred and ninety-six CRS patients, who underwent functional endoscopic sinus surgery (FESS), were enrolled. Prior to FESS, the severity of each patient's CRS was evaluated using a questionnaire, endoscopic examination, acoustic rhinometry, smell test, saccharine transit test, and CT scan. Nasal bacterial cultures were collected from both middle meati using a cotton-tipped stick. Our results showed that the symptom severity complained of by patients and their loss of smell function did not influence the bacterial culture rate. We discovered that the bacterial culture rate was significantly higher in nostrils with nasal polyps than those without polyps, along with nostrils experiencing thick, purulent discharge as opposed to those without discharge. Additionally, this result also occurred in nostrils with a saccharin transit time of more than 30 min than it did in those with a saccharin transit time of less than or equal to 30 min. Both the total endoscopic score and anterior group CT score were significantly higher in nostrils with positive culture than those with negative culture, while the second minimal cross-sectional area (MCA₂) of the nasal cavity was significantly lower in nostrils with positive culture than those with negative culture. Multiple logistic regression analysis showed that both nasal polyps and MCA₂ were the predictors for positive nasal bacterial culture results. It was concluded that nasal polyps and MCA₂ were the predictors for positive nasal bacterial culture results in CRS patients.

Development of a reference data set for assigning Streptococcus and Enterococcus species based on next generation sequencing of the 16S-23S rRNA region

Background

Many members of Streptococcus and Enterococcus genera are clinically relevant opportunistic pathogens warranting accurate and rapid identification for targeted therapy. Currently, the developed method based on next generation sequencing (NGS) of the 16S-23S rRNA region proved to be a rapid, reliable and precise approach for species identification directly from polymicrobial and challenging clinical samples. The introduction of this new method to routine diagnostics is hindered by a lack of the reference sequences for the 16S-23S rRNA region for many bacterial species. The aim of this study was to develop a careful assignment for streptococcal and enterococcal species based on NGS of the 16S-23S rRNA region.

Methods

Thirty two strains recovered from clinical samples and 19 reference strains representing 42 streptococcal species and nine enterococcal species were subjected to bacterial identification by four Sanger-based sequencing methods targeting the genes encoding (i) 16S rRNA, (ii) sodA, (iii) tuf and (iv) rpoB; and NGS of the 16S-23S rRNA region.

Results

This study allowed obtainment and deposition of reference sequences of the 16S-23S rRNA region for 15 streptococcal and 3 enterococcal species followed by enrichment for 27 and 6 species, respectively, for which reference sequences were available in the databases. For Streptococcus, NGS of the 16S-23S rRNA region was as discriminative as Sanger sequencing of the tuf and rpoB genes allowing for an unambiguous identification of 93% of analyzed species. For Enterococcus, sodA, tuf and rpoB genes sequencing allowed for identification of all species, while the NGS-based method did not allow for identification of only one enterococcal species. For both genera, the sequence analysis of the 16S rRNA gene was endowed with a low identification potential and was inferior to that of other tested identification methods. Moreover, in case of phylogenetically related species the sequence analysis of only the intergenic spacer region was not sufficient enough to precisely identify Streptococcus strains at the species level.

Conclusions

Based on the developed reference dataset, clinically relevant streptococcal and enterococcal species can now be reliably identified by 16S-23S rRNA sequences in samples. This study will be useful for introduction of a novel diagnostic tool, NGS of the 16S-23S rRNA region, which undoubtedly is an improvement for reliable culture-independent species identification directly from polymicrobially constituted clinical samples.

Analysis of Sinonasal Microbiota in Exacerbations of Chronic Rhinosinusitis Subgroups

Objective

Microbiome analyses now allow precise determination of the sinus microbiota of patients with exacerbations of chronic rhinosinusitis (CRS). The aim of this report is to describe the sinus microbiota of acute exacerbations in CRS clinical subgroups (with nasal polyps [CRSwNP], without nasal polyps [CRSsNP], and allergic fungal rhinosinusitis [AFRS]).

Study Design

Retrospective chart review.

Setting

Tertiary rhinology practice.

Subjects and Methods

A retrospective review was performed of all patients whose sinus microbiota were assayed via a commercially available microbiome technology during an acute CRS exacerbation during the 2-year period ending December 31, 2016. All samples were sinus aspirates collected under endoscopic visualization in clinic.

Results

Samples from a total of 134 patients (65 CRSsNP, 55 CRSwNP, and 14 AFRS) were reviewed. The observed richness (number of taxa >2% relative abundance) ranged between 1 and 11 taxa, with an average of 3 taxa per specimen. The most common bacteria in all groups were Staphylococcal spp (including Staphylococcus aureus), Streptococcus spp, Pseudomonas spp, and Escherichia spp. S aureus had an increased prevalence in CRSsNP and AFRS as compared with CRSwNP. Otherwise, the sinus microbiota were markedly similar among all 3 clinical subgroups.

Conclusions

Many bacterial types are identified during acute CRS exacerbation according to DNA-based detection techniques. Bacterial richness was remarkably low in all samples. Few differences in the patterns among clinical subgroups were observed. Further investigation is warranted to determine the clinical significance of these observations and their role in current clinical algorithms.

Development and Validation of a Reference Data Set for Assigning Staphylococcus Species Based on Next-Generation Sequencing of the 16S-23S rRNA Region

Many members of the Staphylococcus genus are clinically relevant opportunistic pathogens that warrant accurate and rapid identification for targeted therapy. The aim of this study was to develop a careful assignment scheme for staphylococcal species based on next-generation sequencing (NGS) of the 16S-23S rRNA region. All reference staphylococcal strains were identified at the species level using Sanger sequencing of the 16S rRNA, sodA, tuf, and rpoB genes and NGS of the 16S-23S rRNA region. To broaden the database, an additional 100 staphylococcal strains, including 29 species, were identified by routine diagnostic methods, 16S rRNA Sanger sequencing and NGS of the 16S-23S rRNA region. The results enabled development of reference sequences encompassing the 16S-23S rRNA region for 50 species (including one newly proposed species) and 6 subspecies of the Staphylococcus genus. This study showed sodA and rpoB targets were the most discriminative but NGS of the 16S-23S rRNA region was more discriminative than tuf gene sequencing and much more discriminative than 16S rRNA gene sequencing. Almost all Staphylococcus species could be distinguished when the max score was 99.0% or higher and the sequence similarity between the best and second best species was equal to or >0.2% (min. 9 nucleotides). This study allowed development of reference sequences for 21 staphylococcal species and enrichment for 29 species for which sequences were publicly available. We confirmed the usefulness of NGS of the 16S-23S rRNA region by identifying the whole species content in 45 clinical samples and comparing the results to those obtained using routine diagnostic methods. Based on the developed reference database, all staphylococcal species can be reliably detected based on the 16S-23S rRNA sequences in samples composed of both single species and more complex polymicrobial communities. This study will be useful for introduction of a novel diagnostic tool, which undoubtedly is an improvement for reliable species identification in polymicrobial samples. The introduction of this new method is hindered by a lack of reference sequences for the 16S-23S rRNA region for many bacterial species. The results will allow identification of all Staphylococcus species, which are clinically relevant pathogens.

Study of the impact of long-duration space missions at the International Space Station on the astronaut microbiome

Over the course of a mission to the International Space Station (ISS) crew members are exposed to a number of stressors that can potentially alter the composition of their microbiomes and may have a negative impact on astronauts’ health. Here we investigated the impact of long-term space exploration on the microbiome of nine astronauts that spent six to twelve months in the ISS. We present evidence showing that the microbial communities of the gastrointestinal tract, skin, nose and tongue change during the space mission. The composition of the intestinal microbiota became more similar across astronauts in space, mostly due to a drop in the abundance of a few bacterial taxa, some of which were also correlated with changes in the cytokine profile of crewmembers. Alterations in the skin microbiome that might contribute to the high frequency of skin rashes/hypersensitivity episodes experienced by astronauts in space were also observed. The results from this study demonstrate that the composition of the astronauts’ microbiome is altered during space travel. The impact of those changes on crew health warrants further investigation before humans embark on long-duration voyages into outer space.

Contribution of the Mucosal Microbiota to Bovine Respiratory Health

Recognizing the respiratory tract as a dynamic and complex ecosystem has enhanced our understanding of the pathophysiology of bovine respiratory disease (BRD). There is widespread evidence showing that disease-predisposing factors often disrupt the respiratory microbial ecosystem, provoking atypical colonization patterns and a progressive dysbiosis. The ecological factors that shape the respiratory microbiota, and the influence of these complex communities on bovine respiratory health, are a rich area for research exploration. Here, we review the current status of understanding of the bovine respiratory microbiota, the factors that influence its development and stability, its role in maintaining mucosal homeostasis, and ultimately its contribution to bovine health and disease. Finally, we explore the limitations of current research approaches to the microbiome and discuss potential directions for future research that can help us better understand the role of the respiratory microbiota in the health, welfare, and productivity of livestock.

Relative abundance of nasal microbiota in chronic rhinosinusitis by structured histopathology

BACKGROUND

Chronic rhinosinusitis (CRS) is an inflammatory disease process with several different phenotypes. Recent data has shown that CRS phenotypes maintain distinct nasal microbiota that may predict surgical outcomes. Nasal microbiota and structured histopathologic reporting have the potential to further differentiate subtypes and provide additional insight into the pathophysiology of CRS.

METHODS

Sinus swabs collected during functional endoscopic sinus surgery (FESS) were studied by polymerase chain reaction analysis of 16S ribosomal RNA. A structured histopathology report of 13 variables was utilized to analyze sinus tissue removed during FESS. Histopathology variables and relative abundance of nasal microbiota were compared among CRS patients.

RESULTS

A total of 51 CRS patients who underwent FESS were included. Relative abundance of the Firmicutes phylum in nasal microbiota of CRS patients was associated with presence of neutrophilic infiltrate (27.47 ± 44.75 vs 9.21 ± 11.84, p < 0.029), presence of mucosal ulceration (47.67 ± 45.52 vs 13.27 ± 26.48, p < 0.041), presence of squamous metaplasia (5562.70 ± 2715.66 vs 3563.73 ± 2580.84, p < 0.035), and absence of Charcot-Leyden crystals (5423.00 ± 3320.57 vs 679.94 ± 1653.66, p < 0.001). Relative abundance of the Bacteroidetes phylum in nasal microbiota of CRS patients was associated with increased severity of inflammatory degree (p < 0.004) and presence of mucosal ulceration (p < 0.004).

CONCLUSION

Distinct histopathologic features of CRS are associated with relative abundance of nasal microbiota phyla, specifically Firmicutes and Bacteroidetes. These findings contribute to the growing body of literature on microbiota in sinonasal disease and may have important implications for understanding pathophysiologic mechanisms of CRS subtypes and disease management.

Characterisation of the nasal microbiota in granulomatosis with polyangiitis

OBJECTIVES

Prior studies have suggested a potential link between nasal microbes and granulomatosis with polyangiitis (GPA; Wegener's), but these studies relied on culture-dependent methods. This study comprehensively examined the entire community of nasal microbiota (bacteria and fungi) in participants with GPA compared with healthy controls using deep sequencing methods.

METHODS

16S rRNA and internal transcribed spacer gene sequencing were performed on nasal microbial DNA isolated from nasal swabs of 60 participants with GPA and 41 healthy controls. Alpha and beta diversity were assessed as well as the relative abundance of the most abundant bacterial and fungal taxa. The effects of covariates including disease activity and immunosuppressive therapies on microbial composition were evaluated.

RESULTS

Compared with controls, participants with GPA had a significantly different microbial composition (weighted UniFrac p=0.04) and lower relative abundance of Propionibacterium acnes and Staphylococcus epidermidis (for both, false discovery rate-corrected p=0.02). Disease activity in GPA was associated with a lower abundance of fungal order Malasseziales compared with participants with GPA in remission (p=0.04) and controls (p=0.01). Use of non-glucocorticoid immunosuppressive therapy was associated with 'healthy' nasal microbiota while participants with GPA who were off immunosuppressive therapy had more dysbiosis (weighted UniFrac p=0.01). No difference in the relative abundance of Staphylococcus aureus was observed between GPA and controls.

CONCLUSIONS

GPA is associated with an altered nasal microbial composition, at both the bacterial and fungal levels. Use of immunosuppressive therapies and disease remission are associated with healthy microbial communities.

Chronic Rhinosinusitis: Potential Role of Microbial Dysbiosis and Recommendations for Sampling Sites

Chronic rhinosinusitis (CRS) is an inflammatory condition that affects up to 12% of the human population in developed countries. Previous studies examining the potential role of the sinus bacterial microbiota within CRS infections have found inconsistent results, possibly because of inconsistencies in sampling strategies. The aim of this study was to determine whether the sinus microbiome is altered in CRS and additionally if the middle meatus is a suitable representative site for sampling the sinus microbiome. Swab samples were collected from 12 healthy controls and 21 CRS patients, including all eight sinuses for CRS patients and between one and five sinuses for control subjects. The left and right middle meatus and nostril swabs were also collected. Significant differences in the sinus microbiomes between CRS and control samples were revealed using high-throughput 16S rRNA gene sequencing. The genus Escherichia was over-represented in CRS sinuses, and associations between control patients and Corynebacterium and Dolosigranulum were also identified. Comparisons of the middle meatuses between groups did not reflect these differences, and the abundance of the genus Escherichia was significantly lower at this location. Additionally, intra-patient variation was lower between sinuses than between sinus and middle meatus, which together with the above results suggests that the middle meatus is not an effective representative sampling site.

Therapy of Sinonasal Microbiome in CRS: A Critical Approach

PURPOSE OF REVIEW

Perturbations in local microbiota have been demonstrated in many chronic inflammatory diseases including chronic rhinosinusitis (CRS). The purpose of this paper is to review the latest microbiome research as it pertains to CRS and establish whether there is any evidence supporting the microbiome hypothesis for CRS. Treatment factors that may influence the sinonasal microbiome as well as the role of probiotics are also discussed.

RECENT FINDINGS

Despite significant heterogeneity in study design, tissue sampling, processing and bioinformatics analysis, consistent findings have emerged from the recent literature. Healthy individuals and CRS patients have similar overall bacterial burden of disease and share many common phylum. CRS patients, however, routinely show reductions in markers of biodiversity. Both medical and surgical treatments appear to influence the sinonasal microbiome, with certain bacterial strains associated with better treatment outcomes. The presence of microbial dysbiosis in CRS is now supported by numerous studies. Whether this dysbiosis is a cause or rather an association of the disease process still remains unclear. Although probiotic therapies show early promise, much larger studies are required to establish their real role as a treatment for CRS.