Sinus microbiome diversity depletion and Corynebacterium tuberculostearicum enrichment mediates rhinosinusitis

Gut dysbiosis is associated with metabolism and systemic inflammation in patients with ischemic stroke

The role of metabolic diseases in ischemic stroke has become a primary concern in both research and clinical practice. Increasing evidence suggests that dysbiosis is associated with metabolic diseases. The aim of this study was to investigate whether the gut microbiota, as well as concentrations of organic acids, the major products of dietary fiber fermentation by the gut microbiota, are altered in patients with ischemic stroke, and to examine the association between these changes and host metabolism and inflammation. We analyzed the composition of the fecal gut microbiota and the concentrations of fecal organic acids in 41 ischemic stroke patients and 40 control subjects via 16S and 23S rRNA-targeted quantitative reverse transcription (qRT)-PCR and high-performance liquid chromatography analyses, respectively. Multivariable linear regression analysis was subsequently performed to evaluate the relationships between ischemic stroke and bacterial counts and organic acid concentrations. Correlations between bioclinical markers and bacterial counts and organic acids concentrations were also evaluated. Although only the bacterial counts of Lactobacillus ruminis were significantly higher in stroke patients compared to controls, multivariable analysis showed that ischemic stroke was independently associated with increased bacterial counts of Atopobium cluster and Lactobacillus ruminis, and decreased numbers of Lactobacillus sakei subgroup, independent of age, hypertension, and type 2 diabetes. Changes in the prevalence of Lactobacillus ruminis were positively correlated with serum interleukin-6 levels. In addition, ischemic stroke was associated with decreased and increased concentrations of acetic acid and valeric acid, respectively. Meanwhile, changes in acetic acid concentrations were negatively correlated with the levels of glycated hemoglobin and low-density lipoprotein cholesterol, whereas changes in valeric acid concentrations were positively correlated with the level of high sensitivity C-reactive protein and with white blood cell counts. Together, our findings suggest that gut dysbiosis in patients with ischemic stroke is associated with host metabolism and inflammation.

A systematic review of the sinonasal microbiome in chronic rhinosinusitis

BACKGROUND

The interaction between the host and microorganisms in chronic rhinosinusitis (CRS) is poorly understood and is a growing area of interest. More recently, methodologies have been developed to assess the microbiome without the use of culture by analyzing the bacterial 16S ribosomal RNA gene. We reviewed the microbiome literature to better understand the role of microbes in CRS.

METHODS

Systematic review of studies that used the 16S ribosomal RNA gene deep sequencing.

RESULTS

Nine publications met the search criteria. Eight studies evaluated the microbiome in controls (total, 83 subjects; range, 3-28 per study), whereas six of the studies included patients with CRS (total, 121 patients; range, 7-43 per study). Various sequencing techniques, primers, sample sites, and extraction methods were used. Of the articles that specified the number of taxa in controls, an average of 1587 taxa were identified (range, 911-2330). Significant heterogeneity was noted among the studies; however, Firmicutes, Actinobacteria, and Bacteroides phyla were identified in every sample of control patients and patients with CRS. Three of the studies showed enrichment to some degree of Staphylococcus aureus in patients with CRS. The total bacterial burden in CRS was similar to the controls. One study demonstrated a decrease in diversity, whereas other studies did not show any changes in CRS when compared with controls.

CONCLUSION

Although there are common phyla present in both control patients and patients with CRS, no consistent enrichment of any particular taxon was identified. Our findings indicated that there was no clear single causative microbe in CRS. More studies are needed to better understand the significance of the host interaction with the microbiome and the role it plays in CRS.

Bacterial community collapse: a meta-analysis of the sinonasal microbiota in chronic rhinosinusitis

Chronic rhinosinusitis (CRS) is a common, debilitating condition characterized by long-term inflammation of the nasal cavity and paranasal sinuses. The role of the sinonasal bacteria in CRS is unclear. We conducted a meta-analysis combining and reanalysing published bacterial 16S rRNA sequence data to explore differences in sinonasal bacterial community composition and predicted function between healthy and CRS affected subjects. The results identify the most abundant bacteria across all subjects as Staphylococcus, Propionibacterium, Corynebacterium, Streptococcus and an unclassified lineage of Actinobacteria. The meta-analysis results suggest that the bacterial community associated with CRS patients is dysbiotic and ecological networks fostering healthy communities are fragmented. Increased dispersion of bacterial communities, significantly lower bacterial diversity, and increased abundance of members of the genus Corynebacterium are associated with CRS. Increased relative abundance and diversity of other members belonging to the phylum Actinobacteria and members from the genera Propionibacterium differentiated healthy sinuses from those that were chronically inflamed. Removal of Burkholderia and Propionibacterium phylotypes from the healthy community dataset was correlated with a significant increase in network fragmentation. This meta-analysis highlights the potential importance of the genera Burkholderia and Propionibacterium as gatekeepers, whose presence may be important in maintaining a stable sinonasal bacterial community.

Characterization of Sinus Microbiota by 16S Sequencing from Swabs

New culture-independent microbiology methods are leading to a paradigm shift in our understanding of how the microbial community at the mucosal surface impacts sinonasal health and disease. Whereas traditional culture-based protocols were designed to identify specific pathogens in order to direct antibiotic therapies and eradicate bacteria, newer molecular techniques allow for the identification of both culturable and nonculturable bacteria in diverse communities. As a result of the recent explosion in the use of molecular techniques, we are gaining an understanding of how commensal bacteria may help modulate the host immune response and promote homeostasis. Here, we describe the general workflow of microbiome sequencing including the detailed methods for extracting mixed-community genomic DNA from sinonasal swabs, amplifying bacterial 16S rRNA genes using quantitative PCR, and preparing the samples for next-generation sequencing on the most commonly used sequencing platforms.

Investigation of sinonasal microbiome spatial organization in chronic rhinosinusitis

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. The objective was 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

Eight CRS patients undergoing primary surgery were sampled bilaterally at the anterior nares, middle meatus, nasopharynx, maxillary sinus, frontal sinus, and sphenoid sinus for investigation using broad-range bacterial 16S ribosomal RNA (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.

Host-microbiome interactions in acute and chronic respiratory infections

Respiratory infection is a leading cause of global morbidity and mortality. Understanding the factors that influence risk and outcome of these infections is essential to improving care. We increasingly understand that interactions between the microbial residents of our mucosal surfaces and host regulatory systems is fundamental to shaping local and systemic immunity. These mechanisms are most well defined in the gastrointestinal tract, however analogous systems also occur in the airways. Moreover, we now appreciate that the host-microbiota interactions at a given mucosal surface influence systemic host processes, in turn, affecting the course of infection at other anatomical sites. This review discusses the mechanisms by which the respiratory microbiome influences acute and chronic airway disease and examines the contribution of cross-talk between the gastrointestinal and respiratory compartments to microbe-mucosa interactions.

The bacterial microbiome in chronic rhinosinusitis: Richness, diversity, postoperative changes, and patient outcomes

BACKGROUND

The bacterial microbiome in chronic rhinosinusitis (CRS) remains poorly understood. Microorganisms are believed to be important contributors to the inflammatory response seen in these patients.

OBJECTIVE

To examine the bacterial CRS microbiome by using a pyrosequencing technique and determine the diversity, richness, prevalence, and abundance of bacterial species in these patients. Furthermore, the postoperative changes that occur in the microbiome and correlations with patient outcomes are assessed.

METHODS

Swabs were collected from 23 patients with CRS and 11 controls during surgery. Further postoperative swabs were collected in the CRS group. Bacterial DNA was extracted from the swabs and then sequenced by using 16S ribosomal DNA bacterial tag-encoded FLX amplicon pyrosequencing.

RESULTS

A total of 456 unique bacterial species were detected. No difference was seen for richness or diversity between the study groups (p > 0.05). Diversity declined after surgery in the CRS group (p = 0.01). Propionibacterium acnes and Staphylococcus epidermidis were the most prevalent species. Several significant differences were determined for prevalence and mean relative abundance (MRA) between the study groups. In particular, Acinetobacter johnsonii was more prevalent and had a higher MRA in the controls. Furthermore, the MRA of this species increased after surgery and was associated with improved quality of life.

CONCLUSION

This study characterized the sinonasal microbiome in a group of controls and patients with CRS. Important differences in diversity, prevalence, abundance, and temporal changes were described. Of great interest is the potential association between A. johnsonii and health. These findings provide new insights into the interplay between the microbiome and health in the paranasal sinuses.

Microbiome of the paranasal sinuses: Update and literature review

BACKGROUND

Our understanding of the resident microbiome of the paranasal sinuses has changed considerably in recent years. Once presumed to be sterile, healthy sinus cavities are now known to harbor a diverse assemblage of microorganisms, and, it is hypothesized that alterations in the kinds and quantities of these microbes may play a role in the pathogenesis of chronic rhinosinusitis (CRS).

OBJECTIVES

To review the current literature regarding the sinus microbiome and collate research findings from relevant studies published to date.

METHODS

A systematic literature review was performed on all molecular studies that investigated the microbial communities of the paranasal sinuses. Methods of detection, microbiome composition, and comparative profiling between patients with and without CRS were explored.

RESULTS

A complex consortium of microorganisms has been demonstrated in the sinuses of both patients with and without CRS. However, the latter generally have been characterized by reduced biodiversity compared with controls, with selective enrichment of particular microbes (e.g., Staphylococcus aureus). Such disruptions in the resident microbiome may contribute to disease pathogenesis by enhancing the virulence of potential pathogens and adversely modulating immune responses.

CONCLUSION

The advent of culture-independent molecular approaches has led to a greater appreciation of the intricate microbial ecology of the paranasal sinuses. Microbiota composition, distribution, and abundance impact mucosal health and influence pathogen growth and function. A deeper understanding of the host-microbiome relationship and its constituents may encourage development of new treatment paradigms for CRS, which target restoration of microbiome homeostasis and cultivation of optimal microbial communities.

Evidence of microbiota dysbiosis in chronic rhinosinusitis

BACKGROUND

Despite considerable research, the pathogenesis of chronic rhinosinusitis (CRS) remains poorly understood. Potential microbial roles in the etiology or progression of CRS have long been hypothesized, yet few specific associations have been identified. In this study we investigate associations between patterns in resident bacterial communities and clinical variants of CRS.

METHODS

Bacterial communities were assessed in 94 patients with extensive bilateral CRS undergoing endoscopic sinus surgery (ESS) and 29 controls undergoing ESS for indications other than CRS. Patients were grouped on the basis of phenotypic variants (with or without polyposis) and clinical parameters, including asthma and cystic fibrosis. Bacterial communities were characterized via 16S rRNA gene amplicon sequencing, and quantified by quantitative polymerase chain reaction.

RESULTS

Controls and idiopathic CRS subjects tended to be dominated by members of the genera Corynebacterium and Staphylococcus, together with lower abundances of several other genera, including Streptococcus, Moraxella, and Haemophilus. Aberrant (dysbiotic) bacterial assemblages (with changes in community membership and structure, reduced diversity, and increased bacterial load) and increased inter- and intrasubject variability were more common in subjects with comorbidities such as asthma and cystic fibrosis. Dysbiotic communities were variably dominated by members of the genera Staphylococcus, Streptococcus, Haemophilus, Pseudomonas, Moraxella, or Fusobacterium.

CONCLUSION

Bacterial community dysbiosis was more apparent than specific associations with examined phenotypes or endotypes, and may play a role in the pathogenesis or influence the severity of CRS. Reductions in several common core bacterial taxa, increased inter- and intrasubject variability, reduced bacterial diversity, and increased bacterial load characterized aberrant bacterial communities in CRS.

Features of the bronchial bacterial microbiome associated with atopy, asthma, and responsiveness to inhaled corticosteroid treatment

BACKGROUND

Compositional differences in the bronchial bacterial microbiota have been associated with asthma, but it remains unclear whether the findings are attributable to asthma, to aeroallergen sensitization, or to inhaled corticosteroid treatment.

OBJECTIVES

We sought to compare the bronchial bacterial microbiota in adults with steroid-naive atopic asthma, subjects with atopy but no asthma, and nonatopic healthy control subjects and to determine relationships of the bronchial microbiota to phenotypic features of asthma.

METHODS

Bacterial communities in protected bronchial brushings from 42 atopic asthmatic subjects, 21 subjects with atopy but no asthma, and 21 healthy control subjects were profiled by using 16S rRNA gene sequencing. Bacterial composition and community-level functions inferred from sequence profiles were analyzed for between-group differences. Associations with clinical and inflammatory variables were examined, including markers of type 2-related inflammation and change in airway hyperresponsiveness after 6 weeks of fluticasone treatment.

RESULTS

The bronchial microbiome differed significantly among the 3 groups. Asthmatic subjects were uniquely enriched in members of the Haemophilus, Neisseria, Fusobacterium, and Porphyromonas species and the Sphingomonodaceae family and depleted in members of the Mogibacteriaceae family and Lactobacillales order. Asthma-associated differences in predicted bacterial functions included involvement of amino acid and short-chain fatty acid metabolism pathways. Subjects with type 2-high asthma harbored significantly lower bronchial bacterial burden. Distinct changes in specific microbiota members were seen after fluticasone treatment. Steroid responsiveness was linked to differences in baseline compositional and functional features of the bacterial microbiome.

CONCLUSION

Even in subjects with mild steroid-naive asthma, differences in the bronchial microbiome are associated with immunologic and clinical features of the disease. The specific differences identified suggest possible microbiome targets for future approaches to asthma treatment or prevention.

Composition and immunological significance of the upper respiratory tract microbiota

The intestinal microbiota is essential for nutrient acquisition, immune development, and exclusion of invading pathogens. The upper respiratory tract (URT) microbiota is less well studied and does not appear to abide by many of the paradigms of the gastrointestinal tract. Decades of carriage studies in children have demonstrated that microbe–microbe competition and collusion occurs in the URT. Whether colonization with common pathogens (e.g., Staphylococcus aureus and Streptococcus pneumoniae) alters immune development or susceptibility to respiratory conditions is just beginning to be understood. Herein, we discuss the biogeography of the URT microbiota, the succession and evolution of the microbiota through the life course, and discuss the evidence for microbe–microbe interactions in colonization and infection.

A comprehensive review of the nasal microbiome in chronic rhinosinusitis (CRS)

Chronic rhinosinusitis (CRS) has been known as a disease with strong infectious and inflammatory components for decades. The recent advancement in methods identifying microbes has helped implicate the airway microbiome in inflammatory respiratory diseases such as asthma and COPD. Such studies support a role of resident microbes in both health and disease of host tissue, especially in the case of inflammatory mucosal diseases. Identifying interactive events between microbes and elements of the immune system can help us to uncover the pathogenic mechanisms underlying CRS. Here we provide a review of the findings on the complex upper respiratory microbiome in CRS in comparison with healthy controls. Furthermore, we have reviewed the defects and alterations of the host immune system that interact with microbes and could be associated with dysbiosis in CRS.

The sinonasal bacterial microbiome in health and disease

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.

Dietary modifications for refractory chronic rhinosinusitis? Manipulating diet for the modulation of inflammation

BACKGROUND

An endotype of chronic rhinosinusitis (CRS) refractory to medical and surgical management is characterized by persistent T-helper 1/T-helper 17 inflammation of the sinus mucosa, which potentially facilitates colonization with dysbiotic microbial flora. Dietary interventions that target reduction of systemic inflammation are increasingly recommended as adjuncts to ongoing medical therapy in chronic disorders with a strong inflammatory component, such as cardiac disease, diabetes, and metabolic syndrome. Inflammation-reducing dietary modifications may thus be of benefit in patients with refractory CRS (RCRS).

OBJECTIVE

To identify nonpharmacologic approaches that implicate modification of dietary factors, potentially reducing systemic level of inflammation in RCRS.

METHODS

A systematic review of the literature was undertaken to identify dietary strategies for reducing inflammation in metabolic syndrome, diabetes, and cardiac disease. Mechanistic-based strategies for reducing systemic inflammation were identified and categorized to identify potential therapeutic avenues, which would be applicable to RCRS.

RESULTS

Principal mechanisms for altering inflammation at the systemic level via dietary manipulation center around (1) increased consumption of foods with anti-inflammatory properties, and (2) modulation of the gut microbiome to reduce short-chain fatty acid secretion by dysbiotic gut flora. Recommended dietary modifications to reduce systemic markers of inflammation or to improve RCRS include alteration of macronutrient intake, alterations in consumption of meat and fats, consumption of prebiotics and probiotics, and a low-salicylate diet in the context of aspirin-exacerbated respiratory disease.

CONCLUSION

Dietary modifications may offer a potential nonpharmacologic means of reducing inflammation in patients with RCRS and hence may represent a complementary adjunct to existing medical therapies. Additional prospective studies are required to further validate the concept of dietary modifications in patients with RCRS to support the findings.

A chronic rhinosinusitis-derived isolate of Pseudomonas aeruginosa induces acute and pervasive effects on the murine upper airway microbiome and host immune response

BACKGROUND

Diverse microbial communities colonize healthy sinus mucosa and specific species within these communities are capable of protecting the host from pathogenic infection. However, little is known of the dynamics of upper airway infection and the role of the sinus mucosal microbiome in short- and longer-term outcomes using clinical isolates from patients with chronic rhinosinusitis.

METHODS

We examine microbiome and immune dynamics after murine sinus infection with Pseudomonas aeruginosa EC1, isolated previously from a chronic rhinosinusitis patient. Microbiota profiling (16S rRNA sequencing), histologic, and immunologic analyses [interferon-gamma (IFN-γ) and eotaxin-1 (CCL11) gene expression] were performed at 1, 7, and 10 days postinfection (D1PI, D7PI, and D10PI) in antimicrobial-treated and untreated animals.

RESULTS

At D1PI, P. aeruginosa EC1 dominated the upper airway microbiome and was associated with a significant increase in sinus mucosa goblet cell hyperplasia, mucin hypersecretion (p < 0.001), and IFN-γ expression in antibiotic-treated and untreated animals, although the magnitude of pathogen enrichment was lower in the latter group. Mucin hypersecretion and IFN-γ expression subsided by 7D7PI in both groups of mice, coincident with a depletion of the infectious strain. However, other members of the Pseudomonadaceae family remained significantly enriched (p < 0.05, q < 0.05) in the microbiome at D7PI and D10PI and this perturbation was associated with induction of eotaxin-1 at these later time-points.

CONCLUSION

Murine intranasal P. aeruginosa EC1 infection causes a pervasive shift in the sinus microbiome that persists despite histologic resolution and is associated with a reproducible immunologic shift from an initial IFN-γ response to a temporal induction of eotaxin-1.

Chronic rhinosinusitis: the rationale for current treatments

INTRODUCTION

Chronic rhinosinusitis (CRS) is a broad clinical syndrome linked by mucosal inflammation. Primary treatment modalities are corticosteroids and antibiotics with surgery an option for failures, but the level of supporting evidence is generally low. The primary reason is that CRS is a symptom complex and not a specific disease. Areas covered: The primary treatment modalities for CRS are corticosteroids, antibiotics and surgery. Corticosteroids, which have very broad anti-inflammatory properties, also have the strongest evidence for efficacy. Antibiotics are likely effective in a subpopulation of patients but the various phenotypes and endotypes that make up CRS have thus far been poorly defined. Early surgery as well as biologics may also be more efficacious and cost effective in some phenotypes as well. Expert commentary: A better understanding of the inflammatory pathways that drive CRS will permit investigators to separate patient groups. This will allow for clinical trials that target specific subpopulations and more personalized therapy for CRS patients in the future.

Differential Analysis of the Nasal Microbiome of Pig Carriers or Non-Carriers of Staphylococcus aureus

Staphylococcus aureus is presently regarded as an emerging zoonotic agent due to the spread of specific methicillin-resistant S. aureus (MRSA) clones in pig farms. Studying the microbiota can be useful for the identification of bacteria that antagonize such opportunistic veterinary and zoonotic pathogen in animal carriers. The aim of this study was to determine whether the nasal microbiome of pig S. aureus carriers differs from that of non-carriers. The V3-V5 region of the 16S rRNA gene was sequenced from nasal swabs of 44 S. aureus carriers and 56 non-carriers using the 454 GS FLX titanium system. Carriers and non-carriers were selected on the basis of quantitative longitudinal data on S. aureus carriage in 600 pigs sampled at 20 Danish herds included in two previous studies in Denmark. Raw sequences were analysed with the BION meta package and the resulting abundance matrix was analysed using the DESeq2 package in R to identify operational taxonomic units (OTUs) with differential abundance between S. aureus carriers and non-carriers. Twenty OTUs were significantly associated to non-carriers, including species with known probiotic potential and antimicrobial effect such as lactic acid-producing isolates described among Leuconostoc spp. and some members of the Lachnospiraceae family, which is known for butyrate production. Further 5 OTUs were significantly associated to carriage, including known pathogenic bacteria such as Pasteurella multocida and Klebsiella spp. Our results show that the nasal microbiome of pigs that are not colonized with S. aureus harbours several species/taxa that are significantly less abundant in pig carriers, suggesting that the nasal microbiota may play a role in the individual predisposition to S. aureus nasal carriage in pigs. Further research is warranted to isolate these bacteria and assess their possible antagonistic effect on S. aureus for the pursuit of new strategies to control MRSA in pig farming.

Correlation of T2R38 taste phenotype and in vitro biofilm formation from nonpolypoid chronic rhinosinusitis patients

BACKGROUND

Sinonasal biofilms have been demonstrated in specimens collected from chronic rhinosinusitis (CRS) patients. Mounting evidence suggests that biofilms contribute to therapeutically recalcitrant CRS. Recently, the bitter taste receptor T2R38 has been implicated in the regulation of the sinonasal mucosal innate immune response. TAS2R38 gene polymorphisms affect receptor functionality and contribute to variations seen in sinonasal innate defense as well as taste perception reflected in gustatory sensitivity to the bitter compound phenylthiocarbamide (PTC). In a population of CRS patients with active infection or inflammation, we sought to determine if a correlation between T2R38 phenotype and in vitro biofilm formation existed.

METHODS

Endoscopically guided sinonasal swabs were obtained prospectively from CRS (±polyp) patients with evidence of persistent inflammation or mucopurulence. In vitro biofilm formation was assessed with a modified Calgary Biofilm Detection Assay. Patients' phenotypic (functional) expression of the bitter taste receptor T2R38 was evaluated with a taste test including the compound PTC. Linear regression was used to determine the level of significance between mean in vitro biofilm formation levels and mean PTC taste test intensity ratings across CRS patients.

RESULTS

Sinonasal swabs were obtained from 59 patients, with 42 of the 59 samples demonstrating in vitro biofilm formation. Analysis revealed an inverse linear association between in vitro biofilm formation and PTC taste intensity ratings (p = 0.019) for all patients. This association was exclusively driven by nonpolypoid CRS patients (p = 0.0026).

CONCLUSION

In vitro biofilm formation from sinonasal clinical isolates is inversely correlated with PTC taste sensitivity in nonpolypoid CRS patients.

Bacterial microbiota of the upper respiratory tract and childhood asthma

BACKGROUND

Patients with asthma and healthy controls differ in bacterial colonization of the respiratory tract. The upper airways have been shown to reflect colonization of the lower airways, the actual site of inflammation in asthma, which is hardly accessible in population studies.

OBJECTIVE

We sought to characterize the bacterial communities at 2 sites of the upper respiratory tract obtained from children from a rural area and to relate these to asthma.

METHODS

The microbiota of 327 throat and 68 nasal samples from school-age farm and nonfarm children were analyzed by 454-pyrosequencing of the bacterial 16S ribosomal RNA gene.

RESULTS

Alterations in nasal microbiota but not of throat microbiota were associated with asthma. Children with asthma had lower α- and β-diversity of the nasal microbiota as compared with healthy control children. Furthermore, asthma presence was positively associated with a specific operational taxonomic unit from the genus Moraxella in children not exposed to farming, whereas in farm children Moraxella colonization was unrelated to asthma. In nonfarm children, Moraxella colonization explained the association between bacterial diversity and asthma to a large extent.

CONCLUSIONS

Asthma was mainly associated with an altered nasal microbiota characterized by lower diversity and Moraxella abundance. Children living on farms might not be susceptible to the disadvantageous effect of Moraxella. Prospective studies may clarify whether Moraxella outgrowth is a cause or a consequence of loss in diversity.

Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis

BACKGROUND

Upper respiratory infections (URI) and their complications are a major healthcare burden for pediatric populations. Although the microbiology of the nasopharynx is an important determinant of the complications of URI, little is known of the nasopharyngeal (NP) microbiota of children, the factors that affect its composition, and its precise relationship with URI.

RESULTS

Healthy children (n = 47) aged 49-84 months from a prospective cohort study based in Wisconsin, USA, were examined. Demographic and clinical data and NP swab samples were obtained from participants upon entry to the study. All NP samples were profiled for bacterial microbiota using a phylogenetic microarray, and these data were related to demographic characteristics and upper respiratory health outcomes. The composition of the NP bacterial community of children was significantly related prior to the history of acute sinusitis (R (2) = 0.070, P < 0.009). History of acute sinusitis was associated with significant depletion in relative abundance of taxa including Faecalibacterium prausnitzii and Akkermansia spp. and enrichment of Moraxella nonliquefaciens. Enrichment of M. nonliquefaciens was also a characteristic of baseline NP samples of children who subsequently developed acute sinusitis over the 1-year study period. Time to develop URI was significantly positively correlated with NP diversity, and children who experienced more frequent URIs exhibited significantly diminished NP microbiota diversity (P ≤ 0.05).

CONCLUSIONS

These preliminary data suggest that previous history of acute sinusitis influences the composition of the NP microbiota, characterized by a depletion in relative abundance of specific taxa. Diminished diversity was associated with more frequent URIs.

Chronic Rhinosinusitis with Nasal Polyps

Chronic rhinosinusitis with nasal polyps (CRSwNP) is an important clinical entity diagnosed by the presence of both subjective and objective evidence of chronic sinonasal inflammation. Symptoms include anterior or posterior rhinorrhea, nasal congestion, hyposmia, and/or facial pressure or pain that last for a duration of more than 12 weeks. Nasal polyps are inflammatory lesions that project into the nasal airway, are typically bilateral, and originate from the ethmoid sinus. Males are more likely to be affected than females, but no specific genetic or environmental factors have been strongly linked to the development of this disorder to date. CRSwNP is frequently associated with asthma and allergic rhinitis, but the cellular and molecular mechanisms that contribute to the clinical symptoms are not fully understood. Defects in the sinonasal epithelial cell barrier, increased exposure to pathogenic and colonized bacteria, and dysregulation of the host immune system are all thought to play prominent roles in disease pathogenesis. Additional studies are needed to further explore the clinical and pathophysiological features of CRSwNP so that biomarkers can be identified and novel advances can be made to improve the treatment and management of this disease.

Idiopathic subglottic stenosis is associated with activation of the inflammatory IL-17A/IL-23 axis

OBJECTIVES/HYPOTHESIS

Idiopathic subglottic stenosis (iSGS) is a rare and devastating extrathoracic obstruction involving the lower laryngeal and upper tracheal airway. It arises without known antecedent injury or associated disease process. Persistent mucosal inflammation and a localized fibrotic response are hallmarks of the disease. Despite the initial clinical description of iSGS more than 40 year ago, there have been no substantive investigations into the pathogenesis of this enigmatic and progressive airway obstruction. In these studies, we present the initial characterization of the molecular pathogenesis underlying the fibrosing phenotype of iSGS.

METHODS

Utilizing 20 human iSGS and healthy control specimens, we applied histologic, immunohistochemical, molecular, and immunologic techniques.

RESULTS

We demonstrate significant activation of the canonical IL-23/IL-17A pathway in the tracheal mucosa of iSGS patients, as well as identify γδ T cells as the primary cellular source of IL-17A.

CONCLUSION

Our results suggest that aberrant mucosal immune activation is a component in of the pathogenesis of iSGS. Most critically, our work offers new targets for future therapeutic intervention.

LEVEL OF EVIDENCE

NA Laryngoscope, 126:E356-E361, 2016.

Molecular analysis of idiopathic subglottic stenosis for Mycobacterium species

Objectives/Hypothesis

Idiopathic subglottic stenosis (iSGS) is an unexplained obstruction involving the lower laryngeal and upper tracheal airway. Persistent mucosal inflammation is a hallmark of the disease. Epithelial microbiota dysbiosis is found in other chronic inflammatory mucosal diseases; however, the relationship between tracheal microbiota composition and iSGS is unknown.

Given the critical role for host defense at mucosal barriers, we analyzed tissue specimens from iSGS patients for the presence of microbial pathogens.

Methods

Utilizing 30 human iSGS, 20 intubation‐related tracheal stenosis (iLTS), and 20 healthy control specimens, we applied molecular, immunohistochemical, electron microscopic, immunologic, and Sanger‐sequencing techniques.

Results

With unbiased culture‐independent nucleic acid, protein, and immunologic approaches, we demonstrate that Mycobacterium species are uniquely associated with iSGS. Phylogenetic analysis of the mycobacterial virulence factor rpoB suggests that, rather than Mycobacterium tuberculosis, a variant member of the Mycobacterium tuberculosis complex or a closely related novel mycobacterium is present in iSGS specimens.

Conclusion

These studies identify a novel pathogenic role for established large airway bacteria and provide new targets for future therapeutic intervention.

Level of Evidence

NA Laryngoscope, 127:179–185, 2017

Looking Beyond Respiratory Cultures: Microbiome-Cytokine Signatures of Bacterial Pneumonia and Tracheobronchitis in Lung Transplant Recipients

Bacterial pneumonia and tracheobronchitis are diagnosed frequently following lung transplantation. The diseases share clinical signs of inflammation and are often difficult to differentiate based on culture results. Microbiome and host immune-response signatures that distinguish between pneumonia and tracheobronchitis are undefined. Using a retrospective study design, we selected 49 bronchoalveolar lavage fluid samples from 16 lung transplant recipients associated with pneumonia (n = 8), tracheobronchitis (n = 12) or colonization without respiratory infection (n = 29). We ensured an even distribution of Pseudomonas aeruginosa or Staphylococcus aureus culture-positive samples across the groups. Bayesian regression analysis identified non-culture-based signatures comprising 16S ribosomal RNA microbiome profiles, cytokine levels and clinical variables that characterized the three diagnoses. Relative to samples associated with colonization, those from pneumonia had significantly lower microbial diversity, decreased levels of several bacterial genera and prominent multifunctional cytokine responses. In contrast, tracheobronchitis was characterized by high microbial diversity and multifunctional cytokine responses that differed from those of pneumonia-colonization comparisons. The dissimilar microbiomes and cytokine responses underlying bacterial pneumonia and tracheobronchitis following lung transplantation suggest that the diseases result from different pathogenic processes. Microbiomes and cytokine responses had complementary features, suggesting that they are closely interconnected in the pathogenesis of both diseases.

Fifty Years of Chronic Rhinosinusitis in Children: The Accepted, the Unknown, and Thoughts for the Future

Chronic sinusitis is an often-used term in both lay and medical circumstances. In children, it has significant but largely undefined healthcare costs. Chronic rhinosinusitis (CRS) in children has well demarcated time periods and symptoms, although the actual pathway from normal sinus to CRS is not well understood. There is reasonable consensus as to the standards for diagnosis, the selection of a first-round antibiotic, and length of treatment. However, no recent prospective studies of antibiotics are available. Areas of continued speculation include the following: the microbiome of pediatric CRS, the best use of standard imaging, alternative antibiotic selection, ancillary therapy, and treatment of refractory CRS. In addition, older adolescents can present with a more adult-oriented CRS with or without polyps, suggesting a broader spectrum of disease than is commonly recognized. An accounting of the accepted elements of pediatric rhinosinusitis, as well as areas for future research, is emphasized in this review and, where appropriate, suggestions for potential investigations are offered.

Lung Ischemia-Reperfusion is a Sterile Inflammatory Process Influenced by Commensal Microbiota in Mice

Lung ischemia-reperfusion (IR) complicates numerous clinical processes, such as cardiac arrest, transplantation, and major trauma. These conditions generate sterile inflammation, which can cause or worsen acute lung injury. We previously reported that lung and systemic inflammation in a mouse model of ventilated lung IR depends on Toll-like receptor 4 (TLR-4) signaling and the presence of alveolar macrophages. Here, we tested the hypothesis that the intestinal microbiome has a role in influencing the inflammatory response to lung IR. Lung IR was created in intubated mechanically ventilated mice via reversible left pulmonary artery occlusion followed by reperfusion. Inflammatory markers and histology were tracked during varying periods of reperfusion (from 1 to 24 h). Separate groups of mice were given intestinally localized antibiotics for 8 to 10 weeks and then were subjected to left lung IR and analysis of lungs and plasma for markers of inflammation. Alveolar macrophages from antibiotic-treated or control mice were tested ex vivo for inflammatory responses to bacterial TLR agonists, namely, lipopolysaccharide and Pam3Cys. We found that inflammation generated by left lung IR was rapid in onset and dissipated within 12 to 24 h. Treatment of mice with intestinally localized antibiotics was associated with a marked attenuation of circulating and lung inflammatory markers as well as reduced histologic evidence of infiltrating cells and edema in the lung after IR. Alveolar macrophages from antibiotic-treated mice produced less cytokines ex vivo when stimulated with TLR agonists as compared with those from control mice. Our data indicate that the inflammatory response induced by nonhypoxic lung IR is transient and is strongly influenced by intestinal microbiota. Furthermore, these data suggest that the intestinal microbiome could potentially be manipulated to attenuate the post-IR pulmonary inflammatory response.

Drivers of chronic rhinosinusitis: Inflammation versus infection

Studies of the underlying cause or causes of chronic rhinosinusitis (CRS) over the past 20 or more years have expanded from a focus on systemic immune and allergic mechanisms to an intense search for the underlying drivers of mucosal inflammation. These drivers involve mucosal inflammatory pathways that become activated by allergens, microbial stimuli, or poorly understood exogenous or endogenous stimuli. The holy grail in the study of CRS is to identify specific drivers of mucosal inflammation and translate these into more effective treatment for CRS. Certain deficiencies in local innate immunity have been described in patients with CRS that predispose to increased sinus mucosal bacterial colonization/infection, including deficient local production of antimicrobial lactoferrin and deficient functioning of the bitter taste receptor TAS2R38. Conversely, certain innate factors, namely IL-25, IL-33, and thymic stromal lymphopoietin (TSLP), are elaborated by sinus epithelial cells in response to microbial stimulation or airway injury and promote local TH2 inflammation. The precise physiologic role of these factors in innate or adaptive immunity is unclear, although IL-33 might function as an alarmin triggered by damage-associated molecular patterns. The cytokines IL-25 and TSLP, similarly promote proinflammatory tissue responses. Another feature of epithelial dysregulation in patients with CRS is overproduction of eosinophil-promoting C-C chemokines by sinus epithelium, perhaps driven in part through innate stimuli, as well as TH2 cytokines, such as IL-13. Strategies to reduce the microbial stimulation of maladaptive TH2 inflammation or to suppress the local elaboration of TH2-promoting epithelial factors, such as IL-33, have potential therapeutic benefit in patients with CRS, although the extent to which this is realized in patient care remains limited at present. This rostrum will summarize my views on the major microbial drivers of mucosal inflammation and dysregulation of innate TH2-promoting factors in patients with CRS based on recent experimental data.

Chronic rhinosinusitis pathogenesis

There are a variety of medical conditions associated with chronic sinonasal inflammation, including chronic rhinosinusitis (CRS) and cystic fibrosis. In particular, CRS can be divided into 2 major subgroups based on whether nasal polyps are present or absent. Unfortunately, clinical treatment strategies for patients with chronic sinonasal inflammation are limited, in part because the underlying mechanisms contributing to disease pathology are heterogeneous and not entirely known. It is hypothesized that alterations in mucociliary clearance, abnormalities in the sinonasal epithelial cell barrier, and tissue remodeling all contribute to the chronic inflammatory and tissue-deforming processes characteristic of CRS. Additionally, the host innate and adaptive immune responses are also significantly activated and might be involved in pathogenesis. Recent advancements in the understanding of CRS pathogenesis are highlighted in this review, with special focus placed on the roles of epithelial cells and the host immune response in patients with cystic fibrosis, CRS without nasal polyps, or CRS with nasal polyps.

The role of the local microbial ecosystem in respiratory health and disease

Respiratory tract infections are a major global health concern, accounting for high morbidity and mortality, especially in young children and elderly individuals. Traditionally, highly common bacterial respiratory tract infections, including otitis media and pneumonia, were thought to be caused by a limited number of pathogens including Streptococcus pneumoniae and Haemophilus influenzae. However, these pathogens are also frequently observed commensal residents of the upper respiratory tract (URT) and form-together with harmless commensal bacteria, viruses and fungi-intricate ecological networks, collectively known as the 'microbiome'. Analogous to the gut microbiome, the respiratory microbiome at equilibrium is thought to be beneficial to the host by priming the immune system and providing colonization resistance, while an imbalanced ecosystem might predispose to bacterial overgrowth and development of respiratory infections. We postulate that specific ecological perturbations of the bacterial communities in the URT can occur in response to various lifestyle or environmental effectors, leading to diminished colonization resistance, loss of containment of newly acquired or resident pathogens, preluding bacterial overgrowth, ultimately resulting in local or systemic bacterial infections. Here, we review the current body of literature regarding niche-specific upper respiratory microbiota profiles within human hosts and the changes occurring within these profiles that are associated with respiratory infections.

Effects of a honeybee lactic acid bacterial microbiome on human nasal symptoms, commensals, and biomarkers

BACKGROUND

Lactic acid bacteria (LAB) can restore commensal microbiomes and prevent infections. Arguably, nasal administrations of LAB may therefore be beneficial in chronic rhinosinusitis (CRS). Previous studies have examined effects of topical/nasal LAB in children with secretory otitis media, but little is as yet known about their effects on the human nasal airway. The aim of this pilot study was to examine effects on nasal symptoms and commensal bacteria in healthy subjects of nasal administration of a honeybee LAB microbiome; ie, a mixture of 9 Lactobacillus spp. and 4 Bifidobacterium spp. obtained from the honeybee Apis mellifera. Furthermore, we aimed to assess whether or not the honeybee LAB produced a local inflammatory response.

METHODS

Twenty-two healthy subjects received a single administration of honeybee LAB in a sham-controlled, double-blinded, and crossover design. Using questionnaires, microbiological methods, and nasal lavages, they were assessed regarding symptoms, changes to commensal bacteria, and inflammatory products in nasal lavage fluids.

RESULTS

The honeybee LAB did not produce any symptoms or other untoward effects. No changes were observed of commensal bacteria by the honeybee LAB, and no inflammatory response was detected (compared to sham); ie, unaffected nasal lavage fluid levels of monocyte chemoattractant protein-1 (MCP-1), interleukin-8 (IL-8), monokine induced by interferon-γ (MIG), interleukin-15 (IL-15), epidermal growth factor (EGF), eotaxin, interferon gamma-induced protein-10 (IP-10), and interleukin-1 receptor antagonist (IL-1RA).

CONCLUSION

A single human nasal administration of a honeybee LAB microbiome is well tolerated. Specifically, it does not affect commensal bacteria and does not produce an inflammatory response.

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

OBJECTIVE

Microbiomics in chronic diseases, including chronic rhinosinusitis (CRS), have undergone rapid advances in recent times. The introduction of Next Generation Sequencing (NGS) technology has produced significant clinical insights regarding the bacteriology of these conditions. We review studies that have used 16S rRNA sequencing to specifically investigate the microbiota profiles of patients with CRS in a variety of contexts.

METHODS

Literature review using the CINAHL, MEDLINE, PUBMED, and the Cochrane databases. Papers utilizing 16S-sequencing technology on CRS specimens published between January 1, 1995, and October 31, 2015, were included. Studies limited to only healthy controls were excluded.

RESULTS

Consistent with published studies using non-NGS techniques, the main genera commonly identified from the sinuses of CRS patients included Staphylococcus, Propionibacterium, and Corynebacterium. The microbiome of CRS patients had lower bacterial diversity compared to controls in a number of studies. Also consistent with non-NGS-based studies, Staphylococcus was implicated as an important genus, with highly colonized patients having worse surgical outcomes. Conflicting reports of antibiotic effects on the CRS microbiome were observed. Sampling methods were well investigated, many of the studies reviewed failed to include important methodological detail.

CONCLUSION

While 16S sequencing is a novel microbiological laboratory method, current studies have confirmed our existing understanding of bacteriology of CRS without providing significant additional clinical insight. Complementing 16S studies with more complex NGS methods while developing robust clinical studies aimed at shifting the disrupted CRS microbiome will provide researches with the opportunity to derive further clinical insight and develop new therapeutic targets.

Differences in the paranasal sinuses between germ-free and pathogen-free mice

BACKGROUND

The role of bacteria in the etiology of chronic rhinosinusitis (CRS) is not fully understood. Commensal bacteria may have a significant impact on the development of normal paranasal sinus anatomy and mucosal immunity, as they do in the gut. Studying the paranasal sinuses of germ-free (GF) mice may provide some insight into the effect of commensal bacteria on sinus structure and mucosal function.

METHODS

The paranasal sinuses of 5 GF mice were compared to 5 pathogen-free normal mice. Mice heads underwent computed tomography and images were compared for pneumatization and geometry of the sinuses. Histologically, slides were examined by light microscopy and compared for mucosal thickness, epithelial thickness, cilia, collagen, goblet cells, and nasal-associated lymphatic tissue (NALT).

RESULTS

No radiological differences were seen between groups. Overall, GF mice were found to have thinner mucosa (Δ 15.2 ± 5.2 μm, p = 0.004), thinner epithelium (Δ 5.5 ± 2.6 μm, p = 0.037), more collagen (Δ 5.8% ± 1.6%, p < 0.001), fewer goblet cells (Δ 29.3 ± 5.4, p < 0.001), and less NALT (Δ 14,900 ± 6700 μm(2) , p = 0.04). Subanalysis by region revealed significant differences for GF mice in the middle (thinner mucosa, thinner epithelium, fewer cilia, and more collagen) and posterior (fewer goblet cells) sinus sections.

CONCLUSION

The results of this study demonstrate that commensal microbiota significantly contribute to the structure and function of murine paranasal sinuses. Therefore, changes in commensal microbiota associated with CRS may alter the normal microbe host dialogue in humans and be implicated in the pathogenesis of CRS.

Evolution of the nasopharyngeal microbiota of beef cattle from weaning to 40 days after arrival at a feedlot

Bovine respiratory disease complex (BRDc) is a major cause of morbidity and mortality in beef cattle. There is recent evidence suggesting that the nasopharyngeal microbiota has a key role in respiratory health and disease susceptibility in cattle. However, there is a paucity of knowledge regarding evolution of the nasopharyngeal microbiota when cattle are most likely to develop BRDc (i.e., from weaning to 40days after arrival at a feedlot). The objective was to describe the evolution of the nasopharyngeal microbiota of beef cattle from weaning to 40days after arrival at a feedlot. Deep nasal swabs (DNS) from 30 Angus-cross steers were collected at weaning, on arrival at a feedlot, and at day 40 after arrival. The DNA was extracted from DNS and the hypervariable region V3 of the 16S rRNA gene was amplified and sequenced (Illumina MiSeq platform). Nasopharyngeal microbiota underwent a profound evolution from weaning to arrival at the feedlot and from arrival to day 40, with the abundance of 92 Operational Taxonomic Units (OTUs) significantly changing over time. Mycoplasma (M. dispar and M. bovirhinis) was the most abundant genus in the nasopharynx, accounting for 53% of the total bacterial population. Because an evolving bacterial community may be less capable of resisting colonization by pathogenic bacteria, the instability of the nasopharyngeal microbiota documented in this study might explain why cattle are most likely to be affected with BRDc during the first weeks after weaning and arrival at a feedlot.

Engineering Human Microbiota: Influencing Cellular and Community Dynamics for Therapeutic Applications

The complex relationship between microbiota, human physiology, and environmental perturbations has become a major research focus, particularly with the arrival of culture-free and high-throughput approaches for studying the microbiome. Early enthusiasm has come from results that are largely correlative, but the correlative phase of microbiome research has assisted in defining the key questions of how these microbiota interact with their host. An emerging repertoire for engineering the microbiome places current research on a more experimentally grounded footing. We present a detailed look at the interplay between microbiota and host and how these interactions can be exploited. A particular emphasis is placed on unstable microbial communities, or dysbiosis, and strategies to reestablish stability in these microbial ecosystems. These include manipulation of intermicrobial communication, development of designer probiotics, fecal microbiota transplantation, and synthetic biology.

Influence and effect of the human microbiome in allergy and asthma

PURPOSE OF REVIEW

Studies have illustrated that the healthy human microbiome (i.e. the communities of microbes, their genomic content and interaction with the host) plays a role in the maintenance of immune homeostasis. Perturbation of these communities is an emerging characteristic of an increasing number of inflammatory diseases. The goal of this article is to review the current literature on both respiratory and gut microbiomes and their established relationship with allergy and asthma.

RECENT FINDINGS

Multiple studies have demonstrated airway microbiota dysbiosis, characterized by Proteobacteria expansion in the lower airways, to be a consistent trait of established adult asthma. Members of this phylum are associated with disease features such as bronchial hyperreactivity or corticosteroid resistance. Emerging evidence implicates the neonatal gut microbiome as playing a significant role in the development of childhood atopy, a common precursor to asthma. Murine studies have demonstrated that specific bacterial species (e.g. Lactobacillus johnsonii, Bacteroides fragilis) and microbial metabolites (e.g. the short-chain fatty acid propionate), when supplemented to animals, confer protection against allergen-induced airway disorders.

SUMMARY

The emerging view of atopy and asthma is one consistently related to inappropriate microbial community composition and function in both the airway and gastrointestinal tract. This opens up the possibility that strategies to rationally manipulate microbiota at these sites may represent a novel approach to disease prevention or management.

Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients

Chronic rhinosinusitis (CRS) is a common and potentially debilitating disease characterized by inflammation of the sinus mucosa for longer than 12 weeks. Bacterial colonization of the sinuses and its role in the pathogenesis of this disease is an ongoing area of research. Recent advances in culture-independent molecular techniques for bacterial identification have the potential to provide a more accurate and complete assessment of the sinus microbiome, however there is little concordance in results between studies, possibly due to differences in the sampling location and techniques. This study aimed to determine whether the microbial communities from one sinus could be considered representative of all sinuses, and examine differences between two commonly used methods for sample collection, swabs, and tissue biopsies. High-throughput DNA sequencing of the bacterial 16S rRNA gene was applied to both swab and tissue samples from multiple sinuses of 19 patients undergoing surgery for treatment of CRS. Results from swabs and tissue biopsies showed a high degree of similarity, indicating that swabbing is sufficient to recover the microbial community from the sinuses. Microbial communities from different sinuses within individual patients differed to varying degrees, demonstrating that it is possible for distinct microbiomes to exist simultaneously in different sinuses of the same patient. The sequencing results correlated well with culture-based pathogen identification conducted in parallel, although the culturing missed many species detected by sequencing. This finding has implications for future research into the sinus microbiome, which should take this heterogeneity into account by sampling patients from more than one sinus.

Chronic rhinosinusitis: a microbiome in dysbiosis and the search for alternative treatment options

Chronic rhinosinusitis (CRS) is a common chronic disease. While CRS is a multifactorial disease, many cases involve an imbalance in the sinus bacterial microbiome. This article reviews the composition of the healthy human sinus microbiome compared to the microbiome of CRS patients. Issues with current treatment options, particularly antibiotics, are discussed. Insights into the future of CRS treatment are also explored, principally with regards to probiotics.

Dead or alive: Deoxyribonuclease I sensitive bacteria and implications for the sinus microbiome

BACKGROUND

Recently, there has been tremendous interest in the sinus microbiome and how it relates to disease. However, a lack of a standardized sample collection and DNA extraction methods makes comparison of results across studies nearly impossible. Furthermore, current techniques fail to identify which components of the microbiome are actually alive within the host at the time of sampling.

OBJECTIVE

To develop and optimize a method to differentiate which bacterial species in the human sinus microbiome are live versus dead.

METHODS

Duplicate samples from the middle meatus of patients with healthy sinus tissue and those patients with chronic rhinosinusitis were collected by using brushes (n = 12), swabs (n = 27), and tissue biopsy (n = 8) methods. One sample from each pair was either deoxyribonuclease I- or control-treated before DNA extraction. The relative bacterial versus human composition of each sample was determined. A 16S ribosomal RNA gene analysis was performed on a six-paired sample from patients with healthy sinus tissue.

RESULTS

We found that swabs and brushes collected a higher percentage of bacterial DNA than did tissue biopsy. We also determined that as much as 50% of the bacteria collected in these samples was already dead at the time of collection. The 16S ribosomal RNA gene analysis found significant changes in the relative abundance of taxa identified in the live versus dead bacterial communities of healthy human sinuses.

CONCLUSIONS

Our findings indicated that swabs provided the best quality microbiome samples and that a large portion of the bacteria identified in the sinus were deoxyribonuclease I sensitive. These results highlighted the need for improved techniques such as those presented here, which can differentiate between living and dead bacteria in a sample, a potentially critical distinction when examining changes in sinus innate immune function because both components play important, but distinct, functions. Further studies will determine how these living and dead bacterial populations shift in different disease states and after clinical intervention.

Pathophysiology of chronic rhinosinusitis, pharmaceutical therapy options

Research in immunology has brought great progress in knowledge of inflammatory processes in the last 2 decades, which also has an impact on the upper airways. Our understanding of the pathophysiology of chronic rhinosinusitis developed from a rather mechanistic point of view with a focus on narrow clefts and mucociliary clearance to the appreciation of a complex network of immunological pathways forming the basis of disease. We today differentiate various forms of inflammation, we start to understand complex immune-regulatory networks and the reasons for their failure, and have already developed innovative approaches for therapy for the most severely ill subjects. Due to this new knowledge in inflammation and remodeling processes within mucosal tissue, specifically on the key driving factors, new diagnostic tools and therapeutic approaches for chronic rhinosinusitis have developed; the differentiation of endotypes based on pathophysiological principles will be crucial for the use of innovative therapies, mostly humanized monoclonal antibodies. Several hundred of those antibodies are currently developed for various indications and will impact our specialty as well as pneumology to a great extent.

Composition of symbiotic bacteria predicts survival in Panamanian golden frogs infected with a lethal fungus

Symbiotic microbes can dramatically impact host health and fitness, and recent research in a diversity of systems suggests that different symbiont community structures may result in distinct outcomes for the host. In amphibians, some symbiotic skin bacteria produce metabolites that inhibit the growth of Batrachochytrium dendrobatidis (Bd), a cutaneous fungal pathogen that has caused many amphibian population declines and extinctions. Treatment with beneficial bacteria (probiotics) prevents Bd infection in some amphibian species and creates optimism for conservation of species that are highly susceptible to chytridiomycosis, the disease caused by Bd. In a laboratory experiment, we used Bd-inhibitory bacteria from Bd-tolerant Panamanian amphibians in a probiotic development trial with Panamanian golden frogs, Atelopus zeteki, a species currently surviving only in captive assurance colonies. Approximately 30% of infected golden frogs survived Bd exposure by either clearing infection or maintaining low Bd loads, but this was not associated with probiotic treatment. Survival was instead related to initial composition of the skin bacterial community and metabolites present on the skin. These results suggest a strong link between the structure of these symbiotic microbial communities and amphibian host health in the face of Bd exposure and also suggest a new approach for developing amphibian probiotics.

Microbiome: Paediatricians' perspective

Millions of microorganisms inhabit the human body and affect its homeostasis in multiple ways. Alterations in this microbial community have implications for the health and survival of the human hosts. It is believed that these microorganisms should be included as part of the human genome because of their influence on human physiology hence the term "microbiome" is commonly used to refer to these microbes along with their genetic make-up and their environmental interactions. In this article we attempt to provide an insight into this recently discovered vital organ of the human body which is yet to be fully explored. We herein discuss the composition and role of microbiome in human health and disease with a special emphasis in children and culture-independent techniques employed in mapping of the microbiome. Alteration in the gut microbiome has been associated with causation of several paediatric diseases like infantile colic, necrotizing enterocolitis, asthma, atopy, obesity, type -1 diabetes, and autism. Atopic dermatitis and psoriasis have also been associated with changes in the cutaneous microbiome. Respiratory microbial imbalances during infancy have been linked with wheezing and bronchial asthma. Dysbiosis in the regional microbiome has been linked with caries, periodontitis, and chronic rhinosinusitis. The future therapeutic implications of this rapidly evolving area of research are also highlighted.

Different activations of toll-like receptors and antimicrobial peptides in chronic rhinosinusitis with or without nasal polyposis

Both up- and down-regulation of the Toll-like receptors (TLRs) and antimicrobial peptides (AMPs) of the sinonasal mucosa have already been associated with the pathogenesis of chronic rhinosinusitis with (CRSwNP) or without (CRSsNP) nasal polyps. The objective of this study was to determine the expression of all known TLR and several AMP genes and some selected proteins in association with allergy, asthma and aspirin intolerance (ASA) in CRS subgroups. RT-PCR was applied to measure the mRNA expressions of 10 TLRs, four defensins, lysozyme, cathelicidin and lactoferrin (LTF) in sinonasal samples from patients with CRSsNP (n = 19), CRSwNP [ASA(-): 17; ASA(+): 7] and in control subjects (n = 12). Protein expressions were detected with immunohistochemistry (n = 10). Statistical analysis was done with the Kruskal-Wallis ANOVA, Mann-Whitney U, and Student t test. TLR2, TLR5, TLR6, TLR7, TLR8, TLR9, β-defensins 1 and 4, cathelicidin and LTF mRNA expressions were significantly (p < 0.05) increased in CRSwNP, whereas only TLR2 and LTF were up-regulated in CRSsNP compared to controls. There was no statistical difference in respect of allergy, aspirin intolerance and smoking between CRSsNP, ASA(-) and ASA(+) CRSwNP patients. TLR2, TLR3, TLR4, LTF, β defensin 2 and lysozyme protein expressions were found to be elevated in macrophages of CRSwNP samples (p < 0.05). Gene expression analysis showed markedly different expressions in CRSwNP (6 out of 10 TLR and 4 out of 7 AMP genes were up-regulated) compared to CRSsNP (1/10, 1/7). The distinct activation of the innate immunity may support the concept that CRSsNP and CRSwNP are different subtypes of CRS. These findings were found to be independent from allergy, asthma, smoking, aspirin intolerance and systemic steroid application.