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1.
Sci Rep ; 11(1): 21940, 2021 Nov 09.
Artigo em Inglês | MEDLINE | ID: mdl-34753993

RESUMO

The role of Staphylococcus aureus in the pathogenesis of the chronic sinonasal disease chronic rhinosinusitis (CRS), has not been definitively established. Comparative analyses of S. aureus isolates from CRS with those from control participants may offer insight into a possible pathogenic link between this organism and CRS. The intra- and inter-subject S. aureus strain-level diversity in the sinuses of patients with and without CRS were compared in this cross-sectional study. In total, 100 patients (CRS = 64, control = 36) were screened for S. aureus carriage. The overall carriage prevalence of S. aureus in this cohort was 24% (CRS n = 13, control n = 11). Cultured S. aureus isolates from 18 participants were strain-typed using spa gene sequencing. The bacterial community composition of the middle meatus was assessed using amplicon sequencing targeting the V3V4 hypervariable region of the bacterial 16S rRNA gene. S. aureus isolates cultured from patients were grown in co-culture with the commensal bacterium Dolosigranulum pigrum and characterised. All participants harboured a single S. aureus strain and no trend in disease-specific strain-level diversity was observed. Bacterial community analyses revealed a significant negative correlation in the relative abundances of S. aureus and D. pigrum sequences, suggesting an antagonistic interaction between these organisms. Co-cultivation experiments with these bacteria, however, did not confirm this interaction in vitro. We saw no significant associations of CRS disease with S. aureus strain types. The functional role that S. aureus occupies in CRS likely depends on other factors such as variations in gene expression and interactions with other members of the sinus bacterial community.

2.
Int J Otolaryngol ; 2021: 7428955, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34567126

RESUMO

The purpose of this review is to summarise contemporary knowledge of sinonasal tissue remodelling during chronic rhinosinusitis (CRS), a chronic disease involving long-term inflammation of the paranasal sinuses and nasal passage. The concept of tissue remodelling has significant clinical relevance because of its potential to cause irreversibility in chronic airway tissues. Recent studies have indicated that early surgical treatment of CRS may improve clinical outcome. Tissue remodelling has been described in the literature extensively with no consensus on how remodelling is defined. This review describes various factors implicated in establishing remodelling in sinonasal tissues with a special mention of asthma as a comorbid condition. Some of the main histological features of remodelling include basement membrane thickening and collagen modulation. This may be an avenue of research with regard to targeted therapy against remodelling in CRS.

3.
Respir Res ; 22(1): 106, 2021 Apr 13.
Artigo em Inglês | MEDLINE | ID: mdl-33849523

RESUMO

BACKGROUND: Cystic fibrosis is a debilitating, autosomal recessive disease which results in chronic upper and lower airway infection and inflammation. In this study, four adult patients presenting with cystic fibrosis and chronic rhinosinusitis were recruited. Culture and molecular techniques were employed to evaluate changes in microbial profiles, host gene expression and antimicrobial resistance (AMR) in the upper respiratory tract over time. METHODS: Swab samples from the sinonasal cavity were collected at the time of surgery and at follow-up clinics at regular time intervals for up to 18 months. Nucleic acids were extracted, and DNA amplicon sequencing was applied to describe bacterial and fungal composition. In parallel, RNA was used to evaluate the expression of 17 AMR genes and two inflammatory markers (interleukins 6 and 8) using custom qPCR array cards. Molecular results were compared with routine sinus and sputum culture reports within each patient. RESULTS: Bacterial amplicon sequencing and swab culture reports from the sinonasal cavity were mostly congruent and relatively stable for each patient across time. The predominant species detected in patients P02 and P04 were Pseudomonas aeruginosa, Staphylococcus aureus in patient P03, and a mixture of Enterobacter and S. aureus in patient P01. Fungal profiles were variable and less subject specific than bacterial communities. Increased expressions of interleukins 6 and 8 were observed in all patients throughout the sampling period compared with other measured genes. The most prevalent AMR gene detected was ampC. However, the prevalence of AMR gene expression was low in all patient samples across varying time-points. CONCLUSIONS: We observed a surprising degree of stability of sinonasal microbial composition, and inflammatory and AMR gene expression across all patients post sinus surgery.


Assuntos
Fibrose Cística/microbiologia , Endoscopia/métodos , Microbiota , Procedimentos Cirúrgicos Otorrinolaringológicos , Seios Paranasais/microbiologia , Rinite/microbiologia , Sinusite/microbiologia , Adulto , Doença Crônica , Fibrose Cística/cirurgia , Feminino , Seguimentos , Humanos , Masculino , Pessoa de Meia-Idade , Seios Paranasais/cirurgia , Projetos Piloto , Período Pós-Operatório , Rinite/complicações , Rinite/cirurgia , Sinusite/complicações , Sinusite/cirurgia , Adulto Jovem
4.
Microorganisms ; 9(3)2021 Mar 22.
Artigo em Inglês | MEDLINE | ID: mdl-33810191

RESUMO

Dimethylsulfoniopropionate (DMSP) is one of Earth's most abundant organosulfur molecules. Recently, many marine heterotrophic bacteria were shown to produce DMSP, but few studies have combined culture-dependent and independent techniques to study their abundance, distribution, diversity and activity in seawater or sediment environments. Here we investigate bacterial DMSP production potential in East China Sea (ECS) samples. Total DMSP (DMSPt) concentration in ECS seawater was highest in surface waters (SW) where phytoplankton were most abundant, and it decreased with depth to near bottom waters. However, the percentage of DMSPt mainly apportioned to bacteria increased from the surface to the near bottom water. The highest DMSP concentration was detected in ECS oxic surface sediment (OSS) where phytoplankton were not abundant. Bacteria with the genetic potential to produce DMSP and relevant biosynthesis gene transcripts were prominent in all ECS seawater and sediment samples. Their abundance also increased with depth and was highest in the OSS samples. Microbial enrichments for DMSP-producing bacteria from sediment and seawater identified many novel taxonomic groups of DMSP-producing bacteria. Different profiles of DMSP-producing bacteria existed between seawater and sediment samples and there are still novel DMSP-producing bacterial groups to be discovered in these environments. This study shows that heterotrophic bacteria significantly contribute to the marine DMSP pool and that their contribution increases with water depth and is highest in seabed surface sediment where DMSP catabolic potential is lowest. Furthermore, distinct bacterial groups likely produce DMSP in seawater and sediment samples, and many novel producing taxa exist, especially in the sediment.

5.
Sci Rep ; 10(1): 16422, 2020 10 02.
Artigo em Inglês | MEDLINE | ID: mdl-33009469

RESUMO

Olfactory impairment affects ~ 20% of the population and has been linked to various serious disorders. Microbes in the nasal cavity play a key role in priming the physiology of the olfactory epithelium and maintaining a normal sense of smell by the host. The aim of this study was to explore the link between olfactory dysfunction and nasal bacterial communities. A total of 162 subjects were recruited for this study from a specialized olfactory dysfunction clinic and placed into one of three groups: anosmia, hyposmia or normosmia. Swabs from the nasal middle meatus were collected from each subject then processed for bacterial 16S rRNA gene sequencing. No overall differences in bacterial diversity or composition were observed between the three cohorts in this study. However, the relative abundances of Corynebacterium spp. and Streptococcus spp. were significantly (p < 0.05) different in subjects with olfactory loss. Furthermore, subjects with deficiencies in discriminating between smells (based on discrimination scores) had a lower bacterial diversity (Simpson's evenness p < 0.05). While these results are preliminary in nature, potential bacterial biomarkers for olfactory loss were identified. These findings need to be further validated and biologically tested in animal models.


Assuntos
Seios Paranasais/microbiologia , Seios Paranasais/fisiologia , Olfato/fisiologia , Idoso , Bactérias/genética , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Cavidade Nasal/microbiologia , Transtornos do Olfato/microbiologia , Transtornos do Olfato/fisiopatologia , RNA Ribossômico 16S/genética , Limiar Sensorial/fisiologia
6.
Artigo em Inglês | MEDLINE | ID: mdl-32850496

RESUMO

Human microbiome studies remain focused on bacteria, as they comprise the dominant component of the microbiota. Recent advances in sequencing technology and optimization of amplicon sequencing protocols have allowed the description of other members of the microbiome, including eukaryotes (fungi) and, most recently, archaea. There are no known human-associated archaeal pathogens. Their diversity and contribution to health and chronic respiratory diseases, such as chronic rhinosinusitis (CRS), are unknown. Patients with CRS suffer from long-term sinus infections, and while the microbiota is hypothesized to play a role in its pathogenesis, the exact mechanism is poorly understood. In this cross-sectional study, we applied a recently optimized protocol to describe the prevalence, diversity and abundance of archaea in swab samples from the middle meatus of 60 individuals with and without CRS. A nested PCR approach was used to amplify the archaeal 16S rRNA gene for sequencing, and bacterial and archaeal load (also based on 16S rRNA genes) were estimated using Droplet Digital™ PCR (ddPCR). A total of 16 archaeal amplicon sequence variants (ASVs) from the phyla Euryarchaeota and Thaumarchaeota were identified. Archaeal ASVs were detected in 7/60 individuals, independent of disease state, whereas bacterial ASVs were detected in 60/60. Bacteria were also significantly more abundant than archaea. The ddPCR method was more sensitive than amplicon sequencing at detecting archaeal DNA in samples. Phylogenetic trees were constructed to visualize the evolutionary relationships between archaeal ASVs, isolates and clones. ASVs were placed into phylogenetic clades containing an apparent paucity of human-associated reference sequences, revealing how little studied the human archaeome is. This is the largest study to date to examine the human respiratory-associated archaeome, and provides the first insights into the prevalence, diversity and abundance of archaea in the human sinuses.


Assuntos
Microbiota , Sinusite , Archaea/genética , Estudos Transversais , Humanos , Filogenia , RNA Ribossômico 16S/genética
7.
Xenobiotica ; 50(12): 1443-1450, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32840412

RESUMO

Despite the widespread prescription of antibiotics for patients with chronic rhinosinusitis (CRS), the extent to which drug distribution to the sinonasal mucosa occurs remains largely undefined. Twenty subjects undergoing functional endoscopic sinus surgery (FESS) for CRS were randomized to one of two groups: 1) doxycycline (100 mg daily for seven days) 2) roxithromycin (300 mg daily for seven days). Drug levels were measured using liquid chromatography-tandem mass spectrometry in sinonasal mucus, sinonasal tissues and serum at steady state. Doxycycline concentrations measured in the mucus were significantly lower compared to that in the serum (mean mucus/serum ratio = 0.16, p < 0.001) and the tissue (mean mucus/tissue ratio = 0.18, p < 0.0001). Roxithromycin concentrations in the mucus were also significantly lower compared to that in the serum (mean mucus/serum ratio = 0.37, p = 0.002) and the tissue (mean mucus/tissue ratio = 0.60, p < 0.001). Although the efficacy of doxycycline and roxithromycin in sinonasal mucus in vivo cannot be predicted solely from reported minimum inhibitory concentrations, given the added complexity of bacterial biofilm antimicrobial tolerance, these results suggest that low mucosal penetration of antibiotics may be one of the factors contributing to the limited efficacy of these agents in the treatment of CRS.


Assuntos
Antibacterianos/uso terapêutico , Mucosa Nasal/metabolismo , Sinusite/tratamento farmacológico , Administração Oral , Antibacterianos/administração & dosagem , Antibacterianos/metabolismo , Doença Crônica
8.
Front Microbiol ; 11: 595555, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33414772

RESUMO

Background: Chronic rhinosinusitis (CRS) is a common and debilitating inflammatory condition of the sinuses, afflicting 5% of the general population. Although antibiotics are frequently prescribed for the medical management of CRS, there is surprisingly little evidence to support their efficacy. In this study, we aimed to establish associations between medication usage, the sinus microbiota and patients' clinical outcomes. Methods: Antibiotic prescription patterns for the year before sample collection of 156 CRS patients, 45 disease control patients (mostly requiring septoplasty and inferior turbinate reduction) and 35 healthy control subjects were examined and analyzed together with previously published bacterial 16S rRNA gene amplicon data from our group. Results: The highest antibiotic usage was observed among the two CRS patient categories. Despite heavy antibiotic usage, CRS patients' clinical outcomes as indicated by patient questionnaires and radiologic scores were similar to those patients that did not receive any antibiotics. The sinus microbiota was dominated by members of the bacterial genera Corynebacterium and Staphylococcus in all three cohorts. Bacterial community dispersion as measured by principal coordinate analysis was significantly higher in CRS patients compared to healthy control subjects, but not disease control patients. Pairwise comparisons within cohorts revealed differences in the relative 16S rRNA gene sequence abundances of the genera Staphylococcus and Lawsonella between antibiotic users and non-users. However, overall antibiotic effects were minimal and unpredictable. Conclusion: The unpredictable effects of antibiotic treatment on the sinus microbiota found in this study, together with the lack of differences in patients' symptom scores between cohorts, do not support preoperative antibiotic treatment for CRS patients.

9.
Sci Rep ; 9(1): 17416, 2019 11 22.
Artigo em Inglês | MEDLINE | ID: mdl-31758066

RESUMO

There is a pressing need for longitudinal studies which examine the stability of the sinonasal microbiota. In this study, we investigated bacterial and fungal community composition of the sinuses of four healthy individuals every month for one year, then once every three months for an additional year to capture seasonal variation. Sequencing of bacterial 16S rRNA genes and fungal ITS2 revealed communities that were mainly dominated by members of Actinobacteria and Basidiomycota, respectively. We observed overall shifts in both bacterial and fungal community diversity that were attributable to a combination of individual, seasonal and annual changes. The results suggest that each of the subjects possessed a strong bacterial sinonasal signature, but that fungal communities were less subject specific. Differences in fungal and bacterial diversity between subjects, and which OTUs may be correlated with seasonal differences, were investigated. A small core community that persisted throughout the two year sampling period was identified: Corynebacterium, Propionibacterium and Staphylococcus, and one type of fungus, Malassezia restricta. It is likely that bacterial and fungal airway microbiomes are dynamic and experience natural shifts in diversity with time. The underlying reasons for these shifts appear to be a combination of changes in environmental climate and host factors.


Assuntos
Bactérias , Biodiversidade , Fungos , Microbiota , Seios Paranasais/microbiologia , Estações do Ano , Bactérias/genética , Biologia Computacional/métodos , DNA Espaçador Ribossômico , Fungos/genética , Humanos , Metagenômica , RNA Ribossômico 16S , Análise de Regressão
10.
Int Forum Allergy Rhinol ; 9(12): 1462-1469, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31483577

RESUMO

BACKGROUND: The sinonasal microbiota has been implicated in chronic rhinosinusitis (CRS) pathogenesis, particularly related to the presence of Staphylococcus aureus. Staphylococcus epidermidis is also prevalent within the sinonasal microbiota and may inhibit S. aureus colonization. We investigated polymerase chain reaction (PCR) primer pairs for measuring absolute abundances of S. aureus and S. epidermidis, then compared bacterial community composition and absolute abundances of these species between CRS patients and controls. METHODS: Six candidate Staphylococcus species-specific primer pairs were tested in silico and in vitro against pure bacterial isolates. Quantitative PCR (qPCR) for absolute quantification of S. aureus, S. epidermidis, and overall bacterial load were assessed in 40 CRS (CRS without nasal polyposis [CRSsNP] = 22, CRS with nasal polyposis [CRSwNP] = 18) patients and 14 controls. Amplicon sequencing of the V3-V4 hypervariable regions of the 16S ribosomal RNA (rRNA) bacterial gene were conducted to investigate community composition. RESULTS: Primer pairs targeting the gmk gene of S. aureus and nrd gene from S. epidermidis were the most specific and sensitive primers. S. aureus (CRSsNP = 81.8% occurrence, CRSwNP = 83%, control = 92.9%) and S. epidermidis (CRSsNP = 95.5%, CRSwNP = 100%, control = 92.9%) were very prevalent, as indicated by qPCR results. Both CRSsNP and CRSwNP had significantly (p < 0.05) higher bacterial load when compared with controls (p < 0.05 for both). No significant correlation was observed between S. aureus and S. epidermidis abundances (p > 0.05). CONCLUSION: Bacterial community sequencing detected Staphylococcus-assigned sequences in nearly all patients; however, it could not differentiate between S. aureus and S. epidermidis. Here, we present primer pairs that can distinguish between these species. We report a very high prevalence of S. aureus in both CRS patients and controls.


Assuntos
Seios Paranasais/microbiologia , Rinite/microbiologia , Sinusite/microbiologia , Staphylococcus aureus/isolamento & purificação , Staphylococcus epidermidis/isolamento & purificação , Adulto , Idoso , Doença Crônica , Feminino , Genes Bacterianos , Humanos , Masculino , Pessoa de Meia-Idade , RNA Bacteriano/genética , RNA Ribossômico 16S/genética , Staphylococcus aureus/genética , Staphylococcus epidermidis/genética
12.
mSphere ; 4(1)2019 02 06.
Artigo em Inglês | MEDLINE | ID: mdl-30728283

RESUMO

Chronic rhinosinusitis (CRS) is a heterogeneous condition characterized by persistent sinus inflammation and microbial dysbiosis. This study aimed to identify clinically relevant subgroups of CRS patients based on distinct microbial signatures, with a comparison to the commonly used phenotypic subgrouping approach. The underlying drivers of these distinct microbial clusters were also investigated, together with associations with epithelial barrier integrity. Sinus biopsy specimens were collected from CRS patients (n = 23) and disease controls (n = 8). The expression of 42 tight junction genes was evaluated using quantitative PCR together with microbiota analysis and immunohistochemistry for measuring mucosal integrity and inflammation. CRS patients clustered into two distinct microbial subgroups using probabilistic modelling Dirichlet (DC) multinomial mixtures. DC1 exhibited significantly reduced bacterial diversity and increased dispersion and was dominated by Pseudomonas, Haemophilus, and Achromobacter DC2 had significantly elevated B cells and incidences of nasal polyps and higher numbers of Anaerococcus, Megasphaera, Prevotella, Atopobium, and Propionibacterium In addition, each DC exhibited distinct tight junction gene and protein expression profiles compared with those of controls. Stratifying CRS patients based on clinical phenotypic subtypes (absence or presence of nasal polyps [CRSsNP or CRSwNP, respectively] or with cystic fibrosis [CRSwCF]) accounted for a larger proportion of the variation in the microbial data set than with DC groupings. However, no significant differences between CRSsNP and CRSwNP cohorts were observed for inflammatory markers, beta-dispersion, and alpha-diversity measures. In conclusion, both approaches used for stratifying CRS patients had benefits and pitfalls, but DC clustering provided greater resolution when studying tight junction impairment. Future studies in CRS should give careful consideration to the patient subtyping approach used.IMPORTANCE Chronic rhinosinusitis (CRS) is a major human health problem that significantly reduces quality of life. While various microbes have been implicated, there is no clear understanding of the role they play in CRS pathogenesis. Another equally important observation made for CRS patients is that the epithelial barrier in the sinonasal cavity is defective. Finding a robust approach to subtype CRS patients would be the first step toward unravelling the pathogenesis of this heterogeneous condition. Previous work has explored stratification based on the clinical presentation of the disease (with or without polyps), inflammatory markers, pathology, or microbial composition. Comparisons between the different stratification approaches used in these studies have not been possible due to the different cohorts, analytical methods, or sample sites used. In this study, two approaches for subtyping CRS patients were compared, and the underlying drivers of the heterogeneity in CRS were also explored.


Assuntos
Bactérias/isolamento & purificação , Microbiota , Seios Paranasais/microbiologia , Sinusite/microbiologia , Adulto , Bactérias/classificação , Biópsia , Doença Crônica , Humanos , Inflamação/genética , Membrana Mucosa/imunologia , Membrana Mucosa/microbiologia , Pólipos Nasais/microbiologia , Seios Paranasais/patologia , Sinusite/classificação , Junções Íntimas/genética
13.
Front Immunol ; 9: 2065, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30283438

RESUMO

A complex mix of inflammatory and microbial associations underscores the chronic inflammatory condition chronic rhinosinusitis (CRS), and the etiology remains poorly understood. Recent work has begun to delineate between variants (endotypes) of CRS on the basis of inflammatory biomarkers. This study aimed to assess inflammatory patterns in CRS phenotypes, identify putative endotypes of CRS, and to assess inflammatory associations with the sinonasal microbiota. Ten cytokines and six inflammatory cell types were assessed in mucosal biopsies from 93 CRS subjects and 17 controls via cytometric bead array and immunohistochemical techniques. Putative endotypes were identified via cluster analysis of subjects on the basis of inflammatory markers and comorbidities including polyposis, asthma, and aspirin sensitivity. Finally, previously published bacterial data for this cohort were reanalyzed to evaluate associations with inflammatory markers and CRS subtypes. Inflammatory patterns were highly variable within standard CRS phenotypes. Cluster analysis identified eight subject clusters, with strong delineation on the basis of polyposis and asthma, but also subtle distinctions in inflammatory markers. An association was also identified between depletion of several "health-associated" bacterial taxa, reduced bacterial diversity and increased overall bacterial load, with markers of inflammation and clinical severity. This study contributes to ongoing efforts to define distinct endotypes of CRS on the basis of underlying inflammatory processes, and also offers compelling evidence of a link between bacterial community dysbiosis and inflammation in CRS. Further resolving the heterogeneity of CRS is vital to inform clinical management and personalized treatment approaches.


Assuntos
Inflamação/imunologia , Microbiota/imunologia , Pólipos Nasais/imunologia , Rinite/imunologia , Sinusite/imunologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Bactérias/classificação , Bactérias/genética , Bactérias/imunologia , Doença Crônica , Citocinas/genética , Citocinas/imunologia , Citocinas/metabolismo , Feminino , Variação Genética/imunologia , Humanos , Inflamação/genética , Inflamação/metabolismo , Masculino , Microbiota/genética , Pessoa de Meia-Idade , Pólipos Nasais/genética , Pólipos Nasais/metabolismo , Fenótipo , Rinite/genética , Rinite/metabolismo , Sinusite/genética , Sinusite/metabolismo , Adulto Jovem
14.
Artigo em Inglês | MEDLINE | ID: mdl-29270391

RESUMO

The chronic inflammatory nature of chronic rhinosinusitis (CRS) makes it a morbid condition for individuals with the disease and one whose pathogenesis is poorly understood. To date, proteomic approaches have been applied successfully in a handful of CRS studies. In this study we use a multifaceted approach, including proteomics (iTRAQ labeling) and microbiome (bacterial 16S rRNA gene sequencing) analyses of middle meatus swabs, as well as immune cell analysis of the underlying tissue, to investigate the host-microbe interaction in individuals with CRS (n = 10) and healthy controls (n = 9). Of the total 606 proteins identified in this study, seven were significantly (p < 0.05) more abundant and 104 were significantly lower in the CRS cohort compared with healthy controls. The majority of detected proteins (82% of proteins identified) were not significantly correlated with disease status. Elevated levels of blood and immune cell proteins in the CRS cohort, together with significantly higher numbers of B-cells and macrophages in the underlying tissue, confirmed the inflammatory status of CRS individuals. Protein PRRC2C and Ras-related protein (RAB14) (two of the seven elevated proteins) showed the biggest fold difference between the healthy and CRS groups. Validation of the elevated levels of these two proteins in CRS samples was provided by immunohistochemistry. Members of the bacterial community in the two study cohorts were not associated with PRRC2C, however members of the genus Moraxella did correlate with RAB14 (p < 0.0001, rho = -0.95), which is a protein involved in the development of basement membrane. In addition, significant correlations between certain members of the CRS bacterial community and 33 lower abundant proteins in the CRS cohort were identified. Members of the genera Streptococcus, Haemophilus and Veillonella were strongly correlated with CRS and were significantly associated with a number of proteins with varying functions. The results from this study reveal a strong association between the host and microbes in the sinonasal cavity. Proteins identified as associated with CRS could be new targets for drug therapies and biomarkers for assessment of treatment efficacy.


Assuntos
Interações Hospedeiro-Patógeno , Microbiota , Proteoma/análise , Sinusite/microbiologia , Sinusite/patologia , Adulto , Idoso , Linfócitos B/imunologia , Doença Crônica , Análise por Conglomerados , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Ribossômico/química , DNA Ribossômico/genética , Feminino , Humanos , Macrófagos/imunologia , Masculino , Pessoa de Meia-Idade , Filogenia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Adulto Jovem
15.
Clin Microbiol Rev ; 30(1): 321-348, 2017 01.
Artigo em Inglês | MEDLINE | ID: mdl-27903594

RESUMO

Chronic rhinosinusitis (CRS) encompasses a heterogeneous group of debilitating chronic inflammatory sinonasal diseases. Despite considerable research, the etiology of CRS remains poorly understood, and debate on potential roles of microbial communities is unresolved. Modern culture-independent (molecular) techniques have vastly improved our understanding of the microbiology of the human body. Recent studies that better capture the full complexity of the microbial communities associated with CRS reintroduce the possible importance of the microbiota either as a direct driver of disease or as being potentially involved in its exacerbation. This review presents a comprehensive discussion of the current understanding of bacterial, fungal, and viral associations with CRS, with a specific focus on the transition to the new perspective offered in recent years by modern technology in microbiological research. Clinical implications of this new perspective, including the role of antimicrobials, are discussed in depth. While principally framed within the context of CRS, this discussion also provides an analogue for reframing our understanding of many similarly complex and poorly understood chronic inflammatory diseases for which roles of microbes have been suggested but specific mechanisms of disease remain unclear. Finally, further technological advancements on the horizon, and current pressing questions for CRS microbiological research, are considered.


Assuntos
Bactérias/classificação , Fungos/classificação , Rinite/microbiologia , Sinusite/microbiologia , Anti-Infecciosos/uso terapêutico , Bactérias/crescimento & desenvolvimento , Bactérias/isolamento & purificação , Biofilmes , Ensaios Clínicos como Assunto , Fungos/crescimento & desenvolvimento , Fungos/isolamento & purificação , Humanos , Rinite/tratamento farmacológico , Rinite/virologia , Sinusite/tratamento farmacológico , Sinusite/virologia , Resultado do Tratamento , Vírus/classificação , Vírus/crescimento & desenvolvimento , Vírus/isolamento & purificação
16.
Int Forum Allergy Rhinol ; 7(3): 230-239, 2017 03.
Artigo em Inglês | MEDLINE | ID: mdl-27879060

RESUMO

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.


Assuntos
Disbiose/microbiologia , Rinite/microbiologia , Sinusite/microbiologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Doença Crônica , DNA Bacteriano/genética , Feminino , Humanos , Masculino , Microbiota/genética , Pessoa de Meia-Idade , Cavidade Nasal/microbiologia , RNA Ribossômico 16S/genética , Análise de Sequência de DNA , Adulto Jovem
17.
Environ Microbiol ; 19(1): 381-392, 2017 01.
Artigo em Inglês | MEDLINE | ID: mdl-27902866

RESUMO

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.


Assuntos
Bactérias/isolamento & purificação , Microbiota , Cavidade Nasal/microbiologia , Rinite/microbiologia , Sinusite/microbiologia , Bactérias/classificação , Bactérias/genética , Doença Crônica , Humanos , RNA Ribossômico 16S/genética
18.
PLoS One ; 11(10): e0163666, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27701448

RESUMO

In studies of the human microbiome, faecal samples are frequently used as a non-invasive proxy for the study of the intestinal microbiota. To obtain reliable insights, the need for bacterial DNA of high quality and integrity following appropriate faecal sample collection and preservation steps is paramount. In a study of dietary mineral balance in the context of type 2 diabetes (T2D), faecal samples were collected from healthy and T2D individuals throughout a 13-day residential trial. These samples were freeze-dried, then stored mostly at -20°C from the trial date in 2000/2001 until the current research in 2014. Given the relative antiquity of these samples (~14 years), we sought to evaluate DNA quality and comparability to freshly collected human faecal samples. Following the extraction of bacterial DNA, gel electrophoresis indicated that our DNA extracts were more sheared than extracts made from freshly collected faecal samples, but still of sufficiently high molecular weight to support amplicon-based studies. Likewise, spectrophotometric assessment of extracts revealed that they were of high quality and quantity. A subset of bacterial 16S rRNA gene amplicons were sequenced using Illumina MiSeq and compared against publicly available sequence data representing a similar cohort analysed by the American Gut Project (AGP). Notably, our bacterial community profiles were highly consistent with those from the AGP data. Our results suggest that when faecal specimens are stored appropriately, the microbial profiles are preserved and robust to extended storage periods.


Assuntos
Fezes/microbiologia , Viabilidade Microbiana , Microbiota , Preservação Biológica , Biodiversidade , DNA Bacteriano , Humanos , Metagenoma , Metagenômica , RNA Ribossômico 16S , Fatores de Tempo
19.
Front Microbiol ; 6: 130, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-25741335

RESUMO

The human gut contains dense and diverse microbial communities which have profound influences on human health. Gaining meaningful insights into these communities requires provision of high quality microbial nucleic acids from human fecal samples, as well as an understanding of the sources of variation and their impacts on the experimental model. We present here a systematic analysis of commonly used microbial DNA extraction methods, and identify significant sources of variation. Five extraction methods (Human Microbiome Project protocol, MoBio PowerSoil DNA Isolation Kit, QIAamp DNA Stool Mini Kit, ZR Fecal DNA MiniPrep, phenol:chloroform-based DNA isolation) were evaluated based on the following criteria: DNA yield, quality and integrity, and microbial community structure based on Illumina amplicon sequencing of the V4 region of bacterial and archaeal 16S rRNA genes. Our results indicate that the largest portion of variation within the model was attributed to differences between subjects (biological variation), with a smaller proportion of variation associated with DNA extraction method (technical variation) and intra-subject variation. A comprehensive understanding of the potential impact of technical variation on the human gut microbiota will help limit preventable bias, enabling more accurate diversity estimates.

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