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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.
Front Cell Infect Microbiol ; 11: 585625, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34595125

RESUMO

Background: Chronic rhinosinusitis (CRS) is a globally prevalent inflammatory condition of the paranasal sinuses which severely impairs patients' quality of life. An animal model of unilateral sinusitis by transient sinus occlusion has been described previously in rabbits. The aim of this study was to characterise the sinusitis rabbit model by investigating temporal and bilateral changes in the bacterial community and mucosal inflammation. Methods: Development of sinusitis was achieved by endoscopically placing Merocel ® , a sterile nasal packing material, in the left middle meatus of six New Zealand white rabbits for four weeks. After a total period of 14 weeks, rabbits were assessed for sinusitis by endoscopic examination, magnetic resonance imaging (MRI) and histology. Swabs from the left and right middle meatus were obtained for bacterial community analysis at three time points (week 0, week 4, week 14) during the study. Results: Endoscopic evaluation showed unilateral inflammation in all animals examined after the 4-week blocking period and at week 14. Notably, inflammatory changes were also seen in the contralateral sinus of all animals at week 4. MRI images demonstrated unilateral sinus opacification at week 4 in two rabbits, and partial unilateral sinus opacification at week 14 in one rabbit only. Histological analyses revealed substantial spatial heterogeneity of mucosal inflammation with inconsistent findings across all animals. No significant differences in mucosal inflammatory markers (such as goblet cell hyperplasia, epithelial denudation and oedema) could be identified between nostrils at week 14. The bacterial community in the rabbit sinuses was heavily dominated by Helicobacter at week 0 (baseline). At the end of the blocking period (week 4), bacterial alpha and beta diversity were significantly increased in both nostrils. The bacterial community composition at week 14 had primarily returned to baseline, reflecting the endoscopic and radiological results. Conclusion: This study reaffirmed the ability for development of sinusitis without inoculation of any pathogens in a rabbit model. We were able to demonstrate bilateral sinonasal mucosal inflammation, by inducing unilateral sinus blockage, which resulted in significant changes to the sinonasal bacterial community. These findings may explain some of the clinical observations seen in CRS and warrant further research to reveal potential implications for its therapeutic management.


Assuntos
Seios Paranasais , Sinusite , Animais , Doença Crônica , Humanos , Inflamação , Cavidade Nasal , Seios Paranasais/diagnóstico por imagem , Qualidade de Vida , Coelhos , Sinusite/diagnóstico por imagem
3.
Immun Inflamm Dis ; 9(1): 90-107, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33220024

RESUMO

INTRODUCTION: The pathophysiology and temporal dynamics of affected tissues in chronic rhinosinusitis (CRS) remain poorly understood. Here, we present a multiomics-based time-series assessment of nasal polyp biopsies from three patients with CRS, assessing natural variability over time and local response to systemic corticosteroid therapy. METHODS: Polyp tissue biopsies were collected at three time points over two consecutive weeks. Patients were prescribed prednisone (30 mg daily) for 1 week between Collections 2 and 3. Polyp transcriptome, proteome, and microbiota were assessed via RNAseq, SWATH mass spectrometry, and 16S ribosomal RNA and ITS2 amplicon sequencing. Baseline interpatient variability, natural intrapatient variability over time, and local response to systemic corticosteroids, were investigated. RESULTS: Overall, the highly abundant transcripts and proteins were associated with pathways involved in inflammation, FAS, cadherin, integrin, Wnt, apoptosis, and cytoskeletal signaling, as well as coagulation and B- and T-cell activation. Transcripts and proteins that naturally varied over time included those involved with inflammation- and epithelial-mesenchymal transition-related pathways, and a number of common candidate target biomarkers of CRS. Ten transcripts responded significantly to corticosteroid therapy, including downregulation of TNF, CCL20, and GSDMA, and upregulation of OVGP1, and PCDHGB1. Members of the bacterial genus Streptococcus positively correlated with immunoglobulin proteins IGKC and IGHG1. CONCLUSIONS: Understanding natural dynamics of CRS-associated tissues is essential to provide baseline context for all studies on putative biomarkers, mechanisms, and subtypes of CRS. These data further our understanding of the natural dynamics within nasal polypoid tissue, as well as local changes in response to systemic corticosteroid therapy.


Assuntos
Microbiota , Pólipos Nasais , Rinite , Sinusite , Corticosteroides/uso terapêutico , Humanos , Pólipos Nasais/tratamento farmacológico , Proteínas de Neoplasias , Rinite/tratamento farmacológico , Sinusite/tratamento farmacológico
4.
Sci Rep ; 10(1): 13201, 2020 08 06.
Artigo em Inglês | MEDLINE | ID: mdl-32764634

RESUMO

Xerostomia detrimentally affects the oral health of many head and neck cancer patients who undergo radiotherapy. Its sequelae become an ongoing burden for patients that often manifest as periodontal disease and dental decay. Bacteria play a major role in the pathogenesis of these conditions and here we explore the use of an oral probiotic to beneficially modulate the oral bacterial community post-radiotherapy. In this pilot study, a four-week intervention with oral probiotic lozenges containing Streptococcus salivarius M18 was trialled in seven patients. Post-intervention changes in oral health and in the composition of the plaque and saliva bacterial communities were compared with six patients in a placebo group. An improvement in periodontal screening and plaque index scores was observed in both groups after the intervention period. The oral probiotic lozenges did not significantly impact bacterial community composition or diversity, nor did the probiotic lozenges increase the relative sequence abundance of ZOTU_1 (the probiotic-associated sequence assigned to S. salivarius) detected in the samples. Network analyses suggest negative interactions occurred between ZOTU_1 and species from the periopathogenic genera Campylobacter, Fretibacterium, Selenomonas and Treponema but further investigation is required to more fully understand the beneficial properties of this oral probiotic.


Assuntos
Neoplasias de Cabeça e Pescoço/microbiologia , Neoplasias de Cabeça e Pescoço/radioterapia , Probióticos/farmacologia , Streptococcus salivarius/fisiologia , Administração Oral , Biodiversidade , Estudos de Coortes , Método Duplo-Cego , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Projetos Piloto , Probióticos/administração & dosagem
5.
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
6.
Environ Microbiol ; 22(9): 3985-3999, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32827171

RESUMO

Marine sponge reefs usually comprise a complex array of taxonomically different sponge species, many of these hosting highly diverse microbial communities. The number of microbial species known to occupy a given sponge ranges from tens to thousands, bringing numerous challenges to their analysis. One way to deal with such complexity is to use a core microbiota approach, in which only prevalent and abundant microbes are considered. Here we aimed to test the strength and sensitivity of the core microbiota approach by applying different core definitions to 20 host sponge species. Application of increasingly stringent relative abundance and/or percentage occurrence thresholds to qualify as part of the core microbiota decreased the number of 'core' OTUs and phyla and, consequently, changed both alpha- and beta-diversity patterns. Moreover, microbial co-occurrence patterns explored using correlation networks were also affected by the core microbiota definition. The application of stricter thresholds resulted in smaller and less compartmentalized networks, with different keystone species. These results highlight that the application of different core definitions to phylogenetically disparate host species can result in the drawing of markedly different conclusions. Consequently, we recommend to assess the effects of different core community definitions on the specific system of study before considering its application.


Assuntos
Microbiota/genética , Poríferos/microbiologia , Animais , Bactérias/classificação , Bactérias/genética , Bactérias/isolamento & purificação , Biodiversidade , Metagenoma , Filogenia , Poríferos/classificação
7.
Int Forum Allergy Rhinol ; 10(9): 1057-1064, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32662249

RESUMO

BACKGROUND: Chronic rhinosinusitis (CRS) is a spectrum of complex inflammatory conditions of the sinonasal mucosa. Identification of biomarkers that enable classification and improved delineation among CRS endotypes is of increasing interest. However, the extent to which less invasive sampling methods identify genuine tissue inflammatory patterns is not well understood. The aim of this study was to investigate mucosal swab and cytobrush sampling as less invasive proxies for tissue transcription levels of putative biomarkers of CRS. METHODS: Expression levels of 21 biomarkers of interest were assessed via custom TaqMan array cards from mucosal biopsy, cytobrush, and swab samples, in 32 patients with CRS. Reported expression levels were compared between each of the 3 sample types within each patient. RESULTS: Reported transcription levels from swab samples for IL33, MUC5AC, IL1RN, CXCL8 (IL-8), TNF, IFNG, IL5, OSM, IL1A, and IL17C, and cytobrush levels for IL33, MUC5AC, IL5RA, IL1RN, CXCL8 (IL-8), and IL5 were significantly different to tissue levels from matched biopsy samples. CONCLUSION: Reported expression via swab and cytobrush sampling differed from patterns observed in matched tissue for 10 of 21 and 6 of 21 markers, respectively. Non-biopsy-based studies for these particular markers may therefore not adequately represent tissue inflammatory processes and should be interpreted with caution. Cytobrush samples largely tracked tissue patterns for the remaining target biomarkers. In these cases, cytobrush sampling appears to adequately reflect tissue patterns for several putative biomarkers of CRS, supporting their use in clinical and research settings as a less-invasive proxy for the assessment of mucosal tissue inflammatory transcription patterns.


Assuntos
Pólipos Nasais , Rinite , Sinusite , Biomarcadores , Doença Crônica , Humanos , Mucina-5AC , Rinite/diagnóstico , Sinusite/diagnóstico
8.
mBio ; 11(1)2020 01 07.
Artigo em Inglês | MEDLINE | ID: mdl-31911491

RESUMO

Diet and host phylogeny drive the taxonomic and functional contents of the gut microbiome in mammals, yet it is unknown whether these patterns hold across all vertebrate lineages. Here, we assessed gut microbiomes from ∼900 vertebrate species, including 315 mammals and 491 birds, assessing contributions of diet, phylogeny, and physiology to structuring gut microbiomes. In most nonflying mammals, strong correlations exist between microbial community similarity, host diet, and host phylogenetic distance up to the host order level. In birds, by contrast, gut microbiomes are only very weakly correlated to diet or host phylogeny. Furthermore, while most microbes resident in mammalian guts are present in only a restricted taxonomic range of hosts, most microbes recovered from birds show little evidence of host specificity. Notably, among the mammals, bats host especially bird-like gut microbiomes, with little evidence for correlation to host diet or phylogeny. This suggests that host-gut microbiome phylosymbiosis depends on factors convergently absent in birds and bats, potentially associated with physiological adaptations to flight. Our findings expose major variations in the behavior of these important symbioses in endothermic vertebrates and may signal fundamental evolutionary shifts in the cost/benefit framework of the gut microbiome.IMPORTANCE In this comprehensive survey of microbiomes of >900 species, including 315 mammals and 491 birds, we find a striking convergence of the microbiomes of birds and animals that fly. In nonflying mammals, diet and short-term evolutionary relatedness drive the microbiome, and many microbial species are specific to a particular kind of mammal, but flying mammals and birds break this pattern with many microbes shared across different species, with little correlation either with diet or with relatedness of the hosts. This finding suggests that adaptation to flight breaks long-held relationships between hosts and their microbes.


Assuntos
Evolução Biológica , Aves , Quirópteros , Microbioma Gastrointestinal , Vertebrados , Animais , Biologia Computacional/métodos , Metagenoma , Metagenômica/métodos
9.
Support Care Cancer ; 28(6): 2683-2691, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-31650293

RESUMO

PURPOSE: Oral mucositis (OM) remains a significant complication developed by many patients undergoing radiotherapy (RT) to the head and neck region. Emerging data suggest oral microbes may contribute to the onset and severity of this acute side effect. METHODS: In this study, saliva and oral swabs from head and neck cancer patients undergoing RT were collected. We employed molecular microbiological techniques to study the bacterial communities present in saliva, and both the bacterial and fungal communities present on the buccal mucosa and lateral tongue. Changes in microbiota composition with increasing radiation dose and the presence of mucositis were examined. RESULTS: The data suggest that the salivary microbiota remain stable during RT and are consistently dominated by Streptococcus, Prevotella, Fusobacterium and Granulicatella. Obligate and facultative anaerobic Gram-negative bacilli (GNB) Bacteroidales G2, Capnocytophaga, Eikenella, Mycoplasma and Sneathia, as well as anaerobic GNB in the periopathogenic genera Porphyromonas and Tannerella, were all positively correlated with ≥ grade 2 OM. Significant increases in the relative abundances of Bacteroidales G2, Fusobacterium and Sneathia were identified in buccal mucosa swabs at sites of ≥ grade 2 OM (p < 0.05). Furthermore, the abundance of several GNB (Fusobacterium, Haemophilus, Tannerella, Porphyromonas and Eikenella) on the buccal mucosa may influence patient susceptibility to developing OM. Candida was widely detected in buccal mucosa swabs, regardless of mucositis status. CONCLUSIONS: Our findings support previously hypothesized associations between oral health and the pathogenesis of OM, highlighting the importance of oral health interventions for head and neck cancer patients.


Assuntos
Bactérias/classificação , Candida/isolamento & purificação , Neoplasias de Cabeça e Pescoço/radioterapia , Mucosa Bucal/microbiologia , Saliva/microbiologia , Estomatite/microbiologia , Bactérias/isolamento & purificação , Feminino , Humanos , Masculino , Microbiota , Pessoa de Meia-Idade , Saúde Bucal , Estomatite/etiologia , Língua/microbiologia
10.
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.

11.
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
12.
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
14.
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
16.
Front Microbiol ; 9: 2208, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30283425

RESUMO

Interest in the human microbiome has increased dramatically in the last decade. However, much of this research has focused on bacteria, while the composition and roles of their fungal counterparts remain less understood. Furthermore, a variety of methodological approaches have been applied, and the comparability between studies is unclear. This study compared four primer pairs targeting the small subunit (SSU) rRNA (18S), ITS1, ITS2, and large subunit (LSU) rRNA (26S) genomic regions for their ability to accurately characterize fungal communities typical of the human mycobiota. All four target regions of 21 individual fungal mock community taxa were capable of being amplified adequately and sequenced. Mixed mock community analyses revealed marked variability in the ability of each primer pair to accurately characterize a complex community. ITS target regions outperformed LSU and SSU. Of the ITS regions, ITS1 failed to generate sequences for Yarrowia lipolytica and all three Malassezia species when in a mixed community. These findings were further supported in studies of human sinonasal and mouse fecal samples. Based on these analyses, previous studies using ITS1, SSU, or LSU markers may omit key taxa that are identified by the ITS2 marker. Of methods commonly used in human mycobiota studies to date, we recommend selection of the ITS2 marker. Further investigation of more recently developed fungal primer options will be essential to ultimately determine the optimal methodological approach by which future human mycobiota studies ought to be standardized.

17.
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
18.
Ecology ; 99(9): 1920-1931, 2018 09.
Artigo em Inglês | MEDLINE | ID: mdl-29989167

RESUMO

Anthropogenic stressors are impacting ecological systems across the world. Of particular concern are the recent rapid changes occurring in coral reef systems. With ongoing degradation from both local and global stressors, future reefs are likely to function differently from current coral-dominated ecosystems. Determining key attributes of future reef states is critical to reliably predict outcomes for ecosystem service provision. Here we explore the impacts of changing sponge dominance on coral reefs. Qualitative modelling of reef futures suggests that changing sponge dominance due to increased sponge abundance will have different outcomes for other trophic levels compared with increased sponge dominance as a result of declining coral abundance. By exploring uncertainty in the model outcomes we identify the need to (1) quantify changes in carbon flow through sponges, (2) determine the importance of food limitation for sponges, (3) assess the ubiquity of the recently described "sponge loop," (4) determine the competitive relationships between sponges and other benthic taxa, particularly algae, and (5) understand how changing dominance of other organisms alters trophic pathways and energy flows through ecosystems. Addressing these knowledge gaps will facilitate development of more complex models that assess functional attributes of sponge-dominated reef ecosystems.


Assuntos
Antozoários , Ecossistema , Animais , Carbono , Mudança Climática , Recifes de Corais
19.
Sci Rep ; 8(1): 8128, 2018 05 25.
Artigo em Inglês | MEDLINE | ID: mdl-29802288

RESUMO

The kakapo is a critically endangered, herbivorous parrot endemic to New Zealand. The kakapo hindgut hosts a dense microbial community of low taxonomic diversity, typically dominated by Escherichia fergusonii, and has proven to be a remarkably stable ecosystem, displaying little variation in core membership over years of study. To elucidate mechanisms underlying this robustness, we performed 16S rRNA gene-based co-occurrence network analysis to identify potential interactions between E. fergusonii and the wider bacterial community. Genomic and metagenomic sequencing were employed to facilitate interpretation of potential interactions observed in the network. E. fergusonii maintained very few correlations with other members of the microbiota, and isolates possessed genes for the generation of energy from a wide range of carbohydrate sources, including plant fibres such as cellulose. We surmise that this dominant microorganism is abundant not due to ecological interaction with other members of the microbiota, but its ability to metabolise a wide range of nutrients in the gut. This research represents the first concerted effort to understand the functional roles of the kakapo microbiota, and leverages metagenomic data to contextualise co-occurrence patterns. By combining these two techniques we provide a means for studying the diversity-stability hypothesis in the context of bacterial ecosystems.


Assuntos
Espécies em Perigo de Extinção , Fezes/microbiologia , Metagenômica/métodos , Microbiota , Papagaios/genética , Papagaios/microbiologia , Animais
20.
Artigo em Inglês | MEDLINE | ID: mdl-29517178

RESUMO

BACKGROUND: Antibiotics and corticosteroids are prescribed to patients with chronic rhinosinusitis (CRS) to reduce bacterial burden and mucosal inflammation. Unfortunately, clinical improvement is often short-lived and symptoms frequently recur following cessation of treatment. The impact of these systemic therapies on bacterial communities is not well understood. Improved knowledge of how medical therapies influence the intranasal ecosystem may allow for more effective prescribing and the development of more targeted treatments. METHODS: Twenty patients with CRS were randomized to receive either doxycycline 100 mg twice daily or prednisone 30 mg once daily for 7 days. A further 6 patients with CRS were recruited as untreated controls. Swabs were taken immediately before and after the study period. Symptom scores (22-item Sino-Nasal Outcome Test [SNOT-22]) were recorded. Bacterial communities were characterized using 16S ribosomal RNA (rRNA) gene-targeted amplicon sequencing. Bacterial abundance was estimated using quantitative polymerase chain reaction (PCR) of 16S rRNA gene copies. RESULTS: Bacterial profiles were dominated by members of the genera Corynebacterium and Staphylococcus. Patients treated with either doxycycline or prednisone had variable and unpredictable changes in communities. The average relative abundance of Propionibacterium increased after treatment in the doxycycline treatment group, and Corynebacterium reduced in the prednisone group. Significant differences in clinical scores, bacterial community richness, diversity, and bacterial abundance were not seen after treatment. CONCLUSION: The short-term response of bacterial communities to antibiotic or corticosteroid therapy is unpredictable. This study suggests that the use of systemic therapy in patients with stable CRS should be rationalized to minimize antibiotic-associated morbidity and bacterial dysbiosis.

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