Composition Of Respiratory Microbiota Research Articles

Yinhuang buccal tablet alters airway microbiota composition and metabolite profile in healthy humans

Ethnopharmacological relevancePerturbations in airway microbiota composition and disruption of microbe-metabolite interactions have been observed in respiratory infectious diseases (RIDs). The Yinhuang (YH) buccal tablet, as an ancient Chinese medicinal formula, has been traditionally employed for the management of upper RIDs. However, there is a lack of evidence for the effects of YH buccal tablets on upper respiratory tract microbiota and circulating metabolites. Aim of the studyThe aim of this study was to analyze the changes in respiratory microbiota composition and circulating metabolite profile after YH buccal tablets administration. Materials and methodsThroat swab samples and serum samples were collected from 60 healthy subjects for high-throughput 16S ribosomal RNA gene (16S rRNA) sequencing and non-targeted Ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) analysis. ResultsAirway microbial composition changed significantly after YH administration. The abundance of Actinomyces and Prevotella_7 increased, while the abundance of potentially pathogenic Pseudomonas and Corynebacterium decreased. A total of 168 significant HMDB taxonomic metabolites were identified in serum samples, of which lipid metabolites accounted for the largest proportion. Correlation analysis showed that circulatory metabolites were significantly correlated with changes in airway microbiota composition. ConclusionsYH buccal tablets can inhibit opportunistic pathogens, increase beneficial microorganisms in the upper respiratory tract, and regulate the body's metabolic pathways. These findings provide insights into the mechanism of action of YH buccal tablets in the treatment and prevention of respiratory diseases.

Synergistic anti-infectious bronchitis virus activity of Phillygenin combined Baicalin by modulating respiratory microbiota and improving metabolic disorders

Phillygenin (PHI) and Baicalin (Bai) are the major chemical ingredients extracted from Forsythia suspensa and Scutellaria baicalensis, respectively. The mixture of Forsythia suspensa and Scutellaria baicalensis according to the theories of Traditional Chinese Veterinary Medicine, compounded formulation can effectively exert heat-clearing and detoxifying effect, but the synergistic anti-IBV activity of PHI combined with Bai was unclear. Here, the protection of PHI combined with Bai on avian infectious bronchitis virus (IBV) M41 infection and the change of respiratory microbiota and metabolomics profiles in broilers that infected with IBV were investigated. According to the experimental findings, the combination of PHI and Bai effectively alleviated broilers' slowing-growth weight and respiratory symptoms. This was accompanied by a reduction in viral copies and histopathological changes, as well as an increase of antiviral protein (G3BP1) level in tracheas and anti-IBV antibody levels in serum. In addition, 16s RNA sequencing revealed that IBV infection significantly changed respiratory microbiota composition at different taxonomic levels and respiratory metabolism composition in broilers. Interestingly, PHI combined with Bai modulated the composition of respiratory microfloras, especially the abundance of Firmicutes and Lactobacillaceae were upregulated, as well as the abundance of Proteobacteria was downregulated. The metabolomics results indicated that PHI combined with Bai involved in glucose, lipids, amino acids and nucleotide metabolism during IBV infection. In summary, PHI combined with Bai exhibited a synergistic effect on preventing infectious bronchitis (IB), with the protection being closely associated with the composition of respiratory microbiota and metabolites. Therefore, adding the mixture of PHI and Bai to the chicken drinking water is recommended to prevent and control IB in clinical.

Host-specific signatures of the respiratory microbiota in domestic animals

While the importance of respiratory microbiota in maintaining respiratory health is increasingly recognized, we still lack a comprehensive understanding of the unique characteristics of respiratory microbiota specific to individual hosts. This study aimed to address this gap by analyzing publicly available 16S rRNA gene datasets from various domestic animals (cats, dogs, pigs, donkeys, chickens, sheep, and cattle) to identify host-specific signatures of respiratory microbiota. The findings revealed that cattle and pigs exhibited the highest Shannon diversity index and observed features, indicating a greater microbial variety compared to other animals. Discriminant analysis demonstrated distinct composition of respiratory microbiota across different animals, with no overlapping abundant taxa. The linear discriminant analysis effect size highlighted prevalent host-specific microbiota signatures in different animal species. Moreover, the composition and diversity of respiratory microbiota were significantly influenced by various factors such as individual study, health status, and sampling sites within the respiratory tract. While associations between host and respiratory microbiota have been uncovered, the relative contributions of host and environment in the selection of respiratory microbiota and their impact on host fitness remain unclear. Further investigations involving diverse hosts are necessary to fully comprehend the significance of host-microbial coevolution in maintaining respiratory health.

Distinct respiratory microbiota associates with lung cancer clinicopathological characteristics.

Commensal microbiota dysbiosis is associated with the development of lung cancer. The current studies about composition of respiratory microbiota in lung cancer patients yielded inconsistent results. This study aimed to examine the association between airway microbiota and lung cancer clinicopathological characteristics. Surgically removed lesion tissues from 75 non-small cell lung cancer patients and 7 patients with benign pulmonary diseases were analyzed by 16S rRNA sequencing. Taxonomy, relative abundance, and diversity of respiratory microbiota were compared among lung cancer of different pathology and TNM stages. The effects of antibiotic and cigarette exposure on respiratory microbiota in lung cancer patients were also evaluated. Bacterial relative abundance and alpha- and beta-diversity analysis of lung microbiota showed significant differences among lung cancer of different pathology and benign pulmonary diseases. At the genus level, the abundance differences of 13 taxa between lung squamous cell carcinoma and lung adenocarcinoma, 63 taxa between lung squamous cell carcinoma and benign pulmonary diseases, and 4 taxa between lung adenocarcinoma and benign pulmonary diseases reached statistical significance. In contrast, diversity differences were not as significant across lung cancer of different stages. No significant differences were observed in tissue taxonomic abundances and diversity at all taxonomic levels between lung cancer patients with and without antibiotic exposure 3 months prior to surgery. For lung adenocarcinoma, respiratory bacterial abundance and diversity at all taxonomic levels did not show significant differences between smokers and non-smokers. Our results confirm significantly differential respiratory microbiome taxa, abundance, and diversity in lung cancer of different pathology and some stages. Short-term antibiotic application might play a minor role in molding airway microbiota in lung cancer patients. Composition and diversity of respiratory microbiota in lung adenocarcinoma are not affected by cigarette exposure.

Airway microecology in rifampicin-resistant and rifampicin-sensitive pulmonary tuberculosis patients

BackgroundPulmonary tuberculosis is a chronic infectious disease of the respiratory system. It is still one of the leading causes of death from a single infectious disease, but it has been stuck in the study of a single pathogen. Recent studies have shown that many diseases are associated with disruption of the native microbiota. In this study we investigated the occurrence of tuberculosis and the correlation between drug resistance and respiratory flora. High-throughput 16 S rRNA gene sequencing was used to characterize the respiratory microbiota composition of 30 tuberculosis (TB) affected patients and compared with 30 healthy (H) controls. According to their Gene Xpert results, 30 pulmonary tuberculosis patients were divided into 12 persons in the drug-sensitive group (DS0) and 18 persons in the drug-resistant group (DR0). The microbial flora of the two were compared with the H group.ResultsThe data generated by sequencing showed that Firmicutes, Proteus, Bacteroides, Actinomyces and Fusobacterium were the five main bacterial phyla detected, and they constituted more than 96% of the microbial community. The relative abundances of Fusobacterium, Haemophilus, Porphyromonas, Neisseria, TM7, Spirochetes, SR1, and Tenericutes in the TB group was lower than that of the H group, and Granulicatella was higher than the H group. The PcoA diagrams of the two groups had obvious clustering differences. The Alpha diversity of the TB group was lower than that of the H group, and the Beta diversity was higher than that of the H group (P < 0.05). The relative abundance of Streptococcus in the DS0 group was significantly higher than that in the DR0 group (P < 0.05).ConclusionPulmonary tuberculosis can cause disorders of the respiratory tract microbial flora, in which the relative abundance of Streptococcus was significantly different between rifampicin-sensitive and rifampicin-resistant patients.

Liu Shen Capsule Alters Airway Microbiota Composition and Metabolite Profiles in Healthy Humans.

Alteration in airway microbiota composition and perturbations in microbe-metabolites interactions have been proposed as markers of many diseases. Liu Shen (LS) capsule, a traditional Chinese medicine, was proved as favorable in treating respiratory diseases. However, the effects of the LS capsule in terms of regulating human microorganisms and metabolite profiles are not well known. This study aimed to define and compare the respiratory microbiota composition and circulating and fecal metabolite profiles before and after LS capsule administration. A total of 30 healthy volunteers were recruited. The pharyngeal swab samples were collected for 16S rRNA gene sequencing. The serum and fecal samples were collected to analyze the non-targeted ultra-performance liquid chromatography–tandem mass spectrometry metabolomics. The airway microbial compositions were profoundly altered after LS capsule administration, as evidenced by increased microbial diversity and altered microbial taxa distribution. The increasing abundance of bacterial Bifidobacteria, and Lactobacillus characterized the after-administration groups, and the increasing of abundance bacterial Proteobacteria, Veillonella, Prevotella, Neisseria, and Actinomyces characterized the before-administration groups. Significant discriminations were observed in both serum and fecal metabolic profiles between the before- and after-administration groups. A total number of 134 and 71 significant HMDB taxonomic metabolites including glycerophospholipids, fatty acyls, and prenol lipids in the serum and fecal samples were identified respectively between the before- and after-administration groups. The integrated analysis showed that some altered airway microbiota phylum, such as Bacteroidetes and Proteobacteria, significantly correlated with metabolites in serum and fecal. Hence, our study reported the alternations in the composition and functions of the airway microbial community and the changes in circulating and fecal metabolite profiles after LS capsule administration in healthy humans, thus providing a novel insight into the mechanisms underlying the role of LS capsule treating and preventing related diseases.

Mycoplasma gallisepticum induced inflammation-mediated Th1/Th2 immune imbalance via JAK/STAT signaling pathway in chicken trachea: Involvement of respiratory microbiota

The respiratory microbiota plays a significant role in the host defense against Mycoplasma gallisepticum (MG) infection. The results showed that MG infection changed respiratory microbiota composition, which lead to the tracheal inflammation injury and oxidative stress. MG infection significantly induced immunosuppression in chickens at day 3 and 5 post-infection. In addition, MG infection increased the expressions of pro-inflammatory cytokines in tracheal tissues and activated TLR4 mediated JAK/STAT signaling pathway at day 3 post-infection compared to the control group. Meanwhile, the expressions of pro-inflammatory cytokines were decreased and the expressions of JAK/STAT signaling pathway were decreased at day 5 and day 7 post-infection. On the contrary, the expressions of anti-inflammatory cytokines were significantly decreased at day 3 post-infection and were increased at day 5 and day 7 post-infection in the MG infection group. The antibiotic cocktail group received the respiratory microbiota from the MG infection group, which induced inflammatory injury and oxidative stress, induced mucosal barrier damage by down regulating tight junction-related genes and altered the expressions of mucin, which could be the possible causes of dysregulated immune responses. Importantly, the expressions of pro-inflammatory cytokines were significantly decreased and TLR4 mediated JAK/STAT signaling pathway was downregulated at day 1 and 3 post-transplantation. While, respiratory microbiota transplanted from MG infection significantly increased the expressions of pro-inflammatory cytokines and activated JAK/STAT signaling at day 7 post-transplantation. These results highlighted the role of respiratory microbiota in MG-induced tracheal inflammation injury, and offered a new strategy for the preventive intervention of this disease.

Microbiota - The Unseen Players in Adult Asthmatic Airways.

Modulation of human lung airway physiology by commensal microbiota has become one of the key mechanisms involved in the pathogenesis of adult asthma. Recent evidence suggests that the composition of respiratory microbiota plays a significant role in the manifestation of adult asthma; however, scientific evidence about the relationship between airway microbial diversity and phenotypes of adult asthma is limited. Further research is needed to understand the interactions between the airway microbiota and host immune response to develop microbiota-based strategies in management of adult asthma. This study reviews the advances in culture-independent methods for detection of airway microbiome, the current data about airway microbiota in healthy individuals and in adult patients with asthma with a focus on bacterial communities, and the future research directions in airway microbiome.

Altered respiratory microbiota composition and functionality associated with asthma early in life

BackgroundThe microbiota of the respiratory tract has an important role in maintaining respiratory health. However, little is known on the respiratory microbiota in asthmatic patients among Middle Eastern populations. This study investigated the respiratory microbiota composition and functionality associated with asthma in Emirati subjects.MethodsWe performed 16S rRNA and ITS2-gene based microbial profiling of 40 expectorated sputum samples from adult and pediatric Emirati individuals averaging 52 and 7 years of age, respectively with or without asthma.ResultsWe report bacterial difference belonging to Bacteroidetes, Firmicutes, Fusobacteria and Proteobacteria phyla between asthmatic and non-asthmatic controls. Similarly, fungal difference belonging to Ascomycota, Basidiomycota phyla and other unclassified fungi. Differential abundance testing among asthmatic individuals with relation to Asthma Control Test show a significant depletion of Penicillium aethiopicum and Alternaria spp., among poorly controlled asthmatics. Moreover, data suggest a significant expansion of Malassezia spp. and other unclassified fungi in the airways of those receiving steroids and leukotriene receptor antagonists’ combination therapy, in contrast to those receiving steroids alone. Functional profiling from 16S data showed marked differences between pediatric asthmatic and non-asthmatic controls, with pediatric asthmatic patients showing an increase in amino acid (p-value < 5.03 × 10− 7), carbohydrate (p-value < 4.76 × 10− 7), and fatty acid degradation (p-value < 6.65 × 10− 7) pathways, whereas non-asthmatic controls are associated with increase in amino acid (p-value < 8.34 × 10− 7), carbohydrate (p-value < 3.65 × 10− 7), and fatty acid (p-value < 2.18 × 10− 6) biosynthesis pathways in concordance with enterotype composition.ConclusionsThese differences provide an insight into respiratory microbiota composition in Emirati population and its possible role in the development of asthma early in life. This study provides important information that may eventually lead to the development of screening biomarkers to predict early asthma development and novel therapeutic approaches.

Altered Airway Microbiota Composition in Patients With Pulmonary Hypertension.

Alteration in microbiota composition of respiratory tract has been reported in the progression of many chronic lung diseases, yet, the correlation and causal link between respiratory tract microbiota and the disease development of pulmonary hypertension (PH) remain largely unknown. This study aims to define and compare the respiratory microbiota composition in pharyngeal swab samples between patients with PH and reference subjects. A total of 118 patients with PH and 79 reference subjects were recruited, and the pharyngeal swab samples were collected to sequence the 16S ribosomal RNA (16S rRNA) V3-V4 region of respiratory microbiome. The relative abundances in patients with PH were profoundly different from reference subjects. The Ace and Sobs indexes indicated that the microbiota richness of pharynx value is significantly higher; while the community diversity value is markedly lower in patients with PH, comparing to those of the reference subjects. The microbiota on pharynx showed a different profile between the 2 groups by principal component analysis. The linear discriminant analysis effect size also revealed a significantly higher proportion of Streptococcus, Lautropia, and Ralstonia in patients with PH than reference subjects. The linear discriminant analysis effect size output, which represents the microbial gene functions, suggest genes related to bacterial invasion of epithelial cells, bacterial toxins were enhanced, while genes related to energy metabolism, protein digestion and absorption, and cell division pathways were attenuated in patients with PH versus reference subjects. In summary, our study reports the first systematic definition and divergent profile of the upper respiratory tract microbiota between patients with PH and reference subjects.

Infant respiratory syncytial virus prophylaxis and nasopharyngeal microbiota until 6 years of life: a subanalysis of the MAKI randomised controlled trial

Respiratory syncytial virus (RSV) infection during infancy is suggested to cause long-term wheeze. In turn, wheeze has been associated with bacterial dysbiosis of the respiratory tract. We investigated the effects of RSV prophylaxis with palivizumab in otherwise healthy preterm infants on respiratory microbiota composition at 1 year and 6 years of age. In a multicentre, single-blind, randomised, placebo-controlled trial (the MAKI trial), infants born between 32-35 weeks of gestation, in one university and in 15 regional hospitals in the the Netherlands, were randomly assigned (1:1) to receive palivizumab or placebo during the RSV season of their first year of life. Intramuscular injections of palivizumab 15 mg/kg or placebo were given during one RSV season: either from Oct 1, or from discharge from the neonatal unit until March 10 (minimun of 2 and maximum of 5 injections were given). Children were 6 months old or younger at the start of the RSV season; exclusion criteria included congenital heart disease, bronchopulmonary dysplasia, Down's syndrome, or other serious congenital disorders, use of mechanical ventilation at birth, treatment with surfactant, or physician-diagnosed wheeze before the start of the RSV season. Children were followed up for clinical symptoms until 6 years of age. For this subanalysis, we obtained nasopharyngeal swabs from children aged 1 year and 6 years and analysed them using 16S-rRNA sequencing. At 6 years we also measured reversible airway obstruction. The primary outcome was the effect of palivizumab during infancy on the respiratory microbiota composition at age 1 year and 6 years (intention-to-treat analysis). The trial is registered in the ISRCTN registry, number ISRCTN73641710. From April 1, 2008, to Dec 31, 2010, 429 infants were enrolled in the MAKI trial (n=214 to the palivizumab group; n=215 to the placebo group). At 1 year, we collected swabs and sequenced DNA from 170 (40%) of 429 children, of which 145 (85%) samples had high-quality DNA. The overall microbiota composition was significantly different (R2 1·3%; p=0·0185) between the palivizumab group and the placebo group at 1 year of life; children in the palivizumab group had a significantly lower abundance of the Staphylococcus-dominated cluster (odds ratio 0·28 [95% CI 0·11-0·68]; p=0·00394), an increased abundance of biomarker species, such as Klebsiella, and a more diverse set of oral taxa, including Streptococcus spp, compared with children in the placebo group. At 6 years, we collected swabs and sequenced DNA from 349 (88%) of 395 children who completed follow-up, of which 342 (98%) samples had high-quality DNA. The overall microbiota composition was not significantly different between groups at 6 years (R2 0·6%; p=0·0575); however, children in the palivizumab group had a significantly increased abundance of Haemophilus spp and lower abundance of Moraxella and Neisseriaceae spp compared with children in the placebo group. Absence of PCR-confirmed RSV infection at 1 year was significantly associated with a higher abundance of Haemophilus spp at age 6 years and a significantly lower abundance of Moraxella and Neisseriaceae than children with RSV infection at 1 year. Reversible airway obstruction at 6 years was also positively associated with Haemophilus abundance and negatively associated with the abundance of health-associated taxa, such as Moraxella, Corynebacterium, Dolosigranulum, and Staphylococcus, even after correction for RSV immunoprophylaxis (all: p<0·05). Additionally, reversible airway instruction was associated with significantly higher Streptococcus pneumoniae abundance. Palivizumab in infancy in otherwise healthy preterm infants is associated with persistent effects on the abundance of specific, potentially pathogenic, microbial taxa in the respiratory tract. Several of the palivizumab-associated biomarker species were associated with reversible airway obstruction at age 6 years. These results warrant further studies to establish the long-term ecological effects and health consequences of palivizumab in infancy. MedImmune.

The Composition Alteration of Respiratory Microbiota in Lung Cancer

Background: Previous studies have reported mixed results regarding the composition of respiratory microbiota in lung cancer patients. Therefore, relying on previously published studies, we sought to estimate the relative proportion of respiratory microbiota between lung cancer cases and controls.Methods: MEDLINE, Embase, The Cochrane Library, and Web of Science online databases were systematically searched from inception up to October 14, 2019, to retrieve relevant studies. The relative abundance of each predominant taxon of respiratory microbiota in lung cancer patients and controls was pooled using the reported outcome data.Results: A total of 8 studies comprising 530 participants were included in the final analysis. The pooled phylum level analysis revealed that Bacteroidetes and Proteobacteria were the most abundant bacterial phyla among all participants, recording 17.5%, 47.5% in lung cancer patients, 28.2%, 39.27% in patients with benign pulmonary diseases and 40.62%, 32.09% in healthy controls, respectively. In addition, Actinobacteria and Firmicutes phyla were abundant in lung cancer cases compared to other groups (14.8%, 17.62% for lung cancer versus 13.04%, 13.16% for benign pulmonary nodules and 12.43%, 12.45% for healthy controls). At genus level, Prevotella was predominant in all the participants, and its proportion was relatively lower in cancer patients (25.74% for lung cancer versus 35.59% and 36.75% for benign pulmonary nodules and healthy controls, respectively). Comparatively, Streptococcus was more abundant in lung cancer cases (9.65% in lung cancer versus 7.98%, 7.26% in benign pulmonary nodules and healthy controls).Conclusions: The respiratory microbiota composition of respiratory microbiota significantly differs between lung cancer patients and healthy individuals, and may be used as potential biomarker of lung cancer. In addition, larger sample size, standardized procedures, dynamic monitoring, metabolomics, and culturomics are needed to confirm these results.

The respiratory microbiota: new insights into pulmonary tuberculosis

BackgroundPrevious studies demonstrated that the diversity and composition of respiratory microbiota in TB patients were different from healthy individuals. Therefore, the aim of the present analysis was to estimate the relative proportion of respiratory microbiota at phylum and genus levels among TB cases and healthy controls.MethodsThe PubMed and Google Scholar online databases were searched to retrieve relevant studies for the analysis. The statistical analysis was done using STATA version 11, pooled estimates are presented using graphs. The summary of findings in included studies is also presented in Table 1.ResultsThe phylum level analysis shows that the pooled proportions of Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Crenarchaeota were determined among tuberculosis patients and healthy controls. In brief, Firmicutes, and Proteobacteria were the most abundant bacterial phyla in both TB cases and healthy controls, composing 39.9 and 22.7% in TB cases and 39.4 and 19.5% in healthy controls, respectively. The genus level analysis noted that Streptococcus (35.01%), Neisseria (27.1%), Prevotella (9.02%) and Veillonella (7.8%) were abundant in TB patients. The Prevotella (36.9%), Gammaproteobacteria (22%), Streptococcus (19.2%) and Haemophilus (15.4%) were largely seen in healthy controls. Interestingly, Veillonella, Rothia, Leuconostoc were unique to TB cases, whereas Lactobacillus, and Gammaproteobacteria, Haemophilus, and Actinobacillus were identified only in healthy controls.ConclusionThe composition of the respiratory microbiota in TB patients and healthy controls were quite different. More deep sequencing studies are needed to explore the microbial variation in the respiratory system in connection with TB.

Maturation of the Infant Respiratory Microbiota, Environmental Drivers, and Health Consequences. A Prospective Cohort Study.

Perinatal and postnatal influences are presumed important drivers of the early-life respiratory microbiota composition. We hypothesized that the respiratory microbiota composition and development in infancy is affecting microbiota stability and thereby resistance against respiratory tract infections (RTIs) over time. To investigate common environmental drivers, including birth mode, feeding type, antibiotic exposure, and crowding conditions, in relation to respiratory tract microbiota maturation and stability, and consecutive risk of RTIs over the first year of life. In a prospectively followed cohort of 112 infants, we characterized the nasopharyngeal microbiota longitudinally from birth on (11 consecutive sample moments and the maximum three RTI samples per subject; in total, n = 1,121 samples) by 16S-rRNA gene amplicon sequencing. Using a microbiota-based machine-learning algorithm, we found that children experiencing a higher number of RTIs in the first year of life already demonstrate an aberrant microbial developmental trajectory from the first month of life on as compared with the reference group (0-2 RTIs/yr). The altered microbiota maturation process coincided with decreased microbial community stability, prolonged reduction of Corynebacterium and Dolosigranulum, enrichment of Moraxella very early in life, followed by later enrichment of Neisseria and Prevotella spp. Independent drivers of these aberrant developmental trajectories of respiratory microbiota members were mode of delivery, infant feeding, crowding, and recent antibiotic use. Our results suggest that environmental drivers impact microbiota development and, consequently, resistance against development of RTIs. This supports the idea that microbiota form the mediator between early-life environmental risk factors for and susceptibility to RTIs over the first year of life.

Antibiotic exposure and interpersonal variance mask the effect of ivacaftor on respiratory microbiota composition

BackgroundG551D is a class III mutation of the cystic fibrosis transmembrane regulator (CFTR) that results in impaired chloride channel function in cystic fibrosis (CF). Ivacaftor, a CFTR-potentiating agent improves sweat chloride, weight, lung function, and pulmonary exacerbation rate in CF patients with G551D mutations, but its effect on the airway microbiome remains poorly characterised. MethodsTwenty CF patients with at least one G551D mutation from a single centre were recruited to a 4month double-blind, placebo-controlled, crossover study of ivacaftor with 28days of active treatment. Sputum microbiota composition was assessed by 16S rRNA gene amplicon sequencing and quantitative PCR at five key time points, along with regular clinical review, respiratory function assessment, and peripheral blood testing. ResultsNo significant difference in microbiota composition was observed in subjects following ivacaftor treatment or placebo (PERMANOVA P=0.95, square root ECV=−4.94, 9479 permutations). Microbiota composition variance was significantly greater between subjects, than within subjects over time (P<0.0001, Mann Whitney U test), and an additional within-patient paired assessment of microbiota similarity was therefore performed. Again, change in microbiota composition was not significantly greater during treatment with ivacaftor compared to placebo (Wilcoxon test, P=0.51). A significant change in microbiota composition was however associated with any change in antibiotic exposure, regardless of whether ivacaftor or placebo was administered (P=0.006). In a small, subgroup analysis of subjects whose antibiotic exposure did not change within the study period, a significant reduction in total bacterial load was observed during treatment with ivacaftor (P=0.004, two-tailed paired Student's t-test). ConclusionsThe short-term impact of ivacaftor therapy on sputum microbiota composition in patients with G551D mutations are modest compared to those resulting from antibiotic exposure, and may be masked by changes in antibiotic treatment regimen.

Impact of nasopharyngeal microbiota on the development of respiratory tract diseases.

Knowledge of whether and how respiratory microbiota composition can prime the immune system and provide colonisation resistance, limiting consecutive pathobiont overgrowth and infections, is essential to improving the prevention and therapy of respiratory disorders. Modulation of dysbiotic ecosystems or reconstitution of missing microbes might be a possible measure to reduce respiratory diseases. The aim of this review is to analyse the role of nasopharyngeal microbiota in the development of respiratory tract disease in paediatric-age subjects. PubMed was used to search for all studies published over the last 15years using the following key words: "microbiota" or "microbioma" and "nasopharyngeal" or "respiratory" or "nasal" and "children" or "paediatric" or "infant". Analysis of the literature showed that respiratory microbiota can regulate health and disease development in the respiratory tract. Like the gut microbiota, the respiratory microbiota is established at birth, and early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children. Protective and dangerous bacteria have been identified, and this can be considered the base for developing new approaches to diseases that respond poorly to traditional interventions. Reconstitution of missing microbes can be achieved by the administration of pre- and probiotics. Modulation of respiratory microbiota by favouring colonisation of the upper respiratory tract by beneficial commensals can interfere with the proliferation and activity of resident pathobionts and is a possible new measure to reduce the risk of disease. However, further studies are needed because a deeper understanding of these and related issues can be transferred to clinical practice.

Effect of systemic glucocorticosteroids in the management of asthma and chronic obstructive pulmonary disease exacerbation on respiratory microbiota composition in the period of stability

The purpose of this study is to evaluate the ability of systemic glucocorticosteroids administered during the exacerbation of the disease to have a modifying effect on the qualitative and quantitative composition of the oropharyngeal microbiota. Material and methods. The study included 88 patients with COPD and 50 patients with stable asthma. The patients have had a history of observation for twelve months or more; they are characterized by the absence of exacerbations and systemic antibiotic therapy for four weeks or more prior to inclusion in the study. Also, all patients participating in the study were taken samples of oropharyngeal microbiota for isolating bacterial DNA and sequencing 16S rRNA gene sequences followed by the analysis of the taxonomic composition of the microbiota. Generalized linear model implemented in the R programming language version 3.1.0, glm2 package was used to identify the relationship between taxonomic composition of metagenomes and metadata. Results. The study suggests that the use of systemic glucocorticosteroids administered during the exacerbation of asthma and COPD modifies the composition of the respiratory microbiome in the period of stability increasing the oropharyngeal representation of non-pathogenic bacteria such as Bacteroidetes (including members of the genus Prevotella) and reducing bacterial contamination of oropharyngeal swabs by proteobacteria especially Streptococcus, and Haemophilus, which includes pathogens.

Pneumococcal colonization and carriage

Invited Lecture AbstractsISPPD-0534 Pneumococcal Colonization and Carriage: GENOMICS AND PNEUMOCOCCAL EPIDEMIOLOGY IN THE NASOPHARYNXC. Chewapreecha1, S.R. Harris1, N.J. Croucher2, C. Turner3, P. Marttinen4, L. Cheng5, A. Pessia5, D. Aanensen6, S.J. Salter1, A.E. Mather1, A.J. Page1, D. Harris1, F. Nosten7, D. Goldblatt8, J. Corander5, J. Parkhill1, P. Turner3, S.D. Bentley11Pathogen genomics, The Wellcome Trust Sanger Institute, Cambridge, United Kingdom; 2Center for Communicable Disease Dynamics, Harvard School of Public Health, Boston, USA; 3Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia 4Department of Information and Computer Science, Aalto University, Helsinki, Finland; 5Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland; 6Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom; 7Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Tak, Thailand; 8Immunobiology Unit, Institute of Child Health University College London, London, United KingdomHomologous recombination is one of the main evolutionary forces affecting Streptococcus pneumoniae. The highly recombinogenic nature of this species allows introduction of genetic material with selective advantages in carriage, the state that is a prerequisite for the development of pneumococcal invasive diseases. To study the impact of recombination on the evolution of a carriage pneumococcal population, whole genome sequencing was used to characterize 3,085 pneumococcal carriage isolates from a 2.4 km2 Thai refugee camp collected over a 3-year period. This high sampling density allowed us to characterized genetic exchanges in the pneumococcal population at a high resolution. Recombination ‘hotspots’ showed remarkable consistency between lineages, some of which were associated with drug resistance. Temporal trends in recombination at these sites reflected changes in antibiotic consumption, suggesting recombination facilitates adaptation to changing selection pressures. The highest frequencies of receipt and donation of DNA fragments exchanged through homologous recombination were observed in non-encapsulated lineages, implying a potential role in diversification and adaptation of the overall population played by these non-vaccine target lineages. These findings expand our understanding of pneumococcal population in carriage and help inform the design of future intervention strategies.No conflict of interestISPPD-0550 Pneumococcal Colonization and Carriage: INTERACTIONS BETWEEN STREPTOCOCCUS PNEUMONIAE AND THE RESPIRATORY MICROBIOME IN RELATION TO RESPIRATORY HEALTHD. Bogaert11The NetherlandsIndividuals differ markedly in their susceptibility to and clinical presentation of respiratory infections, despite that most young children and many adults are colonized with potential bacterial pathogens like Streptococcus pneumoniae. The reasons for these individual differences are not yet fully understood, but clearly multifactorial. Besides pathogen-related (virulence)-factors, host-related factors like immune-status and genetic background and environmental factors, a possible fourth factor might be of relevance, i.e. the commensal community of bacteria ‘hosting’ these potential pathogens. The collective genomes of these commensal inhabitants are referred to as the human microbiome. This microbiome contains highly complexity communities of bacteria, which differ between individuals and even more between niches. The human microbiome in general has shown crucial for an appropriate development of our immune system and our mucosal barriers, and for prevention of pathogen adherence and expansion. We studied the development and composition of microbiota of the upper respiratory tract in different age-groups and in relation to environmental and disease characteristics. We observed highly complex and niche-specific communities of bacteria. Even within the upper respiratory tract, the microbiota composition differs depending on the exact anatomical location. Furthermore, the composition of respiratory microbiota varies with host and environmental factors like age, season, infant feeding, and viral presence. Moreover, our data suggest a correlation between the presence and abundance of specific bacteria and stability of microbiota, as well as susceptibility to respiratory infections. Finally, clear evidence has been found for patterns of bacterial interactions within the respiratory microbiota, with a central role played by Streptococci.No conflict of interest

Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children.

Many bacterial pathogens causing respiratory infections in children are common residents of the respiratory tract. Insight into bacterial colonization patterns and microbiota stability at a young age might elucidate healthy or susceptible conditions for development of respiratory disease. To study bacterial succession of the respiratory microbiota in the first 2 years of life and its relation to respiratory health characteristics. Upper respiratory microbiota profiles of 60 healthy children at the ages of 1.5, 6, 12, and 24 months were characterized by 16S-based pyrosequencing. We determined consecutive microbiota profiles by machine-learning algorithms and validated the findings cross-sectionally in an additional cohort of 140 children per age group. Overall, we identified eight distinct microbiota profiles in the upper respiratory tract of healthy infants. Profiles could already be identified at 1.5 months of age and were associated with microbiota stability and change over the first 2 years of life. More stable patterns were marked by early presence and high abundance of Moraxella and Corynebacterium/Dolosigranulum and were positively associated with breastfeeding in the first period of life and with lower rates of parental-reported respiratory infections in the consecutive periods. Less stable profiles were marked by high abundance of Haemophilus or Streptococcus. These findings provide novel insights into microbial succession in the respiratory tract in infancy and link early-life profiles to microbiota stability and respiratory health characteristics. New prospective studies should elucidate potential implications of our findings for early diagnosis and prevention of respiratory infections. Clinical trial registered with www.clinicaltrials.gov (NCT00189020).

The effect of long-term macrolide treatment on respiratory microbiota composition in non-cystic fibrosis bronchiectasis: an analysis from the randomised, double-blind, placebo-controlled BLESS trial

Long-term macrolide treatment has proven benefit in inflammatory airways diseases, but whether it leads to changes in the composition of respiratory microbiota is unknown. We aimed to assess whether long-term, low-dose erythromycin treatment changes the composition of respiratory microbiota in people with non-cystic fibrosis bronchiectasis. Microbiota composition was determined by 16S rRNA gene sequencing of sputum samples from participants in the BLESS trial, a 12-month, double-blind, placebo-controlled trial of twice-daily erythromycin ethylsuccinate (400 mg) in adult patients with non-cystic fibrosis bronchiectasis and at least two infective exacerbations in the preceding year. The primary outcome was within-patient change in respiratory microbiota composition (assessed by Bray-Curtis index) between baseline and week 48, comparing erythromycin with placebo. The BLESS trial is registered with the Australian New Zealand Clinical Trials Registry, number ACTRN12608000460303. The BLESS trial took place between Oct 15, 2008, and Dec 14, 2011. Paired sputum samples were available from 86 randomly assigned patients, 42 in the placebo group and 44 in the erythromycin group. The change in microbiota composition between baseline and week 48 was significantly greater with erythromycin than with placebo (median Bray-Curtis score 0·52 [IQR 0·14-0·78] vs 0·68 [0·46-0·93]; median difference 0·16, 95% CI 0·01-0·33; p=0·03). In patients with baseline airway infection dominated by Pseudomonas aeruginosa, erythromycin did not change microbiota composition significantly. In those with infection dominated by organisms other than P. aeruginosa, erythromycin caused a significant change in microbiota composition (p=0·03 [by analysis of similarity]), representing a reduced relative abundance of Haemophilus influenzae (35·3% [5·5-91·6] vs 6·7% [0·8-74·8]; median difference 12·6%, 95% CI 0·4-28·3; p=0·04; interaction p=0·02) and an increased relative abundance of P aeruginosa (0·02% [0·00-0·33] vs 0·13% [0·01-39·58]; median difference 6·6%, 95% CI 0·1-37·1; p=0·002; interaction p=0·45). Compared with placebo, erythromycin reduced the rate of pulmonary exacerbations over the 48 weeks of the study in patients with P. aeruginosa-dominated infection (median 1 [IQR 0-3] vs 3 [2-5]; median difference -2, 95% CI -4 to -1; p=0·01), but not in those without P. aeruginosa-dominated infection (1 [0-2] vs 1 [0-3]; median difference 0, -1 to 0; p=0·41; interaction p=0·04). Long-term erythromycin treatment changes the composition of respiratory microbiota in patients with bronchiectasis. In patients without P. aeruginosa airway infection, erythromycin did not significantly reduce exacerbations and promoted displacement of H. influenzae by more macrolide-tolerant pathogens including P. aeruginosa. These findings argue for a cautious approach to chronic macrolide use in patients without P. aeruginosa airway infection. Mater Adult Respiratory Research Trust Fund.