Infant airway microbiota and topical immune perturbations in the origins of childhood asthma

Early Origins of Chronic Obstructive Pulmonary Disease: Prenatal and Early Life Risk Factors

The main risk factor for chronic obstructive pulmonary disease (COPD) is active smoking. However, a considerable amount of people with COPD never smoked, and increasing evidence suggests that adult lung disease can have its origins in prenatal and early life. This article reviews some of the factors that can potentially affect lung development and lung function trajectories throughout the lifespan from genetics and prematurity to respiratory tract infections and childhood asthma. Maternal smoking and air pollution exposure were also analyzed among the environmental factors. The adoption of preventive strategies to avoid these risk factors since the prenatal period may be crucial to prevent, delay the onset or modify the progression of COPD lung disease throughout life.

Microbiome and Asthma: Microbial Dysbiosis and the Origins, Phenotypes, Persistence, and Severity of Asthma

The importance of the microbiome, and of the gut-lung axis in the origin and persistence of asthma, is an ongoing field of investigation. The process of microbial colonisation in the first three years of life is fundamental for health, with the first hundred days of life being critical. Different factors are associated with early microbial dysbiosis, such as caesarean delivery, artificial lactation and antibiotic therapy, among others. Longitudinal cohort studies on gut and airway microbiome in children have found an association between microbial dysbiosis and asthma at later ages of life. A low α-diversity and relative abundance of certain commensal gut bacterial genera in the first year of life are associated with the development of asthma. Gut microbial dysbiosis, with a lower abundance of Phylum Firmicutes, could be related with increased risk of asthma. Upper airway microbial dysbiosis, especially early colonisation by Moraxella spp., is associated with recurrent viral infections and the development of asthma. Moreover, the bacteria in the respiratory system produce metabolites that may modify the inception of asthma and is progression. The role of the lung microbiome in asthma development has yet to be fully elucidated. Nevertheless, the most consistent finding in studies on lung microbiome is the increased bacterial load and the predominance of proteobacteria, especially Haemophilus spp. and Moraxella catarrhalis. In this review we shall update the knowledge on the association between microbial dysbiosis and the origins of asthma, as well as its persistence, phenotypes, and severity.

Asthma, obesity, and microbiota: A complex immunological interaction

Obesity and allergic asthma are inflammatory chronic diseases mediated by distinct immunological features, obesity presents a Th1/Th17 profile, asthma is commonly associated with Th2 response. However, when combined, they result in more severe asthma symptoms, greater frequency of exacerbation episodes, and lower therapy responsiveness. These features lead to decreased life quality, associated with higher morbidity/mortality rates.  In addition, obesity prompts specific asthma phenotypes, which can be dependent on atopic status, age, and gender. In adults, obesity is associated with neutrophilic/Th17 profile, while in children, the outcome is diverse, in some cases children with obesity present aggravation of atopy, and Th2 inflammation, and in others an association with a Th1 profile, with reduced IgE levels and eosinophilia. These alterations occur due to a complex group of factors among which the microbiome has been recently explored. Particularly, evidence shows its important role in susceptibility or resistance to asthma development, via gut-lung-axis, and demonstrates its relevance to the immune pathogenesis of the syndrome. Few studies address the relevance of the lung microbiome in shaping the immune response, locally. However, specific bacteria, like Moraxella catarrhalis, Haemophilus influenza, and Streptococcus pneumoniae, correlate with important features of the obese-asthmatic phenotype. Although maternal obesity is known to increase asthma risk in offspring, the impact on lung colonization is unknown. This review details the main key immune mechanisms involved in obesity-aggravated asthma, featuring the effect of maternal obesity in the establishment of gut and lung microbiota of the offspring, acting as potential childhood asthma inducer.

Airborne polystyrene microplastics and nanoplastics induce nasal and lung microbial dysbiosis in mice

Microplastics (MP) and nanoplastics (NP) have been found in multiple environments and creatures. However, their effects on the airway microbiota still remain poorly understood. In this study, a series of bioinformatic and statistical analyses were carried out to explore the influence of airborne MP and NP on the nasal and lung microbiota in mice. Both MP and NP were capable of inducing nasal microbial dysbiosis, and MP had a stronger influence on the lung microbiota than NP. Multiple nasal and lung bacteria were associated with MP and NP groups, among which nasal Staphylococcus and lung Roseburia were most associated with MP group, while nasal Prevotella and lung unclassified_Muribaculaceae were most associated with NP group. The nasal Staphylococcus, lung Roseburia, lung Eggerthella and lung Corynebacterium were associated with both MP and NP groups, which were potential biomarkers of micro/nanoplastics-induced airway dysbiosis. SAR11_Clade_Ia and SAR11_Clade_II were associated with both nasal and lung microbiota in MP group, while no such bacterium was determined in NP group. The relevant results suggest that both airborne MP and NP could induce nasal and lung microbial dysbiosis, and the relevant preventative and curable strategies deserve further investigations.

Association of Severe Bronchiolitis during Infancy with Childhood Asthma Development: An Analysis of the ECHO Consortium

Objective: Many studies have shown that severe (hospitalized) bronchiolitis during infancy is a risk factor for developing childhood asthma. However, the population subgroups at the highest risk remain unclear. Using large nationwide pediatric cohort data, namely the NIH Environmental influences on Child Health Outcomes (ECHO) Program, we aimed to quantify the longitudinal relationship of bronchiolitis hospitalization during infancy with asthma in a generalizable dataset and to examine potential heterogeneity in terms of major demographics and clinical factors. Methods: We analyzed data from infants (age <12 months) enrolled in one of the 53 prospective cohort studies in the ECHO Program during 2001−2021. The exposure was bronchiolitis hospitalization during infancy. The outcome was a diagnosis of asthma by a physician by age 12 years. We examined their longitudinal association and determined the potential effect modifications of major demographic factors. Results: The analytic cohort consisted of 11,762 infants, 10% of whom had bronchiolitis hospitalization. Overall, 15% subsequently developed asthma. In the Cox proportional hazards model adjusting for 10 patient-level factors, compared with the no-bronchiolitis hospitalization group, the bronchiolitis hospitalization group had a significantly higher rate of asthma (14% vs. 24%, HR = 2.77, 95%CI = 2.24−3.43, p < 0.001). There was significant heterogeneity by race and ethnicity (Pinteraction = 0.02). The magnitude of the association was greater in non-Hispanic White (HR = 3.77, 95%CI = 2.74−5.18, p < 0.001) and non-Hispanic Black (HR = 2.39, 95%CI = 1.60−3.56; p < 0.001) infants, compared with Hispanic infants (HR = 1.51, 95%CI = 0.77−2.95, p = 0.23). Conclusions: According to the nationwide cohort data, infants hospitalized with bronchiolitis are at a higher risk for asthma, with quantitative heterogeneity in different racial and ethnic groups.

Asthma and Wheeze Severity and the Oropharyngeal Microbiota in Children and Adolescents

Rationale: There is a major unmet need for improving the care of children and adolescents with severe asthma and wheeze. Identifying factors contributing to disease severity may lead to improved diagnostics, biomarkers, or therapies. The airway microbiota may be such a key factor. Objectives: To compare the oropharyngeal airway microbiota of children and adolescents with severe and mild/moderate asthma/wheeze. Methods: Oropharyngeal swab samples from school-age and preschool children in the European U-BIOPRED (Unbiased BIOmarkers in the PREDiction of respiratory disease outcomes) multicenter study of severe asthma, all receiving severity-appropriate treatment, were examined using 16S ribosomal RNA gene sequencing. Bacterial taxa were defined as amplicon sequence variants. Results: We analyzed 241 samples from four cohorts: A) 86 school-age children with severe asthma; B) 39 school-age children with mild/moderate asthma; C) 65 preschool children with severe wheeze; and D) 51 preschool children with mild/moderate wheeze. The most common bacteria were Streptococcus (mean relative abundance, 33.5%), Veillonella (10.3%), Haemophilus (7.0%), Prevotella (5.9%), and Rothia (5.5%). Age group (school-age vs. preschool) was associated with the microbiota in β-diversity analysis (F = 3.32, P = 0.011) and in a differential abundance analysis (28 significant amplicon sequence variants). Among all children, we found no significant difference in the microbiota between children with severe and mild/moderate asthma/wheeze in univariable β-diversity analysis (F = 1.99, P = 0.08, N = 241), but a significant difference in a multivariable model (F = 2.66, P = 0.035), including the number of exacerbations in the previous year. Age was also significant when expressed as a microbial maturity score (Spearman Rho, 0.39; P = 4.6 × 10^-10); however, this score was not associated with asthma/wheeze severity. Conclusions: There was a modest difference in the oropharyngeal airway microbiota between children with severe and mild/moderate asthma/wheeze across all children but not in individual age groups, and a strong association between the microbiota and age. This suggests the oropharyngeal airway microbiota as an interesting entity in studying asthma severity, but probably without the strength to serve as a biomarker for targeted intervention.

Nasopharyngeal airway dual-transcriptome of infants with severe bronchiolitis and risk of childhood asthma: A multicenter prospective study

BACKGROUND

Severe bronchiolitis (ie, bronchiolitis requiring hospitalization) during infancy is a major risk factor for childhood asthma. However, the exact mechanism linking these common conditions remains unclear.

OBJECTIVES

This study sought to examine the integrated role of airway microbiome (both taxonomy and function) and host response in asthma development in this high-risk population.

METHODS

This multicenter prospective cohort study of 244 infants with severe bronchiolitis (median age, 3 months) examined the infants' nasopharyngeal metatranscriptomes (microbiomes) and transcriptomes (hosts), as well as metabolomes at hospitalization. The longitudinal relationships investigated include (1) major bacterial species (Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis), (2) microbial function, and (3) host response with risks of developing asthma by age 6 years.

RESULTS

First, the abundance of S pneumoniae was associated with greater risks of asthma (P = .01), particularly in infants with nonrhinovirus infection (Pinteraction = .04). Second, of 328 microbial functional pathways that are differentially enriched by asthma development, the top pathways (eg, fatty acid and glycolysis pathways; false discovery rate [FDR] < 1 × 10-12) were driven by these 3 major species (eg, positive association of S pneumoniae with glycolysis; FDR < 0.001). These microbial functional pathways were validated with the parallel metabolome data. Third, 104 transcriptome pathways were differentially enriched (FDR < .05)-for example, downregulated interferon-α and -γ and upregulated T-cell activation pathways. S pneumoniae was associated with most differentially expressed transcripts (eg, DAGLB; FDR < 0.05).

CONCLUSIONS

By applying metatranscriptomic, transcriptomic, and metabolomic approaches to a multicenter cohort of infants with bronchiolitis, this study found an interplay between major bacterial species, their function, and host response in the airway, and their longitudinal relationship with asthma development.

Microbial dysbiosis and childhood asthma development: Integrated role of the airway and gut microbiome, environmental exposures, and host metabolic and immune response

Asthma is a chronic and heterogeneous respiratory disease with many risk factors that typically originate during early childhood. A complex interplay between environmental factors and genetic predisposition is considered to shape the lung and gut microbiome in early life. The growing literature has identified that changes in the relative abundance of microbes (microbial dysbiosis) and reduced microbial diversity, as triggers of the airway-gut axis crosstalk dysregulation, are associated with asthma development. There are several mechanisms underlying microbial dysbiosis to childhood asthma development pathways. For example, a bacterial infection in the airway of infants can lead to the activation and/or dysregulation of inflammatory pathways that contribute to bronchoconstriction and bronchial hyperresponsiveness. In addition, gut microbial dysbiosis in infancy can affect immune development and differentiation, resulting in a suboptimal balance between innate and adaptive immunity. This evolving dysregulation of secretion of pro-inflammatory mediators has been associated with persistent airway inflammation and subsequent asthma development. In this review, we examine current evidence around associations between the airway and gut microbial dysbiosis with childhood asthma development. More specifically, this review focuses on discussing the integrated roles of environmental exposures, host metabolic and immune responses, airway and gut microbial dysbiosis in driving childhood asthma development.

The developing airway and gut microbiota in early life is influenced by age of older siblings

BACKGROUND

Growing up with siblings has been linked to numerous health outcomes and is also an important determinant for the developing microbiota. Nonetheless, research into the role of having siblings on the developing microbiota has mainly been incidental.

RESULTS

Here, we investigate the specific effects of having siblings on the developing airway and gut microbiota using a total of 4497 hypopharyngeal and fecal samples taken from 686 children in the COPSAC2010 cohort, starting at 1 week of age and continuing until 6 years of age. Sibship was evaluated longitudinally and used for stratification. Microbiota composition was assessed using 16S rRNA gene amplicon sequencing of the variable V4 region. We found siblings in the home to be one of the most important determinants of the developing microbiota in both the airway and gut, with significant differences in alpha diversity, beta diversity, and relative abundances of the most abundant taxa, with the specific associations being particularly apparent during the first year of life. The age gap to the closest older sibling was more important than the number of older siblings. The signature of having siblings in the gut microbiota at 1 year was associated with protection against asthma at 6 years of age, while no associations were found for allergy.

CONCLUSIONS

Having siblings is one of the most important factors influencing a child's developing microbiota, and the specific effects may explain previously established associations between siblings and asthma and infectious diseases. As such, siblings should be considered in all studies involving the developing microbiota, with emphasis on the age gap to the closest older sibling rather than the number of siblings. Video abstract.

Respiratory and Intestinal Microbiota in Pediatric Lung Diseases-Current Evidence of the Gut-Lung Axis

The intestinal microbiota is known to influence local immune homeostasis in the gut and to shape the developing immune system towards elimination of pathogens and tolerance towards self-antigens. Even though the lung was considered sterile for a long time, recent evidence using next-generation sequencing techniques confirmed that the lower airways possess their own local microbiota. Since then, there has been growing evidence that the local respiratory and intestinal microbiota play a role in acute and chronic pediatric lung diseases. The concept of the so-called gut–lung axis describing the mutual influence of local microbiota on distal immune mechanisms was established. The mechanisms by which the intestinal microbiota modulates the systemic immune response include the production of short-chain fatty acids (SCFA) and signaling through pattern recognition receptors (PRR) and segmented filamentous bacteria. Those factors influence the secretion of pro- and anti-inflammatory cytokines by immune cells and further modulate differentiation and recruitment of T cells to the lung. This article does not only aim at reviewing recent mechanistic evidence from animal studies regarding the gut–lung axis, but also summarizes current knowledge from observational studies and human trials investigating the role of the respiratory and intestinal microbiota and their modulation by pre-, pro-, and synbiotics in pediatric lung diseases.

The Role of Early Life Microbiota Composition in the Development of Allergic Diseases

Allergic diseases are becoming a major healthcare issue in many developed nations, where living environment and lifestyle are most predominantly distinct. Such differences include urbanized, industrialized living environments, overused hygiene products, antibiotics, stationary lifestyle, and fast-food-based diets, which tend to reduce microbial diversity and lead to impaired immune protection, which further increase the development of allergic diseases. At the same time, studies have also shown that modulating a microbiocidal community can ameliorate allergic symptoms. Therefore, in this paper, we aimed to review recent findings on the potential role of human microbiota in the gastrointestinal tract, surface of skin, and respiratory tract in the development of allergic diseases. Furthermore, we addressed a potential therapeutic or even preventive strategy for such allergic diseases by modulating human microbial composition.

Controlled human infection with Neisseria lactamica in late pregnancy to measure horizontal transmission and microbiome changes in mother-neonate pairs: a single-arm interventional pilot study protocol

INTRODUCTION

Infant upper respiratory microbiota are derived partly from the maternal respiratory tract, and certain microbiota are associated with altered risk of infections and respiratory disease. Neisseria lactamica is a common pharyngeal commensal in young children and is associated with reduced carriage and invasive disease by Neisseria meningitidis. Nasal inoculation with N. lactamica safely and reproducibly reduces N. meningitidis colonisation in healthy adults. We propose nasal inoculation of pregnant women with N. lactamica, to establish if neonatal pharyngeal colonisation occurs after birth, and to characterise microbiome evolution in mother-infant pairs over 1 month post partum.

METHODS AND ANALYSIS

20 healthy pregnant women will receive nasal inoculation with N. lactamica (wild type strain Y92-1009) at 36-38 weeks gestation. Upper respiratory samples, as well as optional breastmilk, umbilical cord blood and infant venous blood samples, will be collected from mother-infant pairs over 1 month post partum. We will assess safety, N. lactamica colonisation (by targeted PCR) and longitudinal microevolution (by whole genome sequencing), and microbiome evolution (by 16S rRNA gene sequencing).

ETHICS AND DISSEMINATION

This study has been approved by the London Central Research Ethics Committee (21/PR/0373). Findings will be published in peer-reviewed open-access journals as soon as possible.

TRIAL REGISTRATION NUMBER

NCT04784845.

Immune dysfunction induced by 2,6-dichloro-1,4-benzoquinone, an emerging water disinfection byproduct, due to the defects of host-microbiome interactions

2,6-dichloro-1,4-benzoquinone (DCBQ), as an emerging water disinfection byproducts (DBPs), has posed potential risks via the digestion system. However, little is known about the toxicity of DCBQ on the gut microbiome, which plays a critical role on human health. This study has comprehensively investigated the impact of DCBQ on the intestinal microbiome, metabolic functions, and immunity after the mice orally exposure to DCBQ at the concentration of 31.25, 62.5 and 125 mg/kg body weight for 28 days. Our results indicated that DCBQ exposure has perturbed the balance between T helper (Th) 1 mediated pro-inflammatory response and Th2 mediated anti-inflammatory response in mice, especially inducing the activation of immune system toward a Th2 response. DCBQ group has induced gut microbiota dysbiosis, and at phylum level, Proteobacteria was relatively less abundant compared with that in the control group. Furthermore, DCBQ exposure has dramatically perturbed metabolites profiles which were involved in 28 metabolic pathways, such as amino acids biosynthesis and metabolism, lipid metabolism. In particular, the altered gut microbiota showed strong correlations with both the altered metabolites and the altered immunological variables after DCBQ exposure. This study provides evidence on the adverse effects and mechanisms of water disinfection byproduct DCBQ through the interaction of immune-microbiome-metabolome, highlighting the importance to assess DBPs-associated risks.

Heterogeneous Condition of Asthmatic Children Patients: A Narrative Review

Currently, asthma represents the most common chronic disorder in children, showing an increasingly consistent burden worldwide. Childhood asthma, similar to what happens in adults, is a diversified disease with a great variability of phenotypes, according to genetic predisposition of patients, age, severity of symptoms, grading of risk, and comorbidities, and cannot be considered a singular well-defined disorder, but rather a uniquely assorted disorder with variable presentations throughout childhood. Despite several developments occurring in recent years in pediatric asthma, above all, in the management of the disease, some essential areas, such as the improvement of pediatric asthma outcomes, remain a hot topic. Most treatments of the type 2 (T2) target phenotype of asthma, in which IL-4, IL-5, and IL-13 modulate the central signals of inflammatory reactions. Although, there may be an unresolved need to identify new biomarkers used as predictors to improve patient stratification using disease systems and to aid in the selection of treatments. Moreover, we are globally facing many dramatic challenges, including climate change and the SARS-CoV2 pandemic, which have a considerable impact on children and adolescent asthma. Preventive strategies, including allergen immunotherapy and microbiome evaluation, and targeted therapeutic strategies are strongly needed in this population. Finally, the impact of asthma on sleep disorders has been reviewed.

Informatic analysis of the pulmonary microecology in non-cystic fibrosis bronchiectasis at three different stages

This study explored the impact of pulmonary microecological changes on disease progression in non-cystic fibrosis bronchiectasis (nCFB). A careful search of the NCBI BioProject database revealed the 16S rRNA-based microbiological testing results of 441 pulmonary sputum samples from patients in the relatively stable (baseline), acute exacerbation, or recovery stage. After preliminary analysis and screening, we selected 152 samples for further analyses, including determination of the operational taxonomic unit (OTU) distribution at the phylum, class, order, family and genus levels, community structure, alpha diversity, beta diversity, microbial multivariables, correlations, and community structure after the abundances of intragroup samples were averaged. The recovery group showed significant differences in pulmonary microbiological changes (P < 0.05) compared with the other groups. There were 30 differentially abundant OTUs, with 27 and 7 at the genus and phylum levels, respectively. The Chao1 value of the recovery group was comparable to that of the baseline group, and the Shannon and Simpson values of the recovery group were the highest. Rhodococcus in Actinobacteria was positively correlated with Ochrobactrum in Firmicutes. The differences in pulmonary microecological changes at different nCFB stages may serve as a biologically predictive indicator of nCFB progression.

Early life inter-kingdom interactions shape the immunological environment of the airways

BACKGROUND

There is increasing evidence that the airway microbiome plays a key role in the establishment of respiratory health by interacting with the developing immune system early in life. While it has become clear that bacteria are involved in this process, there is a knowledge gap concerning the role of fungi. Moreover, the inter-kingdom interactions that influence immune development remain unknown. In this prospective exploratory human study, we aimed to determine early post-natal microbial and immunological features of the upper airways in 121 healthy newborns.

RESULTS

We found that the oropharynx and nasal cavity represent distinct ecological niches for bacteria and fungi. Breastfeeding correlated with changes in microbiota composition of oropharyngeal samples with the greatest impact upon the relative abundance of Streptococcus species and Candida. Host transcriptome profiling revealed that genes with the highest expression variation were immunological in nature. Multi-omics factor analysis of host and microbial data revealed unique co-variation patterns.

CONCLUSION

These data provide evidence of a diverse multi-kingdom microbiota linked with local immunological characteristics in the first week of life that could represent distinct trajectories for future respiratory health.

TRIAL REGISTRATION

NHS Health Research Authority, IRAS ID 199053. Registered 5 Oct 2016. https://www.hra.nhs.uk/planning-and-improving-research/application-summaries/research-summaries/breathing-together/ Video abstract.

The preliminary investigation of potential response biomarkers to PAHs exposure on childhood asthma

BACKGROUND

Exposure to polycyclic aromatic hydrocarbons (PAHs) is a potential risk factor for asthma prevalence. This study aims to explore whether PAHs exposure is associated with childhood asthma by altering microbial diversity and metabolic profiles.

METHODS

Thirty children with asthma and 30 children as control in Nanjing, China were recruited. Urinary 1-hydroxypyrene (1-OHPyr) level was determined by UPLC-Orbitrap-MS as a PAHs exposure biomarker. Logistic regression was conducted to investigate the association between 1-OHPyr and childhood asthma. Microbial diversity was analyzed by 16S rRNA gene sequencing. Metabolic profiles were obtained by UPLC-Orbitrap-MS methods. Differential microbiota and metabolites were screened and selected as response biomarkers or intermediates. Mediation analysis was conducted to assess the association between PAHs and asthma mediated by intermediates.

RESULTS

Participating children with and without asthma aged 6.43 ± 2.23 years. The urinary 1-OHPyr level ranged from 0.10 to 1.51 μmol/mol (creatinine corrected) in the participants. The urinary 1-OHPyr level was associated with childhood asthma (OR = 7.21, 95% CI: 1.03-50.42 per 1 μmol/mol unit). Microbial diversity was decreased in the group with asthma and there was a significant shift in the abundance of Proteobacteria (at the phylum level), Veillonella and Prevotella (at the genus level). The enrichment pathway analysis showed that differentially expressed metabolites were involved in purine metabolism, amino acid metabolism, and lipid and fatty acid metabolism. The urinary 1-OHPyr level was associated with the abundance of Actinomyces sp. oral clone IO076 and 7-methylguanine that showed a mediation effect on the association between urinary 1-OHPyr levels and childhood asthma by mediation analysis.

CONCLUSIONS

Urinary 1-OHPyr exposure was associated with childhood asthma, microbial diversity, and metabolic profiles. Microbial diversity and metabolic profiles may be intermediates as response biomarkers to PAHs exposure in childhood asthma. Further research is needed to confirm these study results and determine the underlying mechanism.

Association of upper airway bacterial microbiota and asthma: systematic review

Individual studies have suggested that upper airway dysbiosis may be associated with asthma or its severity. We aimed to systematically review studies that evaluated upper airway bacterial microbiota in relation to asthma, compared to nonasthmatic controls. Searches used MEDLINE, Embase, and Web of Science Core Collection. Eligible studies included association between asthma and upper airway dysbiosis; assessment of composition and diversity of upper airway microbiota using 16S rRNA or metagenomic sequencing; upper airway samples from nose, nasopharynx, oropharynx or hypopharynx. Study quality was assessed and rated using the Newcastle-Ottawa scale. A total of 249 publications were identified; 17 in the final analysis (13 childhood asthma and 4 adult asthma). Microbiome richness was measured in 6 studies, species diversity in 12, and bacterial composition in 17. The quality of evidence was good and fair. The alpha-diversity was found to be higher in younger children with wheezing and asthma, while it was lower when asthmatic children had rhinitis or mite sensitization. In children, Proteobacteria and Firmicutes were higher in asthmatics compared to controls (7 studies), and Moraxella, Streptococcus, and Haemophilus were predominant in the bacterial community. In pooled analysis, nasal Streptococcus colonization was associated with the presence of wheezing at age 5 (p = 0.04). In adult patients with asthma, the abundance of Proteobacteria was elevated in the upper respiratory tract (3 studies). Nasal colonization of Corynebacterium was lower in asthmatics (2 studies). This study demonstrates the potential relationships between asthma and specific bacterial colonization in the upper airway in adult and children with asthma.

Relationship of the lung microbiome with PD-L1 expression and immunotherapy response in lung cancer

Background

Lung cancer is the primary cause of cancer-related deaths worldwide. The human lung serves as a niche to a unique and dynamic bacterial community that is related to the development of multiple diseases. Here, we investigated the differences in the lung microbiomes of patients with lung cancer.

Methods

16S rRNA sequencing was performed to evaluate the respiratory tract microbiome present in the bronchoalveolar lavage fluid. Patients were stratified based on programmed death-ligand 1 (PD-L1) expression levels and immunotherapy responses.

Results

In total, 84 patients were prospectively analyzed, of which 59 showed low (< 10%), and 25 showed high (≥ 10%) PD-L1 expression levels. The alpha and beta diversities did not significantly differ between the two groups. Veillonella dispar was dominant in the high-PD-L1 group; the population of Neisseria was significantly higher in the low-PD-L1 group than in the high-PD-L1 group. In the immunotherapy responder group, V. dispar was dominant, while Haemophilus influenzae and Neisseria perflava were dominant in the non-responder group.

Conclusion

The abundances of Neisseria and V. dispar differed significantly in relation to PD-L1 expression levels and immunotherapy responses.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12931-021-01919-1.

The Influence of FUT2 and FUT3 Polymorphisms and Nasopharyngeal Microbiome on Respiratory Infections in Breastfed Bangladeshi Infants from the Microbiota and Health Study

Acute respiratory infections (ARIs) are one of the most common causes of morbidity and mortality in young children. The aim of our study was to examine whether variation in maternal FUT2 (α1,2-fucosyltransferase 2) and FUT3 (α1,3/4-fucosyltransferase 3) genes, which shape fucosylated human milk oligosaccharides (HMOs) in breast milk, are associated with the occurrence of ARIs in breastfed infants as well as the influence of the nasopharyngeal microbiome on ARI risk. Occurrences of ARIs were prospectively recorded in a cohort of 240 breastfed Bangladeshi infants from birth to 2 years. Secretor and Lewis status was established by sequencing of FUT2/3 genes. The nasopharyngeal microbiome was characterized by shotgun metagenomics, complemented by specific detection of respiratory pathogens; 88.6% of mothers and 91% of infants were identified as secretors. Maternal secretor status was associated with reduced ARI incidence among these infants in the period from birth to 6 months (incidence rate ratio [IRR], 0.66; 95% confidence interval [CI], 0.47 to 0.94; P = 0.020), but not at later time periods. The nasopharyngeal microbiome, despite precise characterization to the species level, was not predictive of subsequent ARIs. The observed risk reduction of ARIs among infants of secretor mothers during the predominant breastfeeding period is consistent with the hypothesis that fucosylated oligosaccharides in human milk contribute to protection against respiratory infections. However, we found no evidence that modulation of the nasopharyngeal microbiome influenced ARI risk. IMPORTANCE The observed risk reduction of acute respiratory infections (ARIs) among infants of secretor mothers during the predominant breastfeeding period is consistent with the hypothesis that fucosylated oligosaccharides in human milk contribute to protection against respiratory infections. Respiratory pathogens were only weak modulators of risk, and the nasopharyngeal microbiome did not influence ARI risk, suggesting that the associated protective effects of human milk oligosaccharides (HMOs) are not conveyed via changes in the nasopharyngeal microbiome. Our observations add to the evidence for a role of fucosylated HMOs in protection against respiratory infections in exclusively or predominantly breastfed infants in low-resource settings. There is no indication that the nasopharyngeal microbiome substantially modulates the risk of subsequent mild ARIs. Larger studies are needed to provide mechanistic insights on links between secretor status, HMOs, and risk of respiratory infections.

Neonatal airway immune profiles and asthma and allergy endpoints in childhood

BACKGROUND

The immune system plays a key role in the pathogenesis of asthma and allergy, but the role of the airway cytokine and chemokine composition in vivo in early life prior to symptom development has not been described previously. Here, we aimed to examine whether the neonatal airway immune composition associates with development of allergy and asthma in childhood.

METHODS

We measured unstimulated levels of 20 immune mediators related to the Type 1, Type 2, Type 17, or regulatory immune pathways in the airway mucosal lining fluid of 620 one-month-old healthy neonates from the COPSAC₂₀₁₀ birth cohort. Allergy and asthma were diagnosed at our research clinic by predefined algorithms and objective assessments at age 6 years. Principal component analyses were used to describe the airway cytokine and chemokine composition.

RESULTS

A neonatal airway immune profile particularly characterized by enhanced IL-1β and reduced CCL26 was significantly associated with later development of elevated specific IgE to inhaled allergens, a positive skin prick test, and allergic rhinitis, but not with food sensitization. Conversely, reduced Type 17 immune-associated markers, including IL-1β and CXCL8, showed trend of association with development of early asthma endpoints.

CONCLUSIONS

Development of early asthma endpoints and inhalant allergy during the first 6 years of life seems associated with distinctly perturbed airway immune profiles in neonatal life, which is suggestive of an early origin and different pathogenesis of childhood asthma and allergy. These exploratory findings suggest pre- and perinatal life as an important window of opportunity for prevention of asthma and inhalant allergy.

The airway microbiome and pediatric asthma

PURPOSE OF REVIEW

Asthma is the most common chronic disease of childhood. Investigations of the lower and upper airway microbiomes have significantly progressed over recent years, and their roles in pediatric asthma are becoming increasingly clear.

RECENT FINDINGS

Early studies identified the existence of upper and lower airway microbiomes, including imbalances in both associated with pediatric asthma. The infant airway microbiome may offer predictive value for the development of asthma in later childhood, and it may also be influenced by external factors such as respiratory viral illness. The airway microbiome has also been associated with the clinical course of asthma, including rates of exacerbation and level of control. Advances in -omics sciences have enabled improved identification of the airway microbiome's relationships with host response and function in children with asthma. Investigations are now moving toward the application of the above findings to explore risk modification and treatment options.

SUMMARY

The airway microbiome provides an intriguing window into pediatric asthma, offering insights into asthma diagnosis, clinical course, and perhaps treatment. Further investigation is needed to solidify these associations and translate research findings into clinical practice.

Interrupting the Conversation: Implications for Crosstalk Between Viral and Bacterial Infections in the Asthmatic Airway

Asthma is a heterogeneous, chronic respiratory disease affecting 300 million people and is thought to be driven by different inflammatory endotypes influenced by a myriad of genetic and environmental factors. The complexity of asthma has rendered it challenging to develop preventative and disease modifying therapies and it remains an unmet clinical need. Whilst many factors have been implicated in asthma pathogenesis and exacerbations, evidence indicates a prominent role for respiratory viruses. However, advances in culture-independent detection methods and extensive microbial profiling of the lung, have also demonstrated a role for respiratory bacteria in asthma. In particular, airway colonization by the Proteobacteria species Nontypeable Haemophilus influenzae (NTHi) and Moraxella catarrhalis (Mcat) is associated with increased risk of developing recurrent wheeze and asthma in early life, poor clinical outcomes in established adult asthma and the development of more severe inflammatory phenotypes. Furthermore, emerging evidence indicates that bacterial-viral interactions may influence exacerbation risk and disease severity, highlighting the need to consider the impact chronic airway colonization by respiratory bacteria has on influencing host responses to viral infection. In this review, we first outline the currently understood role of viral and bacterial infections in precipitating asthma exacerbations and discuss the underappreciated potential impact of bacteria-virus crosstalk in modulating host responses. We discuss the mechanisms by which early life infection may predispose to asthma development. Finally, we consider how infection and persistent airway colonization may drive different asthma phenotypes, with a view to identifying pathophysiological mechanisms that may prove tractable to new treatment modalities.

Cytokine Stimulation via MRGPRX2 Occurs with Lower Potency than by FcεRI-aggregation but with Similar Dependence on the ERK1/2 Module in Human Skin Mast Cells

Skin mast cells (MCs) contribute to chronic dermatoses that partially rely on MC-derived cytokines. The discovery of MRGPRX2 explains MC-dependent symptoms independently of FcεRI-activation. Here, we investigated whether MRGPRX2 can elicit cytokines, determined its relative potency versus FcεRI and addressed the underlying mechanisms. MRGPRX2-activation by compound 48/80 or Substance P on skin MCs induced TNF-α, IL-8, IL-13, CCL1, CCL2 mRNA and protein, yet induction was typically reduced compared with FcεRI-crosslinking. Generally, cytokine secretion required de-novo-synthesis with maximum accumulation at ≈8 h. Addressing key kinases revealed robust, rapid (1 min), and lasting (30 min) phosphorylation of ERK1/2 following MRGPRX2-ligation, while pp38, and pAKT signals were weaker, and pJNK hardly detectable. The kinase spectrum following FcεRI-aggregation was comparable, but responses considerably delayed. The MEK/ERK pathway was essential for all cytokines examined and four inhibitors of this module gave complete suppression. Variable and weaker contribution was found for PI3K>JNK>p38. Strikingly, cytokine profiles and signaling prerequisites were similar for MRGPRX2 and FcεRI and likely mainly dictated by the MC subset. Collectively, in skin MCs, the physiological producers of MRGPRX2, agonist binding elicits cytokines, yet less efficiently than FcεRI-aggregation. MRGPRX2-associated inflammation may thus be less tissue-destructive than responses to allergic challenge.

Clinical factors associated with composition of lung microbiota and important taxa predicting clinical prognosis in patients with severe community-acquired pneumonia

Few studies have described the key features and prognostic roles of lung microbiota in patients with severe community-acquired pneumonia (SCAP). We prospectively enrolled consecutive SCAP patients admitted to ICU. Bronchoscopy was performed at bedside within 48 h of ICU admission, and 16S rRNA gene sequencing was applied to the collected bronchoalveolar lavage fluid. The primary outcome was clinical improvements defined as a decrease of 2 categories and above on a 7-category ordinal scale within 14 days following bronchoscopy. Sixty-seven patients were included. Multivariable permutational multivariate analysis of variance found that positive bacteria lab test results had the strongest independent association with lung microbiota (R² = 0.033; P = 0.018), followed by acute kidney injury (AKI; R² = 0.032; P = 0.011) and plasma MIP-1β level (R² = 0.027; P = 0.044). Random forest identified that the families Prevotellaceae, Moraxellaceae, and Staphylococcaceae were the biomarkers related to the positive bacteria lab test results. Multivariable Cox regression showed that the increase in α-diversity and the abundance of the families Prevotellaceae and Actinomycetaceae were associated with clinical improvements. The positive bacteria lab test results, AKI, and plasma MIP-1β level were associated with patients’ lung microbiota composition on ICU admission. The families Prevotellaceae and Actinomycetaceae on admission predicted clinical improvements.

Microbial and clinical factors are related to recurrence of symptoms after childhood lower respiratory tract infection

Childhood lower respiratory tract infections (LRTI) are associated with dysbiosis of the nasopharyngeal microbiota, and persistent dysbiosis following the LRTI may in turn be related to recurrent or chronic respiratory problems.

Therefore, we aimed to investigate microbial and clinical predictors of early recurrence of respiratory symptoms as well as recovery of the microbial community following hospital admission for LRTI in children.

To this end, we collected clinical data and characterised the nasopharyngeal microbiota of 154 children (4 weeks–5 years old) hospitalised for a LRTI (bronchiolitis, pneumonia, wheezing illness or mixed infection) at admission and 4–8 weeks later. Data were compared to 307 age-, sex- and time-matched healthy controls.

During follow-up, 66% of cases experienced recurrence of (mild) respiratory symptoms. In cases with recurrence of symptoms during follow-up, we found distinct nasopharyngeal microbiota at hospital admission, with higher levels of Haemophilus influenzae/haemolyticus, Prevotella oris and other gram-negatives and lower levels of Corynebacterium pseudodiphtheriticum/propinquum and Dolosigranulum pigrum compared with healthy controls. Furthermore, in cases with recurrence of respiratory symptoms, recovery of the microbiota was also diminished. Especially in cases with wheezing illness, we observed a high rate of recurrence of respiratory symptoms, as well as diminished microbiota recovery at follow-up.

Together, our results suggest a link between the nasopharyngeal microbiota composition during LRTI and early recurrence of respiratory symptoms, as well as diminished microbiota recovery after 4–8 weeks. Future studies should investigate whether (speed of) ecological recovery following childhood LRTI is associated with long-term respiratory problems.

Composition of nasopharyngeal microbiota during LRTI in children is related to recurring respiratory symptoms in the following months, and to incomplete microbiota recovery. Future research may pinpoint host and microbial predictors of clinical outcomes.https://bit.ly/3aInAwN

Delivery mode and gut microbial changes correlate with an increased risk of childhood asthma

There have been reports of associations between cesarean section delivery and the risk of childhood asthma, potentially mediated through changes in the gut microbiota. We followed 700 children in the Copenhagen Prospective Studies on Asthma in Childhood₂₀₁₀ (COPSAC₂₀₁₀) cohort prospectively from birth. We examined the effects of cesarean section delivery on gut microbial composition by 16S rRNA gene amplicon sequencing during the first year of life. We then explored whether gut microbial perturbations due to delivery mode were associated with a risk of developing asthma in the first 6 years of life. Delivery by cesarean section was accompanied by marked changes in gut microbiota composition at one week and one month of age, but by one year of age only minor differences persisted compared to vaginal delivery. Increased asthma risk was found in children born by cesarean section only if their gut microbiota composition at 1 year of age still retained a cesarean section microbial signature, suggesting that appropriate maturation of the gut microbiota could mitigate against the increased asthma risk associated with gut microbial changes due to cesarean section delivery.

Host-microbiome intestinal interactions during early life: considerations for atopy and asthma development

PURPOSE OF REVIEW

The body's largest microbial community, the gut microbiome, is in contact with mucosal surfaces populated with epithelial, immune, endocrine and nerve cells, all of which sense and respond to microbial signals. These mutual interactions have led to a functional coevolution between the microbes and human physiology. Examples of coadaptation are anaerobes Bifidobacteria and Bacteroides, which have adjusted their metabolism to dietary components of human milk, and infant immune development, which has evolved to become reliant on the presence of beneficial microbes. Current research suggests that specific composition of the early-life gut microbiome aligns with the maturation of host immunity. Disruptions of natural microbial succession patterns during gut colonization are a consistent feature of immune-mediated diseases, including atopy and asthma.

RECENT FINDINGS

Here, we catalog recent birth cohorts documenting associations between immune dysregulation and microbial alterations, and summarize the evidence supporting the role of the gut microbiome as an etiological determinant of immune-mediated allergic diseases.

SUMMARY

Ecological concepts that describe microbial dynamics in the context of the host environment, and a portray of immune and neuroendocrine signaling induced by host-microbiome interactions, have become indispensable in describing the molecular role of early-life microbiome in atopy and asthma susceptibility.

Airway immune mediator levels during asthma-like symptoms in young children and their possible role in response to azithromycin

BACKGROUND

Asthma-like symptoms in young children are orchestrated by the local airway immune response, but current knowledge largely relies on in vitro airway models. Azithromycin has been shown to reduce the duration of episodes with asthma-like symptoms, but efficacy may depend on the individual child's immune response.

OBJECTIVES

To investigate in vivo upper airway immune mediator levels during episodes with asthma-like symptoms in young children and their ability to predict the clinical response to azithromycin treatment.

METHODS

A total of 535 children aged 0-3 years from the Copenhagen Prospective Studies of Asthma in Childhood-2010 mother-child cohort were examined for immune mediator levels in samples of nasal epithelial lining fluid during episodes with asthma-like symptoms as well as in the asymptomatic state. In a sub-study, children with recurrent asthma-like symptoms were randomized to either a 3-day course of oral azithromycin (10 mg/kg; n = 32) or placebo (n = 38). In the current study, we compared the pretreatment immune mediator levels with the clinical response to treatment with azithromycin in an exploratory post hoc analysis.

RESULTS

The immune mediator concentrations during vs outside episodes were significantly upregulated for IFN-ɣ (ratio 1.73), TNF-α (ratio 2.05), IL-1β (ratio 1.45), IL-10 (ratio 1.97), while CCL22 (ratio 0.65) was downregulated. Low levels of TNF-α and IL-10 and high levels of CCL22 predicted better treatment response to azithromycin (P-values < .05).

CONCLUSION

Upper airway immune mediator levels were altered during episodes of asthma-like symptoms, and levels of TNF-α, CCL22, and IL-10 may predict the response to azithromycin treatment.

Manipulating the infant respiratory microbiomes to improve clinical outcomes: A review of the literature

BACKGROUND

The association between infant respiratory microbiota and disease (including respiratory tract infections and asthma) is increasingly recognised, although the mechanism remains unclear. Respiratory infections and asthma account for a large proportion of infant morbidity and mortality, so the possibility of preventing disease or modifying clinical outcomes by manipulating microbiome development warrants investigation.

OBJECTIVES AND METHODS

We identified studies that investigated the efficacy of live bacteria (probiotics or human challenge) or their substrates to modify respiratory colonisation or clinical outcomes in infants.

ELIGIBILITY CRITERIA

Interventional studies involving infants under one year of age, administration of live bacteria or their substrates, and outcome measures including bacterial colonisation, microbiome profile, or respiratory disease phenotypes.

RESULTS AND LIMITATIONS

Some bacterial interventions can reduce infant respiratory infections, although none have been shown to reduce asthma incidence. The literature is heterogeneous in design and quality, precluding meaningful meta-analysis.

CONCLUSIONS

Upper respiratory tract infant microbiome manipulation may alter outcomes in respiratory tract infection, but further well-conducted research is needed to confirm this. Improved regulation of proprietary bacterial products is essential for further progress.

Early Microbial-Immune Interactions and Innate Immune Training of the Respiratory System during Health and Disease

Over the past two decades, several studies have positioned early-life microbial exposure as a key factor for protection or susceptibility to respiratory diseases. Birth cohorts have identified a strong link between neonatal bacterial colonization of the nasal airway and gut with the risk for respiratory infections and childhood asthma. Translational studies have provided companion mechanistic insights on how viral and bacterial exposures in early life affect immune development at the respiratory mucosal barrier. In this review, we summarize and discuss our current understanding of how early microbial–immune interactions occur during infancy, with a particular focus on the emergent paradigm of “innate immune training”. Future human-based studies including newborns and infants are needed to inform the timing and key pathways implicated in the development, maturation, and innate training of the airway immune response, and how early microbiota and virus exposures modulate these processes in the respiratory system during health and disease.

Early Life Microbiota and Respiratory Tract Infections

Over the last decade, it has become clear that respiratory and intestinal tract microbiota are related to pathogenesis of respiratory tract infections (RTIs). Host and environmental factors can drive respiratory microbiota maturation in early life, which in turn is related to consecutive susceptibility to RTIs. Moreover, during RTIs, including viral bronchiolitis, the local microbiome appears to play an immunomodulatory role through complex interactions, though causality has not yet been fully demonstrated. The microbiota is subsequently associated with recovery after RTIs and can be related to persistent or long-term sequelae. In this Review, we explore the epidemiological evidence supporting these associations and link to mechanistic insights. The long-term consequences of childhood RTIs and the comprehensive role of the microbiota at various stages in RTI pathogenesis call for early life preventative and therapeutic interventions to promote respiratory health.

A rich meconium metabolome in human infants is associated with early-life gut microbiota composition and reduced allergic sensitization

Microbiota maturation and immune development occur in parallel with, and are implicated in, allergic diseases, and research has begun to demonstrate the importance of prenatal influencers on both. Here, we investigate the meconium metabolome, a critical link between prenatal exposures and both early microbiota and immune development, to identify components of the neonatal gut niche that contribute to allergic sensitization. Our analysis reveals that newborns who develop immunoglobulin E (IgE)-mediated allergic sensitization (atopy) by 1 year of age have a less-diverse gut metabolome at birth, and specific metabolic clusters are associated with both protection against atopy and the abundance of key taxa driving microbiota maturation. These metabolic signatures, when coupled with early-life microbiota and clinical factors, increase our ability to accurately predict whether or not infants will develop atopy. Thus, the trajectory of both microbiota colonization and immune development are significantly affected by metabolites present in the neonatal gut at birth.

Metabolic diversity is reduced in newborns that develop allergic sensitization

Gut microbiota maturation is reduced within infants that develop allergic sensitization

Meconium metabolites are associated with important taxa for microbiota maturation

Nutritional immunity: the impact of metals on lung immune cells and the airway microbiome during chronic respiratory disease

Nutritional immunity is the sequestration of bioavailable trace metals such as iron, zinc and copper by the host to limit pathogenicity by invading microorganisms. As one of the most conserved activities of the innate immune system, limiting the availability of free trace metals by cells of the immune system serves not only to conceal these vital nutrients from invading bacteria but also operates to tightly regulate host immune cell responses and function. In the setting of chronic lung disease, the regulation of trace metals by the host is often disrupted, leading to the altered availability of these nutrients to commensal and invading opportunistic pathogenic microbes. Similarly, alterations in the uptake, secretion, turnover and redox activity of these vitally important metals has significant repercussions for immune cell function including the response to and resolution of infection. This review will discuss the intricate role of nutritional immunity in host immune cells of the lung and how changes in this fundamental process as a result of chronic lung disease may alter the airway microbiome, disease progression and the response to infection.

Asthma in the Precision Medicine Era: Biologics and Probiotics

Asthma is a major global health issue. Over 300 million people worldwide suffer from this chronic inflammatory airway disease. Typical clinical symptoms of asthma are characterized by a recurrent wheezy cough, chest tightness, and shortness of breath. The main goals of asthma management are to alleviate asthma symptoms, reduce the risk of asthma exacerbations, and minimize long-term medicinal adverse effects. However, currently available type 2 T helper cells (Th2)-directed treatments are often ineffective due to the heterogeneity of the asthma subgroups, which manifests clinically with variable and poor treatment responses. Personalized precision therapy of asthma according to individualized clinical characteristics (phenotype) and laboratory biomarkers (endotype) is the future prospect. This mini review discusses the molecular mechanisms underlying asthma pathogenesis, including the hot sought-after topic of microbiota, add-on therapies and the potential application of probiotics in the management of asthma.

The changes of respiratory microbiome between mild and severe asthma patients

Due to the increased number of patients suffering from asthma, the mechanism of this disease has been subject to much attention from the public and finding a cure for this disease is urgent. A changed abundance of the microbiome has been proven to play an important role in the genesis and development of asthma. In this study, the abundance and the function of the microbiome were studied. It was found that there were significant changes in the components and the function of the microbiome when asthma changed from mild to severe. This study could help us to better understand the relationship between asthma and the respiratory microbiome.

Nasopharyngeal microbiome analyses in otitis-prone and otitis-free children

OBJECTIVES

About 10-15% children develop frequent acute otitis media (AOM) confirmed by tympanocentesis. These children are designated sOP (stringently defined otitis-prone) because all AOM episodes have been microbiologically confirmed. The cause of otitis-proneness in sOP children is multi-factorial, including frequent otopathogen nasopharyngeal (NP) colonization and deficiency in innate and adaptive immune responses. A largely unexplored contributor to otitis proneness is NP microbiome composition. Since the microbiome modulates otopathogen NP colonization and immune responses, we hypothesized that the NP microbiome composition in sOP children might be dysregulated.

METHODS

We performed 16S rRNA sequencing to analyze microbiome composition in 157 NP samples from 28 sOP and 68 AOM-free children when they were 6 months or 12 months old and healthy. Bioinformatic approaches were employed to examine the composition difference between the two populations and its correlation with changes in levels of inflammatory cytokines.

RESULTS

A different global microbiome profile and reduced alpha diversity was observed in the NP microbiome of sOP children when 6 months old, compared with that from AOM-free children of the same age. This difference was resolved when groups were compared at 12 months old. We found 4 bacterial genera-Bacillus, Veillonella, Gemella, and Prevotella-correlated with higher levels of pro-inflammatory cytokines in the NP. Those 4 bacterial genera were in lower abundance in sOP compared to AOM-free children.

CONCLUSION

Dysbiosis occurs in the NP microbiome of sOP children at an early age even when they were healthy. This dysbiosis correlates with a lower inflammatory state in the NP of these children.

Decreased miRNA-320e correlates with allergy in children with otitis media with effusion

OBJECTIVE

Otitis media with effusion (OME) is a common childhood disease and the main cause of conductive hearing loss in this age group. Many factors predispose to OME but allergy is still widely disputed. The answer may lay in the molecular mechanisms of ear exudate formation and the recent studies showed miRNAs might take part in it. MiRNAs are also potent regulators of allergic response. As miRNAs are present in the middle ear, we hypothesized their expression differs between allergic and non-allergic patients and reflects the difference in pathomechanism of effusion formation between these two groups.

MATERIALS AND METHODS

This study aimed to establish the expression of 5 different miRNAs (miR-223-3p, miR-451a, miR-16-5p, miR-320e, miR-25-3p) in ear exudates in children diagnosed with OME. The allergy group consisted of 18 patients whereas the non-allergic group had 36 patients. MicroRNA was isolated from the middle ear fluid collected during myringotomy and transcribed into cDNA. MiRNA expression was measured with TaqMan™ MicroRNA Assays and analyzed with DataAssist software. The comparative CT method was used for calculating the relative quantification of gene expression based on the endogenous control gene expression (U6 snRNA-001973).

RESULTS

MiR-320e expression was significantly decreased in allergic children with OME. Other studied miRNAs also showed reduced expression in allergic children, but the decrease was not significant.

CONCLUSIONS

MiRNA expression differs between children with and without allergy in the course of OME, but further studies are needed to explain the exact role of miR-320e and its target genes in OME pathology in allergic patients.

The intersect of genetics, environment, and microbiota in asthma-perspectives and challenges

In asthma, a significant portion of the interaction between genetics and environment occurs through microbiota. The proposed mechanisms behind this interaction are complex and at times contradictory. This review covers recent developments in our understanding of this interaction: the "microbial hypothesis" and the "farm effect"; the role of endotoxin and genetic variation in pattern recognition systems; the interaction with allergen exposure; the additional involvement of host gut and airway microbiota; the role of viral respiratory infections in interaction with the 17q21 and CDHR3 genetic loci; and the importance of in utero and early-life timing of exposures. We propose a unified framework for understanding how all these phenomena interact to drive asthma pathogenesis. Finally, we point out some future challenges for continued research in this field, in particular the need for multiomic integration, as well as the potential utility of asthma endotyping.

Interactions of Bacteriophages and Bacteria at the Airway Mucosa: New Insights Into the Pathophysiology of Asthma

The airway epithelium is the primary site where inhaled and resident microbiota interacts between themselves and the host, potentially playing an important role on allergic asthma development and pathophysiology. With the advent of culture independent molecular techniques and high throughput technologies, the complex composition and diversity of bacterial communities of the airways has been well-documented and the notion of the lungs' sterility definitively rejected. Recent studies indicate that the microbial composition of the asthmatic airways across the spectrum of disease severity, differ significantly compared with healthy individuals. In parallel, a growing body of evidence suggests that bacterial viruses (bacteriophages or simply phages), regulating bacterial populations, are present in almost every niche of the human body and can also interact directly with the eukaryotic cells. The triptych of airway epithelial cells, bacterial symbionts and resident phages should be considered as a functional and interdependent unit with direct implications on the respiratory and overall homeostasis. While the role of epithelial cells in asthma pathophysiology is well-established, the tripartite interactions between epithelial cells, bacteria and phages should be scrutinized, both to better understand asthma as a system disorder and to explore potential interventions.

NOD1 sensing of house dust mite-derived microbiota promotes allergic experimental asthma

BACKGROUND

Asthma severity has been linked to exposure to gram-negative bacteria from the environment that are recognized by NOD1 receptor and are present in house dust mite (HDM) extracts. NOD1 polymorphism has been associated with asthma.

OBJECTIVE

We sought to evaluate whether either host or HDM-derived microbiota may contribute to NOD1-dependent disease severity.

METHODS

A model of HDM-induced experimental asthma was used and the effect of NOD1 deficiency was evaluated. Contribution of host microbiota was evaluated by fecal transplantation. Contribution of HDM-derived microbiota was assessed by 16S ribosomal RNA sequencing, mass spectrometry analysis, and peptidoglycan depletion of the extracts.

RESULTS

In this model, loss of the bacterial sensor NOD1 and its adaptor RIPK2 improved asthma features. Such inhibitory effect was not related to dysbiosis caused by NOD1 deficiency, as shown by fecal transplantation of Nod1-deficient microbiota to wild-type germ-free mice. The 16S ribosomal RNA gene sequencing and mass spectrometry analysis of HDM allergen, revealed the presence of some muropeptides from gram-negative bacteria that belong to the Bartonellaceae family. While such HDM-associated muropeptides were found to activate NOD1 signaling in epithelial cells, peptidoglycan-depleted HDM had a decreased ability to instigate asthma in vivo.

CONCLUSIONS

These data show that NOD1-dependent sensing of HDM-associated gram-negative bacteria aggravates the severity of experimental asthma, suggesting that inhibiting the NOD1 signaling pathway may be a therapeutic approach to treating asthma.

Exposure to ultrafine particles and oral flora, respiratory function, and biomarkers of inflammation: A panel study in children

Particulate matter (PM) is the most important air pollution problem that leads to substantial health effects. However, very few studies focused on the effects of ultrafine particles (UFPs, particles< 0.1 μm) on children respiratory health. We performed a panel study with 3 rounds of follow-up among 65 pupils at the Elementary School Affiliated to Shanghai Normal University in China from November 2018 to June 2019. Real-time concentrations of UFPs were measured in the campus. In each visit, we detected biomarkers in saliva and microflora in buccal mucosa, fractional exhaled nitric oxide (FeNO) and lung function. We applied a linear mixed-effect (LME) model to examine the associations of UFPs and each health outcome. We found increased levels of FeNO and tumor necrosis factor-α (TNF-α) and reduced lung function in association with higher UFP exposure. For each interquartile range increase of UFPs, the largest changes were found in lag 0-72 h for forced vital capacity [-69.02 ml (95% CI: -114.20, -23.84)], TNF-α [13.41 pg/ml (95% CI: 7.08, 19.73)], and FeNO [26.85% (95% CI: 11.84%, 43.88%)]. UFP exposure was associated with reduced diversity in buccal microflora with largest reduction in lag 0-72 h [12.24 (95% CI: 7.76, 16.71) for Ace index; 8.78 (95% CI: 2.96, 14.60) for Chao1 index]. UFP exposure was also associated with increased Streptococcus, Gemella, and decreased Actinomyces. Short-term UFP exposures may impair the respiratory system by inducing inflammation, decreasing lung function and attenuating buccal microbe diversity in children.

Cardiorespiratory performance capacity and airway microbiome in patients following primary repair of esophageal atresia

BACKGROUND

Patients following repair of an esophageal atresia (EA) or tracheoesophageal fistula (TEF) carry an increased risk of long-term cardiopulmonary malaise. The role of the airway microbiome in EA/TEF patients remains unclear.

METHODS

All EA/TEF patients treated between 1980 and 2010 were invited to a prospective clinical examination, spirometry, and spiroergometry. The airway microbiome was determined from deep induced sputum by 16 S rRNA gene sequencing. The results were compared to a healthy age- and sex-matched control group.

RESULTS

Nineteen EA/TEF patients with a mean age of 24.7 ± 7 years and 19 age- and sex-matched controls were included. EA/TEF patients showed a significantly lower muscle mass, lower maximum vital capacity (VC_max), and higher rates of restrictive ventilation disorders. Spiroergometry revealed a significantly lower relative performance capacity and lower peak VO₂ in EA/TEF patients. Alpha- and beta-diversity of the airway microbiome did not differ significantly between the two groups. Linear discriminant effect size analysis revealed significantly enriched species of Prevotella_uncultured, Streptococcus_anginosus, Prevotella_7_Prevotella_enoeca, and Mogibacterium_timidum.

CONCLUSION

EA/TEF patients frequently suffer from restrictive ventilation disorders and impaired cardiopulmonary function associated with minor alterations of the airway microbiome. Long-term examinations of EA/TEF patients seem to be necessary in order to detect impaired cardiopulmonary function.

IMPACT

The key messages of the present study are a significantly decreased VC_max and exercise performance, as well as airway microbiome differences in EA/TEF patients. This study is the first to present parameters of lung function and exercise performance in combination with airway microbiome analysis with a mean follow-up of 24 years in EA/TEF patients. Prospective, long-term studies are needed to unravel possible interactions between alterations of the airway microbiome and impaired pulmonary function in EA/TEF patients.

Urbanized microbiota in infants, immune constitution, and later risk of atopic diseases

BACKGROUND

Urbanization is linked with an increased burden of asthma and atopic traits. A putative mechanism is insufficient exposure to beneficial microbes early in life, leading to immune dysregulation, as was previously shown for indoor microbial exposures.

OBJECTIVE

Our aim was to investigate whether urbanization is associated with the microbiota composition in the infants' body and early immune function, and whether these contribute to the later risk of asthma and atopic traits.

METHODS

We studied the prospective Copenhagen Prospective Studies on Asthma in Childhood 2010₂₀₁₀ mother-child cohort of 700 children growing up in areas with different degrees of urbanization. During their first year of life, airway and gut microbiotas, as well as immune marker concentrations, were defined. When the children were 6 years of age, asthma and atopic traits were diagnosed by pediatricians.

RESULTS

In adjusted analyses, the risk of asthma and aeroallergen sensitization were increased in urban infants. The composition of especially airway but also gut microbiotas differed between urban and rural infants. The living environment-related structure of the airway microbiota was already associated with immune mediator concentrations at 1 month of age. An urbanized structure of the airway and gut microbiotas was associated with an increased risk of asthma coherently during multiple time points and also with the risks of eczema and sensitization.

CONCLUSION

Our findings suggest that urbanization-related changes in the infant microbiota may elevate the risk of asthma and atopic traits, probably via cross talk with the developing immune system. The airways may facilitate this effect, as they are open for colonization by environmental airborne microbes and serve as an immune interface.

The infant pharyngeal microbiomes: origin, impact and manipulation

PURPOSE OF REVIEW

There has been an exponential increase in research into infant microbiome evolution, and it appears that pharyngeal microbiota are associated with clinical phenotypes (e.g. infection and asthma). Although broad consensus views are emerging, significant challenges and uncertainties remain.

RECENT FINDINGS

Infant pharyngeal microbiome research is limited by low biomass, high temporal diversity and lack of agreed standards for sampling, DNA sequencing and taxonomic reporting. Analysis of amplicon sequence variants and improved cost and availability of whole-genome sequencing are promising options for improving taxonomic resolution of such studies. Infant respiratory microbiomes arise, at least in part, from maternal flora (e.g. the respiratory tract and breastmilk), and are associated with environmental and clinical factors (e.g. mode of feeding and delivery, siblings, daycare attendance, birth season and antibiotic usage). Interventional research to modify the infant pharyngeal microbiota has recently been reported, using dietary supplements.

SUMMARY

Further work is needed to improve characterization of the infant pharyngeal microbiomes, including routes of bacterial acquisition, role of environmental factors and associations with disease phenotypes. Methodological standards are desirable to facilitate more reproducible, comparable research. Improved understanding may enable manipulation of infant pharyngeal microbiota to improve clinical outcomes.

Biomarkers for diagnosis and prediction of therapy responses in allergic diseases and asthma

Modern health care requires a proactive and individualized response to diseases, combining precision diagnosis and personalized treatment. Accordingly, the approach to patients with allergic diseases encompasses novel developments in the area of personalized medicine, disease phenotyping and endotyping, and the development and application of reliable biomarkers. A detailed clinical history and physical examination followed by the detection of IgE immunoreactivity against specific allergens still represents the state of the art. However, nowadays, further emphasis focuses on the optimization of diagnostic and therapeutic standards and a large number of studies have been investigating the biomarkers of allergic diseases, including asthma, atopic dermatitis, allergic rhinitis, food allergy, urticaria and anaphylaxis. Various biomarkers have been developed by omics technologies, some of which lead to a better classification of distinct phenotypes or endotypes. The introduction of biologicals to clinical practice increases the need for biomarkers for patient selection, prediction of outcomes and monitoring, to allow for an adequate choice of the duration of these costly and long‐lasting therapies. Escalating healthcare costs together with questions about the efficacy of the current management of allergic diseases require further development of a biomarker‐driven approach. Here, we review biomarkers in diagnosis and treatment of asthma, atopic dermatitis, allergic rhinitis, viral infections, chronic rhinosinusitis, food allergy, drug hypersensitivity and allergen immunotherapy with a special emphasis on specific IgE, the microbiome and the epithelial barrier. In addition, EAACI guidelines on biologicals are discussed within the perspective of biomarkers.

Can we prevent allergic disease? Understanding the links between the early life microbiome and allergic diseases of childhood

PURPOSE OF REVIEW

The microbiome and immune system are intrinsically linked, and during infancy these crucial biological systems undergo a concurrent and expansive maturation process. As these maturation processes progress, some children develop a sequence of IgE-mediated immune disorders termed the 'Allergic March', and unfortunately the prevalence of these lifelong and burdensome allergic conditions has increased over the past half century. Our current treatment strategies are unable to prevent or cure components of the Allergic March. However, recent discoveries have enhanced our mechanistic understanding of early-life microbiota-immune interactions with exciting implications for preventing these allergic disorders.

RECENT FINDINGS

The current review will detail recent literature regarding perinatal factors (e.g. birth mode, antibiotic exposure, breastmilk seeding of the microbiota, built environment) that shape the infant gut microbiota composition. Furthermore, we will discuss new findings that have highlighted immune cells which are particularly sensitive to microbial influences in utero and during the early-life window of development.

SUMMARY

As our understanding of the dynamic relationship between the developing infant microbiota and immune system grows, a priority toward preserving critical early-life interactions may provide life-long protection to these diseases in the future.

European Respiratory Society International Congress 2020: highlights from best-abstract awardees

#ERSCongress 2020 best-abstract awardees summarise their virtual European Respiratory Society International Congress experience and views on the evolving field of research for their respective assembly https://bit.ly/3kJ9JrJ.

Epigenetic landscape links upper airway microbiota in infancy with allergic rhinitis at 6 years of age

BACKGROUND

The upper airways present a barrier to inhaled allergens and microbes, which alter immune responses and subsequent risk for diseases, such as allergic rhinitis (AR).

OBJECTIVE

We tested the hypothesis that early-life microbial exposures leave a lasting signature in DNA methylation that ultimately influences the development of AR in children.

METHODS

We studied upper airway microbiota at 1 week, 1 month, and 3 months of life, and measured DNA methylation and gene expression profiles in upper airway mucosal cells and assessed AR at age 6 years in children in the Copenhagen Prospective Studies on Asthma in Childhood birth cohort.

RESULTS

We identified 956 AR-associated differentially methylated CpGs in upper airway mucosal cells at age 6 years, 792 of which formed 3 modules of correlated differentially methylated CpGs. The eigenvector of 1 module was correlated with the expression of genes enriched for lysosome and bacterial invasion of epithelial cell pathways. Early-life microbial diversity was lower at 1 week (richness P = .0079) in children with AR at age 6 years, and reduced diversity at 1 week was also correlated with the same module's eigenvector (ρ = -0.25; P = 3.3 × 10-5). We show that the effect of microbiota richness at 1 week on risk for AR at age 6 years was mediated in part by the epigenetic signature of this module.

CONCLUSIONS

Our results suggest that upper airway microbial composition in infancy contributes to the development of AR during childhood, and this trajectory is mediated, at least in part, through altered DNA methylation patterns in upper airway mucosal cells.

Developmental patterns in the nasopharyngeal microbiome during infancy are associated with asthma risk

Background

Studies indicate that the nasal microbiome may correlate strongly with the presence or future risk of childhood asthma.

Objectives

In this study, we tested whether developmental trajectories of the nasopharyngeal microbiome in early life and the composition of the microbiome during illnesses were related to risk of childhood asthma.

Methods

Children participating in the Childhood Origins of Asthma study (N = 285) provided nasopharyngeal mucus samples in the first 2 years of life, during routine healthy study visits (at 2, 4, 6, 9, 12, 18, and 24 months of age), and during episodes of respiratory illnesses, all of which were analyzed for respiratory viruses and bacteria. We identified developmental trajectories of early-life microbiome composition, as well as predominant bacteria during respiratory illnesses, and we correlated these with presence of asthma at 6, 8, 11, 13, and 18 years of age.

Results

Of the 4 microbiome trajectories identified, a Staphylococcus-dominant microbiome in the first 6 months of life was associated with increased risk of recurrent wheezing by age 3 years and asthma that persisted throughout childhood. In addition, this trajectory was associated with the early onset of allergic sensitization. During wheezing illnesses, detection of rhinoviruses and predominance of Moraxella were associated with asthma that persisted throughout later childhood.

Conclusion

In infancy, the developmental composition of the microbiome during healthy periods and the predominant microbes during acute wheezing illnesses are both associated with the subsequent risk of developing persistent childhood asthma.