The microbiome in asthma

[The lung microbiota. Review]

In the last 20years, culture-independent DNA-based techniques ("shotgun sequencing") demonstrated that complex microbial communities reside on most epithelial surfaces, including the lower airways. Until the amniotic sac ruptures, a fetus is considered to be essentially sterile. Many factors affect the composition of the lung microbiota: inheritance, mode of delivery, diet, and age-related changes in adults. It interacts with the digestive and oropharyngeal microbiotas. Animal models show that these interactions play a role in innate pulmonary immunity and modulation of the inflammatory response. The microbial composition of the airway microbiota differs between healthy children and those with chronic lung disease. The advances in the comprehension of microbiome changes have resulted in new approaches concerning the microbiota for treatment and prevention of disease.

Ribosomal PCR assay of excised intervertebral discs from patients undergoing single-level primary lumbar microdiscectomy

PURPOSE

To determine the presence of infectious microorganisms in the herniated discs of immunocompetent patients, using methodology that we hoped would be of higher sensitivity and specificity than has been reported in the past. Recent studies have demonstrated a significant rate of positive cultures for low virulent organisms in excised HNP samples (range 19-53%). These studies have served as the theoretical basis for a pilot trial, and then, a well done prospective randomized trial that demonstrated that systemic treatment with antibiotics may yield lasting improvements in a subset of patients with axial back pain. Whether the reported positive cultures in discectomy specimens represent true positives is as yet not proven, and critically important if underlying the basis of therapeutic approaches for chronic low back pain.

METHODS

This consecutive case series from a single academic center included 44 patients with radiculopathy and MRI findings of lumbar HNP. Patients elected for lumbar microdiscectomy after failure of conservative management. All patients received primary surgery at a single spinal level in the absence of immune compromise. Excised disc material was analyzed with a real-time PCR assay targeting the 16S ribosomal RNA gene followed by amplicon sequencing. No concurrent cultures were performed. Inclusion criteria were as follows: sensory or motor symptoms in a single lumbar nerve distribution; positive physical examination findings including positive straight leg raise test, distributional weakness, and/or a diminished deep tendon reflexes; and magnetic resonance imaging of the lumbar spine positive for HNP in a distribution correlating with the radicular complaint.

RESULTS

The PCR assay for the 16S rRNA sequence was negative in all 44 patients (100%). 95% CI 0-8%.

CONCLUSIONS

Based on the data presented here, there does not appear to be a significant underlying rate of bacterial disc infection in immunocompetent patients presenting with radiculopathy from disc herniation.

Infection-mediated asthma: etiology, mechanisms and treatment options, with focus on Chlamydia pneumoniae and macrolides

Asthma is a chronic respiratory disease characterized by reversible airway obstruction and airway hyperresponsiveness to non-specific bronchoconstriction agonists as the primary underlying pathophysiology. The worldwide incidence of asthma has increased dramatically in the last 40 years. According to World Health Organization (WHO) estimates, over 300 million children and adults worldwide currently suffer from this incurable disease and 255,000 die from the disease each year. It is now well accepted that asthma is a heterogeneous syndrome and many clinical subtypes have been described. Viral infections such as respiratory syncytial virus (RSV) and human rhinovirus (hRV) have been implicated in asthma exacerbation in children because of their ability to cause severe airway inflammation and wheezing. Infections with atypical bacteria also appear to play a role in the induction and exacerbation of asthma in both children and adults. Recent studies confirm the existence of an infectious asthma etiology mediated by Chlamydia pneumoniae (CP) and possibly by other viral, bacterial and fungal microbes. It is also likely that early-life infections with microbes such as CP could lead to alterations in the lung microbiome that significantly affect asthma risk and treatment outcomes. These infectious microbes may exacerbate the symptoms of established chronic asthma and may even contribute to the initial development of the clinical onset of the disease. It is now becoming more widely accepted that patterns of airway inflammation differ based on the trigger responsible for asthma initiation and exacerbation. Therefore, a better understanding of asthma subtypes is now being explored more aggressively, not only to decipher pathophysiologic mechanisms but also to select treatment and guide prognoses. This review will explore infection-mediated asthma with special emphasis on the protean manifestations of CP lung infection, clinical characteristics of infection-mediated asthma, mechanisms involved and antibiotic treatment outcomes.

The microbiome in respiratory medicine: current challenges and future perspectives

The healthy lung has previously been considered to be a sterile organ because standard microbiological culture techniques consistently yield negative results. However, culture-independent techniques report that large numbers of microorganisms coexist in the lung. There are many unknown aspects in the field, but available reports show that the lower respiratory tract microbiota: 1) is similar in healthy subjects to the oropharyngeal microbiota and dominated by members of the Firmicutes, Bacteroidetes and Proteobacteria phyla; 2) shows changes in smokers and well-defined differences in chronic respiratory diseases, although the temporal and spatial kinetics of these changes are only partially known; and 3) shows relatively abundant non-cultivable bacteria in chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, cystic fibrosis and bronchiectasis, with specific patterns for each disease. In all of these diseases, a loss of diversity, paralleled by an over-representation of Proteobacteria (dysbiosis), has been related to disease severity and exacerbations. However, it is unknown whether dysbiosis is a cause or a consequence of the damage to bronchoalveolar surfaces.Finally, little is known about bacterial functionality and the interactions between viruses, fungi and bacteria. It is expected that future research in bacterial gene expressions, metagenomics longitudinal analysis and host-microbiome animal models will help to move towards targeted microbiome interventions in respiratory diseases.

Household siblings and nasal and fecal microbiota in infants

BACKGROUND

Early-life exposure to older siblings is associated with a lower risk of asthma. To date, no study has addressed the impact of having siblings on both the airway and fecal microbiota during infancy. The aim of this study was therefore to profile the nasal airway and fecal microbiota in infants, and to examine the association between having siblings and microbiota profile.

METHODS

We conducted a cross-sectional study of 105 healthy infants (aged <1 year). Using 16S rRNA gene sequencing and an unbiased clustering approach to the nasal airway and fecal samples, we identified microbiota profiles and then determined the association between having siblings and microbiome profile.

RESULTS

Overall, the median age was 3.4 months (IQR, 2.0-4.7 months); 43% had siblings in the household. Unbiased clustering of nasal airway microbiota identified three profiles: Moraxella dominant (43%), Corynebacterium/Dolosigranulum dominant (36%), and mixed (21%). Infants with siblings were more likely to have a Moraxella-dominant profile than Corynebacterium/Dolosigranulum-dominant profile (76% vs 18%), while those without siblings had the opposite pattern (18% vs 50%; P < 0.001, multivariable-adjusted). Fecal microbiota consisted of three profiles: Bifidobacterium dominant (39%), Escherichia dominant (31%), and Enterobacter dominant (30%). Infants with siblings were more likely to have a Bifidobacterium-dominant profile than Escherichia-dominant profile (49% vs 24%) while those without siblings had the opposite pattern (32% vs 37%; P = 0.04, multivariable-adjusted).

CONCLUSIONS

In this cross-sectional study, infants with siblings were more likely to have a Moraxella-dominant nasal microbiota profile and Bifidobacterium-dominant fecal microbiota profile. These findings should facilitate further investigation of the interplay between early-life environmental exposure, the microbiome, and childhood asthma.

Metabolomics analysis identifies different metabotypes of asthma severity

In this study, we sought to determine whether asthma has a metabolic profile and whether this profile is related to disease severity.We characterised the serum from 22 healthy individuals and 54 asthmatics (12 mild, 20 moderate, 22 severe) using liquid chromatography-high-resolution mass spectrometry-based metabolomics. Selected metabolites were confirmed by targeted mass spectrometry assays of eicosanoids, sphingolipids and free fatty acids.We conclusively identified 66 metabolites; 15 were significantly altered with asthma (p≤0.05). Levels of dehydroepiandrosterone sulfate, cortisone, cortisol, prolylhydroxyproline, pipecolate and N-palmitoyltaurine correlated significantly (p<0.05) with inhaled corticosteroid dose, and were further shifted in individuals treated with oral corticosteroids. Oleoylethanolamide increased with asthma severity independently of steroid treatment (p<0.001). Multivariate analysis revealed two patterns: 1) a mean difference between controls and patients with mild asthma (p=0.025), and 2) a mean difference between patients with severe asthma and all other groups (p=1.7×10^-4). Metabolic shifts in mild asthma, relative to controls, were associated with exogenous metabolites (e.g. dietary lipids), while those in moderate and severe asthma (e.g. oleoylethanolamide, sphingosine-1-phosphate, N-palmitoyltaurine) were postulated to be involved in activating the transient receptor potential vanilloid type 1 (TRPV1) receptor, driving TRPV1-dependent pathogenesis in asthma.Our findings suggest that asthma is characterised by a modest systemic metabolic shift in a disease severity-dependent manner, and that steroid treatment significantly affects metabolism.

Basic Definitions and Concepts: Organization of the Gut Microbiome

New claims are frequently made for a role for the microbiome in a disease or disorder previously considered remote from the gut. The microbiome has been linked to such seemingly unrelated entities as depression, anorexia nervosa, autism, Parkinson disease, allergy, and asthma. Although many of these proposals have been based on animal studies, explorations of the microbiome in human disease continue to proliferate, facilitated by technologies that provide a detailed assessment of the microbial inhabitants of our gastrointestinal tract and their biological activities and metabolic products. With these technologies come new terminologies, which are identified in this article.

Nasopharyngeal Microbiome Diversity Changes over Time in Children with Asthma

BACKGROUND

The nasopharynx is a reservoir for pathogens associated with respiratory illnesses such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome of infants and adults during health and disease; less is known, however, about the composition and temporal dynamics (i.e., longitudinal variation) of microbiotas from children and adolescents. Here we use NGS technology to characterize the nasopharyngeal microbiomes of asthmatic children and adolescents (6 to 18 years) and determine their stability over time.

METHODS

Two nasopharyngeal washes collected 5.5 to 6.5 months apart were taken from 40 children and adolescents with asthma living in the Washington D.C. area. Sequence data from the 16S-V4 rRNA gene region (~250 bp) were collected from the samples using the MiSeq platform. Raw data were processed in mothur (SILVA123 reference database) and Operational Taxonomic Units (OTU)-based alpha- and beta-diversity metrics were estimated. Relatedness among samples was assessed using PCoA ordination and Procrustes analyses. Differences in microbial diversity and taxon mean relative proportions were assessed using linear mixed effects models. Core microbiome analyses were also performed to identify stable and consistent microbes of the nasopharynx.

RESULTS AND DISCUSSION

A total of 2,096,584 clean 16S sequences corresponding to an average of 167 OTUs per sample were generated. Representatives of Moraxella*, Staphylococcus*, Dolosigranulum, Corynebacterium, Prevotella, Streptococcus*, Haemophilus*, Fusobacterium* and a Neisseriaceae genus accounted for 86% of the total reads. These nine genera have been previously found in the nasopharynxes of both infants and adults, but in different proportions. OTUs from the five genera highlighted (*) above defined the nasopharyngeal core microbiome at the 95% level. No significant differences in alpha- and beta-diversity were observed between seasons, but bacterial mean relative proportions of Haemophilus, Moraxella, Staphylococcus and Corynebacterium varied significantly between summer-fall and age groups (inter-patient variation). Additionally, OTUs varied significantly within patients between time points in 35 of the 40 patients analyzed. Future cross-sectional studies should be mindful of the temporal dynamics of the nasopharyngeal microbiota.

Personalised medicine in asthma: from curative to preventive medicine

The concept of asthma has changed substantially in recent years. Asthma is now recognised as a heterogeneous entity that is complex to treat. The subdivision of asthma, provided by "cluster" analyses, has revealed various groups of asthma patients who share phenotypic features. These phenotypes underlie the need for personalised asthma therapy because, in contrast to the previous approach, treatment must be tailored to the individual patient. Determination of the patient's asthma phenotype is therefore essential but sometimes challenging, particularly in elderly patients with a multitude of comorbidities and a complex exposure history. This review first describes the various asthma phenotypes, some of which were defined empirically and others through cluster analysis, and then discusses personalisation of the patient's diagnosis and therapy, addressing in particular biological therapies and patient education. This personalised approach to curative medicine should make way in the coming years for personalised preventive and predictive medicine, focused on subjects at risk who are not yet ill, with the aim of preventing asthma before it occurs. The concept of personalised preventive medicine may seem a long way off, but is it really?

[Association between risk factors during maternal pregnancy and the neonatal period and childhood bronchial asthma]

OBJECTIVE

To study the association of the risk factors during maternal pregnancy and the neonatal period with childhood bronchial asthma.

METHODS

A total of 306 children with asthma (asthma group) and 250 healthy children (control group) were enrolled. Their clinical data during the neonatal period and the maternal data during pregnancy were retrospectively studied.

RESULTS

The univariate analysis showed that there were significant differences in the rates of maternal use of antibiotics during pregnancy, use of antibiotics and probiotics during the neonatal period, preterm birth, cesarean section, low birth weight, and breast feeding (>6 months) between the asthma and control groups (P<0.05). The multivariate logistic regression analysis showed that use of antibiotics during pregnancy (OR=3.908, 95%CI: 1.277-11.962), use of antibiotics during neonatal period (OR=24.154, 95%CI: 7.864-74.183), preterm birth (OR=8.535, 95%CI: 2.733-26.652), and cesarean section (OR=4.588, 95%CI: 2.887-7.291) were independent risk factors for childhood asthma. The use of probiotics during the neonatal period (OR=0.014, 95%CI: 0.004-0.046) and breast feeding (>6 months) (OR=0.161, 95%CI: 0.103-0.253) were protective factors for childhood asthma.

CONCLUSIONS

The early prevention of childhood asthma can be improved by reducing the use of antibiotics during pregnancy, reducing cesarean section, avoiding abuse of antibiotics during the neonatal period, trying breast feeding and taking probiotics in early stage.

Prenatal Maternal Stress and the Risk of Asthma in Children

Emerging evidence indicate that maternal prenatal stress (MPS) can result in a range of long-term adverse effects in the offspring. The underlying mechanism of MPS is not fully understood. However, its complexity is emphasized by the number of purportedly involved pathways namely, placental deregulated metabolism of maternal steroids, impaired maturation of fetal HPA axis, imbalanced efflux of commensal bacteria across the placenta, and skewed immune development toward Th2. Fetal programming probably exerts a pivotal role in the end result of the above pathways through the modulation of gene expression. In this review, we highlight the current knowledge from epidemiological and experimental studies regarding the effects of MPS on asthma development in the offspring.

Conjugated linoleic acids suppress inflammatory response and ICAM-1 expression through inhibition of NF-κB and MAPK signaling in human bronchial epithelial cells

Conjugated linoleic acids (CLAs) comprise a group of natural unsaturated fatty acids. CLA was reported to have anti-asthma, anti-adiposity, and anti-tumor effects. The present study aimed to evaluate the suppressive effects of cis-9, trans-11-CLA (c9,t11-CLA) on the expression of proinflammatory cytokines and intercellular adhesion molecule 1 (ICAM-1) in TNF-α-stimulated human bronchial epithelial (BEAS-2B) cells. After treating with various doses of c9,t11-CLA (12.5-100 μg ml(-1)), BEAS-2B cells were induced into an inflamed state by adding TNF-α or TNF-α/IL-4. The presence of c9,t11-CLA significantly suppressed the secretion of cytokines IL-6, IL-8, CCL5, and MCP-1. We also found that c9,t11-CLA inhibited ICAM-1 expression, and decreased monocyte adhesion to inflamed bronchial epithelial cells. Interestingly, c9,t11-CLA attenuated the phosphorylation of mitogen-activated protein kinase (MAPK) and down-regulated the activation of nuclear factor-κB (NF-κB). These results suggested that the anti-inflammatory effects of c9,t11-CLA were mediated by inhibiting proinflammatory cytokines, chemokines, and ICAM-1 expression by blocking NF-κB transcription regulation and by attenuating MAPK signaling pathways.

Vitamin D and pulmonary function in obese asthmatic children

OBJECTIVE

Asthma-related morbidity is higher among children with vitamin D deficiency and obesity, morbidities that frequently co-exist among minority children. However, the effect of co-existent obesity and vitamin D deficiency on pulmonary function is poorly understood.

METHODS

We compared percent-predicted values of pulmonary function across vitamin D categories among 72 obese and 71 normal-weight Hispanic and African-American children with asthma recruited at an urban children's hospital. Serum cytokines associated with Th1 and Th2 inflammation and 25-hydroxyvitamin D (25-OHD) were quantified in fasting serum. 25-OHD levels ≥30 ng/ml were categorized as sufficient, <30 and ≥20 ng/ml as insufficient, and <20 ng/ml as deficient. The role of inflammation was investigated by regression analysis.

RESULTS

Vitamin D deficiency was present in 50% of children and did not differ by obese status. Forced Expiratory Volume in the first second (84.5 ± 9.4 vs. 94.8 ± 8.4, P < 0.001), and Functional Residual Capacity (67.5 ± 20.1 vs. 79.3 ± 19, P = 0.01) were lower among vitamin D deficient obese asthmatics than their sufficient counterparts, and Total Lung Capacity was lower than their insufficient counterparts (86.9 ± 14.3 vs. 96.6 ± 10, P = 0.01); similar associations were not observed in normal-weight asthmatics and were not influenced by systemic inflammation. No association between Th1 and Th2 inflammatory measures, vitamin D deficiency, and pulmonary function tests was found.

CONCLUSIONS

Vitamin D deficiency was associated with pulmonary function deficits among obese children, but not among normal-weight children with asthma, an association that was independent of Th1 and Th2 serum inflammatory measures. Vitamin D deficiency may be one potential mechanism underlying the obese-asthma phenotype. Pediatr Pulmonol. 2016;51:1276-1283. © 2016 Wiley Periodicals, Inc.

Gut-lung axis: The microbial contributions and clinical implications

Gut microbiota interacts with host immune system in ways that influence the development of disease. Advances in respiratory immune system also broaden our knowledge of the interaction between host and microbiome in the lung. Increasing evidence indicated the intimate relationship between the gastrointestinal tract and respiratory tract. Exacerbations of chronic gut and lung disease have been shown to share key conceptual features with the disorder and dysregulation of the microbial ecosystem. In this review, we discuss the impact of gut and lung microbiota on disease exacerbation and progression, and the recent understanding of the immunological link between the gut and the lung, the gut-lung axis.

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

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

Microbes and asthma: Opportunities for intervention

The worldwide incidence and prevalence of asthma continues to increase. Asthma is now understood as an umbrella term for different phenotypes or endotypes, which arise through different pathophysiologic pathways. Understanding the many factors contributing to development of the disease is important for the identification of novel therapeutic targets for the treatment of certain asthma phenotypes. The hygiene hypothesis has been formulated to explain the increasing prevalence of allergic disease, including asthma. This hypothesis postulates that decreased exposure at a young age to certain infectious agents as a result of improved hygiene, increased antibiotic use and vaccination, and changes in lifestyle and dietary habits is associated with changes in the immune system, which predispose subjects to allergy. Many microbes, during their coevolution with human subjects, developed mechanisms to manipulate the human immune system and to increase their chances of survival. Improving models of asthma, as well as choosing adequate end points in clinical trials, will lead to a more complete understanding of the underlying mechanisms, thus providing an opportunity to devise primary and secondary interventions at the same time as identifying new molecular targets for treatment. This article reports the discussion and conclusion of a workshop under the auspices of the Netherlands Lung Foundation to extend our understanding of how modulation of the immune system by bacterial, parasitic, and viral infections might affect the development of asthma and to map out future lines of investigation.

Human gut microbiota plays a role in the metabolism of drugs

BACKGROUND AND AIMS

The gut microbiome, an aggregate genome of trillions of microorganisms residing in the human gastrointestinal tract, is now known to play a critical role in human health and predisposition to disease. It is also involved in the biotransformation of xenobiotics and several recent studies have shown that the gut microbiota can affect the pharmacokinetics of orally taken drugs with implications for their oral bioavailability.

METHODS

Review of Pubmed, Web of Science and Science Direct databases for the years 1957-2016.

RESULTS AND CONCLUSIONS

Recent studies make it clear that the human gut microbiota can play a major role in the metabolism of xenobiotics and, the stability and oral bioavailability of drugs. Over the past 50 years, more than 30 drugs have been identified as a substrate for intestinal bacteria. Questions concerning the impact of the gut microbiota on drug metabolism, remain unanswered or only partially answered, namely (i) what are the molecular mechanisms and which bacterial species are involved? (ii) What is the impact of host genotype and environmental factors on the composition and function of the gut microbiota, (iii) To what extent is the composition of the intestinal microbiome stable, transmissible, and resilient to perturbation? (iv) Has past exposure to a given drug any impact on future microbial response, and, if so, for how long? Answering such questions should be an integral part of pharmaceutical research and personalised health care.

Bile signalling promotes chronic respiratory infections and antibiotic tolerance

Despite aggressive antimicrobial therapy, many respiratory pathogens persist in the lung, underpinning the chronic inflammation and eventual lung decline that are characteristic of respiratory disease. Recently, bile acid aspiration has emerged as a major comorbidity associated with a range of lung diseases, shaping the lung microbiome and promoting colonisation by Pseudomonas aeruginosa in Cystic Fibrosis (CF) patients. In order to uncover the molecular mechanism through which bile modulates the respiratory microbiome, a combination of global transcriptomic and phenotypic analyses of the P. aeruginosa response to bile was undertaken. Bile responsive pathways responsible for virulence, adaptive metabolism, and redox control were identified, with macrolide and polymyxin antibiotic tolerance increased significantly in the presence of bile. Bile acids, and chenodeoxycholic acid (CDCA) in particular, elicited chronic biofilm behaviour in P. aeruginosa, while induction of the pro-inflammatory cytokine Interleukin-6 (IL-6) in lung epithelial cells by CDCA was Farnesoid X Receptor (FXR) dependent. Microbiome analysis of paediatric CF sputum samples demonstrated increased colonisation by P. aeruginosa and other Proteobacterial pathogens in bile aspirating compared to non-aspirating patients. Together, these data suggest that bile acid signalling is a leading trigger for the development of chronic phenotypes underlying the pathophysiology of chronic respiratory disease.

Dietary silver nanoparticles can disturb the gut microbiota in mice

Background

Humans are increasingly exposed via the diet to Ag nanoparticles (NP) used in the food industry. Because of their anti-bacterial activity, ingested Ag NP might disturb the gut microbiota that is essential for local and systemic homeostasis. We explored here the possible impact of dietary Ag NP on the gut microbiota in mice at doses relevant for currently estimated human intake.

Methods

Mice were orally exposed to food (pellets) supplemented with increasing doses of Ag NP (0, 46, 460 or 4600 ppb) during 28 d. Body weight, systemic inflammation and gut integrity were investigated to determine overall toxicity, and feces DNA collected from the gut were analyzed by Next Generation Sequencing (NGS) to assess the effect of Ag NP on the bacterial population. Ag NP were characterized alone and in the supplemented pellets by scanning transmission electron microscopy (STEM) and energy dispersive X-ray analysis (EDX).

Results

No overall toxicity was recorded in mice exposed to Ag NP. Ag NP disturbed bacterial evenness (α-diversity) and populations (β-diversity) in a dose-dependent manner. Ag NP increased the ratio between Firmicutes (F) and Bacteroidetes (B) phyla. At the family level, Lachnospiraceae and the S24-7 family mainly accounted for the increase in Firmicutes and decrease in Bacteroidetes, respectively. Similar effects were not observed in mice identically exposed to the same batch of Ag NP-supplemented pellets aged during 4 or 8 months and the F/B ratio was less or not modified. Analysis of Ag NP-supplemented pellets showed that freshly prepared pellets released Ag ions faster than aged pellets. STEM-EDX analysis also showed that Ag sulfidation occurred in aged Ag NP-supplemented pellets.

Conclusions

Our data indicate that oral exposure to human relevant doses of Ag NP can induce microbial alterations in the gut. The bacterial disturbances recorded after Ag NP are similar to those reported in metabolic and inflammatory diseases, such as obesity. It also highlights that Ag NP aging in food, and more specifically sulfidation, can reduce the effects of Ag NP on the microbiota by limiting the release of toxic Ag ions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12989-016-0149-1) contains supplementary material, which is available to authorized users.

Lung Microbiome Analysis in Steroid-Naїve Asthma Patients by Using Whole Sputum

Background

Although recent metagenomic approaches have characterized the distinguished microbial compositions in airways of asthmatics, these results did not reach a consensus due to the small sample size, non-standardization of specimens and medication status. We conducted a metagenomics approach by using terminal restriction fragment length polymorphism (T-RFLP) analysis of the induced whole sputum representing both the cellular and fluid phases in a relative large number of steroid naïve asthmatics.

Methods

Induced whole sputum samples obtained from 36 healthy subjects and 89 steroid-naїve asthma patients were analyzed through T-RFLP analysis.

Results

In contrast to previous reports about microbiota in the asthmatic airways, the diversity of microbial composition was not significantly different between the controls and asthma patients (p=0.937). In an analysis of similarities, the global R-value showed a statistically significant difference but a very low separation (0.148, p=0.002). The dissimilarity in the bacterial communities between groups was 28.74%, and operational taxonomic units (OTUs) contributing to this difference were as follows: OTU 789 (Lachnospiraceae), 517 (Comamonadaceae, Acetobacteraceae , and Chloroplast), 633 (Prevotella), 645 (Actinobacteria and Propionibacterium acnes), 607 (Lactobacillus buchneri, Lactobacillus otakiensis, Lactobacillus sunkii, and Rhodobacteraceae), and 661 (Acinetobacter, Pseudomonas, and Leptotrichiaceae), and they were significantly more prevalent in the sputum of asthma patients than in the sputum of the controls.

Conclusion

Before starting anti-asthmatic treatment, the microbiota in the whole sputum of patients with asthma showed a marginal difference from the microbiota in the whole sputum of the controls.

The Fecal Microbiota Profile and Bronchiolitis in Infants

BACKGROUND

Little is known about the association of gut microbiota, a potentially modifiable factor, with bronchiolitis in infants. We aimed to determine the association of fecal microbiota with bronchiolitis in infants.

METHODS

We conducted a case-control study. As a part of multicenter prospective study, we collected stool samples from 40 infants hospitalized with bronchiolitis. We concurrently enrolled 115 age-matched healthy controls. By applying 16S rRNA gene sequencing and an unbiased clustering approach to these 155 fecal samples, we identified microbiota profiles and determined the association of microbiota profiles with likelihood of bronchiolitis.

RESULTS

Overall, the median age was 3 months, 55% were male, and 54% were non-Hispanic white. Unbiased clustering of fecal microbiota identified 4 distinct profiles: Escherichia-dominant profile (30%), Bifidobacterium-dominant profile (21%), Enterobacter/Veillonella-dominant profile (22%), and Bacteroides-dominant profile (28%). The proportion of bronchiolitis was lowest in infants with the Enterobacter/Veillonella-dominant profile (15%) and highest in the Bacteroides-dominant profile (44%), corresponding to an odds ratio of 4.59 (95% confidence interval, 1.58-15.5; P = .008). In the multivariable model, the significant association between the Bacteroides-dominant profile and a greater likelihood of bronchiolitis persisted (odds ratio for comparison with the Enterobacter/Veillonella-dominant profile, 4.24; 95% confidence interval, 1.56-12.0; P = .005). In contrast, the likelihood of bronchiolitis in infants with the Escherichia-dominant or Bifidobacterium-dominant profile was not significantly different compared with those with the Enterobacter/Veillonella-dominant profile.

CONCLUSIONS

In this case-control study, we identified 4 distinct fecal microbiota profiles in infants. The Bacteroides-dominant profile was associated with a higher likelihood of bronchiolitis.

A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs

Inflammation can directly and indirectly modulate the bacterial composition of the microbiome. Although studies of inflammation primarily focus on its function to negatively select against potential pathogens, some bacterial species have the ability to exploit inflammatory byproducts for their benefit. Inflammatory cells release reactive nitrogen species as antimicrobial effectors against infection, but some facultative anaerobes can also utilize the increase in extracellular nitrate in their environment for anaerobic respiration and growth. This phenomenon has been studied in the gastrointestinal tract, where blooms of facultative anaerobic Gammaproteobacteria, primarily Escherichia coli, often occur during colonic inflammation. In cystic fibrosis, Pseudomonas aeruginosa, another Gammaproteobacteria facultative anaerobe, can reduce nitrogen for anaerobic respiration and it blooms in the airways of the chronically inflamed cystic fibrosis lung. This review focuses on the evidence that inflammation can provide terminal electron acceptors for anaerobic respiration and can support blooms of facultative anaerobes, such as E. coli and P. aeruginosa in distinct, but similar, environments of the inflamed gastrointestinal and respiratory tracts.

IL-17A enhances IL-13 activity by enhancing IL-13-induced signal transducer and activator of transcription 6 activation

BACKGROUND

Increased IL-17A production has been associated with more severe asthma; however, the mechanisms whereby IL-17A can contribute to IL-13-driven pathology in asthmatic patients remain unclear.

OBJECTIVE

We sought to gain mechanistic insight into how IL-17A can influence IL-13-driven responses.

METHODS

The effect of IL-17A on IL-13-induced airway hyperresponsiveness, gene expression, mucus hypersecretion, and airway inflammation was assessed by using in vivo models of IL-13-induced lung pathology and in vitro culture of murine fibroblast cell lines and primary fibroblasts and human epithelial cell lines or primary human epithelial cells exposed to IL-13, IL-17A, or both.

RESULTS

Compared with mice given intratracheal IL-13 alone, those exposed to IL-13 and IL-17A had augmented airway hyperresponsiveness, mucus production, airway inflammation, and IL-13-induced gene expression. In vitro, IL-17A enhanced IL-13-induced gene expression in asthma-relevant murine and human cells. In contrast to the exacerbating influence of IL-17A on IL-13-induced responses, coexposure to IL-13 inhibited IL-17A-driven antimicrobial gene expression in vivo and in vitro. Mechanistically, in both primary human and murine cells, the IL-17A-driven increase in IL-13-induced gene expression was associated with enhanced IL-13-driven signal transducer and activator of transcription 6 activation.

CONCLUSIONS

Our data suggest that IL-17A contributes to asthma pathophysiology by increasing the capacity of IL-13 to activate intracellular signaling pathways, such as signal transducer and activator of transcription 6. These data represent the first mechanistic explanation of how IL-17A can directly contribute to the pathogenesis of IL-13-driven pathology.

Vitamin E and the risk of childhood asthma

INTRODUCTION

Asthma, a heterogeneous disease with multiple phenotypes, remains a significant health problem. Present treatments are not curative and prevention should be our ultimate goal. Vitamin E supplementation presents a potential easy and cheap preventive therapy but the results of studies are confusing and sometimes contradictory. Clarification is needed.

AREAS COVERED

Animal studies and research in pregnant women suggest enhanced lifetime resistance to asthma with appropriate fetal exposure to vitamin E. Vitamin E's preventive role is complex and includes functional variations of the different isoforms. Expert commentary: We review the most recent literature on the role of vitamin E isoforms on: lung inflammation, immune development, animal and clinical studies during pregnancy, and the potential influence of vitamin E isoforms on asthma development in offspring. We point out where data are seemingly contradictory, explain why this is so, and comment on where further clarifying research is needed and its future direction.

The Microbiome of Animals: Implications for Conservation Biology

In recent years the human microbiome has become a growing area of research and it is becoming clear that the microbiome of humans plays an important role for human health. Extensive research is now going into cataloging and annotating the functional role of the human microbiome. The ability to explore and describe the microbiome of any species has become possible due to new methods for sequencing. These techniques allow comprehensive surveys of the composition of the microbiome of nonmodel organisms of which relatively little is known. Some attention has been paid to the microbiome of insect species including important vectors of pathogens of human and veterinary importance, agricultural pests, and model species. Together these studies suggest that the microbiome of insects is highly dependent on the environment, species, and populations and affects the fitness of species. These fitness effects can have important implications for the conservation and management of species and populations. Further, these results are important for our understanding of invasion of nonnative species, responses to pathogens, and responses to chemicals and global climate change in the present and future.

Airway Microbiota in Severe Asthma and Relationship to Asthma Severity and Phenotypes

BACKGROUND

The lower airways harbor a community of bacterial species which is altered in asthma.

OBJECTIVES

We examined whether the lower airway microbiota were related to measures of asthma severity.

METHODS

We prospectively recruited 26 severe asthma, 18 non-severe asthma and 12 healthy subjects. DNA was extracted from induced sputum and PCR amplification of the V3-V5 region of bacterial 16S rRNA gene was performed.

RESULTS

We obtained 138,218 high quality sequences which were rarefied at 133 sequences/sample. Twenty OTUs had sequences ≥1% of total. There were marked differences in the distribution of Phyla between groups (P = 2.8x10-118). Bacteroidetes and Fusobacteria were reduced in non-severe and severe asthmatic groups. Proteobacteria were more common in non-severe asthmatics compared to controls (OR = 2.26; 95% CI = 1.94-2.64) and Firmicutes were increased in severe asthmatics compared to controls (OR = 2.15; 95%CI = 1.89-2.45). Streptococcal OTUs amongst the Firmicutes were associated with recent onset asthma, rhinosinusitis and sputum eosinophilia.

CONCLUSIONS

Sputum microbiota in severe asthma differs from healthy controls and non-severe asthmatics, and is characterized by the presence of Streptococcus spp with eosinophilia. Whether these organisms are causative for the pathophysiology of asthma remains to be determined.

Asthma and bronchiectasis exacerbation

Bronchiectasis and asthma are common respiratory diseases worldwide. However, the influence of asthma on bronchiectasis remains unclear. The objective of this study is to analyse the effects of asthma on bronchiectasis exacerbation.Data from inpatients diagnosed with bronchiectasis with or without asthma at Shanghai Pulmonary Hospital (Shanghai, China) between January 2013 and December 2014 were retrospectively collected and analysed. 249 patients with only bronchiectasis and 214 patients with both bronchiectasis and asthma were included in the study. Follow-up records were used to evaluate the effect of asthma on bronchiectasis exacerbation.The variables found to be independently associated with bronchiectasis exacerbations were age (OR 1.07, 95% CI 1.03-1.11; p<0.001), duration of symptoms (OR 1.06, 95% CI 1.03-1.09; p<0.001), the presence of asthma (OR 2.6, 95% CI 1.15-5.88; p=0.021), forced expiratory volume in 1 s <50% predicted (OR 4.03, 95% CI 1.75-9.26; p=0.001), isolation of Pseudomonas aeruginosa in sputum (OR 2.41, 95% CI 1.00-5.79; p=0.05) and lung lesion extension to more than two lobes (OR 2.73, 95% CI 1.16-6.45; p=0.022).The existence of asthma was associated with an independent increase in risk of bronchiectasis exacerbation.

The respiratory microbiome: an underappreciated player in the human response to inhaled pollutants?

PURPOSE

Microbial communities in or on the body (i.e., the microbiome) are highly physiologically active and influence human health. Although environmental scientists are increasingly aware of the gut microbiome, the respiratory microbiome's role in the human response to inhaled pollutants is largely unknown.

METHODS

We reviewed the literature and present mechanisms by which the microbiome might mediate or modify human responses to inhaled pollutants.

RESULTS

The respiratory microbiome has been shown to influence chronic lung disease exacerbations, and increasing evidence indicates a role in disease development. Research also suggests that the respiratory microbiome could plausibly metabolize inhaled pollutants or modulate host inflammatory responses to exposure. Because these responses depend on the microbes present, defining the composition of the resident microbiome and how microbial communities shift with exposure may help to explain variations in susceptibility to inhaled pollutants. Although more research is needed, significant measurement challenges remain for large epidemiologic studies of the respiratory microbiome.

CONCLUSIONS

The respiratory microbiome is likely an underexplored intermediate and potential cause of individual susceptibility to inhaled irritants/toxicants. Characterizing the microbiome's role in the human response to inhaled exposures could improve our understanding of the casual agents of exposure and suggest novel public health interventions.

The relationship between prior antimicrobial prescription and meningitis: a case-control study

BACKGROUND

Recent research into the role of the human microbiome in maintaining health has identified the potentially harmful impact of antimicrobials.

AIM

The association with bacterial and viral meningitis following antimicrobial prescription during the previous year was investigated to determine whether antimicrobials have a deleterious effect on the nasopharyngeal microbiome.

DESIGN AND SETTING

A case-control study (1:4 cases to controls) was conducted examining the rate of previous antimicrobial exposure in cases of meningitis and in a matched control group. Data from a UK primary care clinical database were analysed using conditional logistic regression.

RESULTS

A total of 7346 cases of meningitis were identified, 3307 (45%) viral, 1812 (25%) bacterial, and 2227 (30%) unspecified. The risks of viral (adjusted odds ratio [AOR] 2.45; 95% confidence interval [CI] = 2.24 to 2.68) or bacterial (AOR 1.98; 95% CI = 1.71 to 2.30) meningitis were both increased following antimicrobial prescription in the preceding year. Patients who received ≥4 antimicrobial prescriptions in the preceding year were at significantly increased risk of all types of meningitis (AOR 2.85; 95% CI = 2.44 to 3.34), bacterial meningitis (AOR 3.06; 95% CI = 2.26 to 4.15) and viral meningitis (AOR 3.23; 95% CI = 2.55 to 4.08) compared to their matched controls.

CONCLUSION

There was an increased risk of meningitis following antimicrobial prescription in the previous year. It is possible that this increase was due to an effect of antimicrobials on the microbiome or reflected an increased general susceptibility to infections in these patients.

Relative Importance and Additive Effects of Maternal and Infant Risk Factors on Childhood Asthma

Background

Environmental exposures that occur in utero and during early life may contribute to the development of childhood asthma through alteration of the human microbiome. The objectives of this study were to estimate the cumulative effect and relative importance of environmental exposures on the risk of childhood asthma.

Methods

We conducted a population-based birth cohort study of mother-child dyads who were born between 1995 and 2003 and were continuously enrolled in the PRIMA (Prevention ofRSV: Impact onMorbidity andAsthma) cohort. The individual and cumulative impact of maternal urinary tract infections (UTI) during pregnancy, maternal colonization with group B streptococcus (GBS), mode of delivery, infant antibiotic use, and older siblings at home, on the risk of childhood asthma were estimated using logistic regression. Dose-response effect on childhood asthma risk was assessed for continuous risk factors: number of maternal UTIs during pregnancy, courses of infant antibiotics, and number of older siblings at home. We further assessed and compared the relative importance of these exposures on the asthma risk. In a subgroup of children for whom maternal antibiotic use during pregnancy information was available, the effect of maternal antibiotic use on the risk of childhood asthma was estimated.

Results

Among 136,098 singleton birth infants, 13.29% developed asthma. In both univariate and adjusted analyses, maternal UTI during pregnancy (odds ratio [OR] 1.2, 95% confidence interval [CI] 1.18, 1.25; adjusted OR [AOR] 1.04, 95%CI 1.02, 1.07 for every additional UTI) and infant antibiotic use (OR 1.21, 95%CI 1.20, 1.22; AOR 1.16, 95%CI 1.15, 1.17 for every additional course) were associated with an increased risk of childhood asthma, while having older siblings at home (OR 0.92, 95%CI 0.91, 0.93; AOR 0.85, 95%CI 0.84, 0.87 for each additional sibling) was associated with a decreased risk of childhood asthma, in a dose-dependent manner. Compared with vaginal delivery, C-section delivery increased odds of childhood asthma by 34% (OR 1.34, 95%CI 1.29, 1.39) in the univariate analysis and 11% after adjusting for other environmental exposures and covariates (AOR 1.11, 95%CI 1.06, 1.15). Maternal GBS was associated with a significant increased risk of childhood asthma in the univariate analysis (OR 1.27, 95%CI 1.19, 1.35), but not in the adjusted analysis (AOR 1.03, 95%CI 0.96, 1.10). In the subgroup analysis of children whose maternal antibiotic use information was available, maternal antibiotic use was associated with an increased risk of childhood asthma in a similar dose-dependent manner in the univariate and adjusted analyses (OR 1.13, 95%CI 1.12, 1.15; AOR 1.06, 95%CI 1.05, 1.08 for every additional course). Compared with infants with the lowest number of exposures (no UTI during pregnancy, vaginal delivery, at least five older siblings at home, no antibiotics during infancy), infants with the highest number of exposures (at least three UTIs during pregnancy, C-section delivery, no older siblings, eight or more courses of antibiotics during infancy) had a 7.77 fold increased odds of developing asthma (AOR: 7.77, 95%CI: 6.25, 9.65). Lastly, infant antibiotic use had the greatest impact on asthma risk compared with maternal UTI during pregnancy, mode of delivery and having older siblings at home.

Conclusion

Early-life exposures, maternal UTI during pregnancy (maternal antibiotic use), mode of delivery, infant antibiotic use, and having older siblings at home, are associated with an increased risk of childhood asthma in a cumulative manner, and for those continuous variables, a dose-dependent relationship. Compared with in utero exposures, exposures occurring during infancy have a greater impact on the risk of developing childhood asthma.

Innate Immune Signaling Activated by MDR Bacteria in the Airway

Health care-associated bacterial pneumonias due to multiple-drug resistant (MDR) pathogens are an important public health problem and are major causes of morbidity and mortality worldwide. In addition to antimicrobial resistance, these organisms have adapted to the milieu of the human airway and have acquired resistance to the innate immune clearance mechanisms that normally prevent pneumonia. Given the limited efficacy of antibiotics, bacterial clearance from the airway requires an effective immune response. Understanding how specific airway pathogens initiate and regulate innate immune signaling, and whether this response is excessive, leading to host-induced pathology may guide future immunomodulatory therapy. We will focus on three of the most important causes of health care-associated pneumonia, Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumoniae, and review the mechanisms through which an inappropriate or damaging innate immune response is stimulated, as well as describe how airway pathogens cause persistent infection by evading immune activation.

Lower Neighborhood Socioeconomic Status Associated with Reduced Diversity of the Colonic Microbiota in Healthy Adults

In the United States, there are persistent and widening socioeconomic gaps in morbidity and mortality from chronic diseases. Although most disparities research focuses on person-level socioeconomic-status, mounting evidence suggest that chronic diseases also pattern by the demographic characteristics of neighborhoods. Yet the biological mechanisms underlying these associations are poorly understood. There is increasing recognition that chronic diseases share common pathogenic features, some of which involve alterations in the composition, diversity, and functioning of the gut microbiota. This study examined whether socioeconomic-status was associated with alpha-diversity of the colonic microbiota. Forty-four healthy adults underwent un-prepped sigmoidoscopy, during which mucosal biopsies and fecal samples were collected. Subjects’ zip codes were geocoded, and census data was used to form a composite indicator of neighborhood socioeconomic-status, reflecting household income, educational attainment, employment status, and home value. In unadjusted analyses, neighborhood socioeconomic-status explained 12–18 percent of the variability in alpha-diversity of colonic microbiota. The direction of these associations was positive, meaning that as neighborhood socioeconomic-status increased, so did alpha-diversity of both the colonic sigmoid mucosa and fecal microbiota. The strength of these associations persisted when models were expanded to include covariates reflecting potential demographic (age, gender, race/ethnicity) and lifestyle (adiposity, alcohol use, smoking) confounds. In these models neighborhood socioeconomic-status continued to explain 11–22 percent of the variability in diversity indicators. Further analyses suggested these patterns reflected socioeconomic variations in evenness, but not richness, of microbial communities residing in the sigmoid. We also found indications that residence in neighborhoods of higher socioeconomic-status was associated with a greater abundance of Bacteroides and a lower abundance of Prevotella, suggesting that diet potentially underlies differences in microbiota composition. These findings suggest the presence of socioeconomic variations in colonic microbiota diversity. Future research should explore whether these variations contribute to disparities in chronic disease outcomes.

Dendritic cells revisited in human allergic rhinitis and asthma

The role of dendritic cells (DCs) in airway allergy has been studied for 15 years; recent data has highlighted the cross talk with airway epithelial cells and environmental factors (allergens, virus) during the inception and exacerbation of allergic asthma. Although murine models have provided key information, it remains uncertain to what extent these basic mechanisms take place in human allergic disease, notably with regard to different clinical phenotypes. In the present review, we discuss new evidence regarding mechanisms of DC regulation in the mouse which could be important in human asthma. Finally, after discussing the effects of current therapies on DC biology, we focus on pathways that could represent targets for future therapies.

Potential association of vacuum cleaning frequency with an altered gut microbiota in pregnant women and their 2-year-old children

BACKGROUND

Westernized lifestyle and hygienic behavior have contributed to dramatic changes in the human-associated microbiota. This particularly relates to indoor activities such as house cleaning. We therefore investigated the associations between washing and vacuum cleaning frequency and the gut microbiota composition in a large longitudinal cohort of mothers and their children. The gut microbiota composition was determined using 16S ribosomal RNA (rRNA) gene Illumina deep sequencing.

RESULTS

We found that high vacuum cleaning frequency about twice or more a week was associated with an altered gut microbiota composition both during pregnancy and for 2-year-old children, while there were no associations with house washing frequency. In total, six Operational Taxonomic Units (OTUs) showed significant False Discovery Rate (FDR) corrected associations with vacuum cleaning frequency for mothers (two positive and four negative) and five for 2-year-old children (four positive and one negative). For mothers and the 2-year-old children, OTUs among the dominant microbiota (average >5 %) showed correlation to vacuum cleaning frequency, with an increase in Faecalibacterium prausnitzii for mothers (p = 0.013, FDR corrected), and Blautia sp. for 2-year children (p = 0.012, FDR corrected).

CONCLUSIONS

Bacteria showing significant associations are among the dominant gut microbiota, which may indicate indirect immunomodulation of the gut microbiota possibly through increased allergen (dust mites) exposure as a potential mechanism. However, further exploration is needed to unveil mechanistic details.

The Tasmanian devil microbiome-implications for conservation and management

BACKGROUND

The Tasmanian devil, the world's largest carnivorous marsupial, is at risk of extinction due to devil facial tumour disease (DFTD), a fatal contagious cancer. The Save the Tasmanian Devil Program has established an insurance population, which currently holds over 600 devils in captive facilities across Australia. Microbes are known to play a crucial role in the health and well-being of humans and other animals, and increasing evidence suggests that changes in the microbiota can influence various aspects of host physiology and development. To improve our understanding of devils and facilitate management and conservation of the species, we characterised the microbiome of wild devils and investigated differences in the composition of microbial community between captive and wild individuals.

RESULTS

A total of 1,223,550 bacterial 16S ribosomal RNA (rRNA) sequences were generated via Roche 454 sequencing from 56 samples, including 17 gut, 15 skin, 18 pouch and 6 oral samples. The devil's gut microbiome was dominated by Firmicutes and showed a high Firmicutes-to-Bacteroidetes ratio, which appears to be a common feature of many carnivorous mammals. Metabolisms of carbohydrates, amino acids, energy, cofactors and vitamins, nucleotides and lipids were predicted as the most prominent metabolic pathways that the devil's gut flora contributed to. The microbiota inside the female's pouch outside lactation was highly similar to that of the skin, both co-dominated by Firmicutes and Proteobacteria. The oral microbiome had similar proportions of Proteobacteria, Bacteroidetes, Firmicutes and Fusobacteria.

CONCLUSIONS

Compositional differences were observed in all four types of microbiota between devils from captive and wild populations. Certain captive devils had significantly lower levels of gut bacterial diversity than wild individuals, and the two groups differed in the proportion of gut bacteria accounting for the metabolism of glycan, amino acids and cofactors and vitamins. Further studies are underway to investigate whether alterations in the microbiome of captive devils can have impacts on their ability to adapt and survive following re-introduction to the wild.

Exercise and gut immune function: evidence of alterations in colon immune cell homeostasis and microbiome characteristics with exercise training

There is robust evidence that habitual physical activity is anti-inflammatory and protective against developing chronic inflammatory disease. Much less is known about the effects of habitual moderate exercise in the gut, the compartment that has the greatest immunological responsibility and interactions with the intestinal microbiota. The link between the two has become evident, as recent studies have linked intestinal dysbiosis, or the disproportionate balance of beneficial to pathogenic microbes, with increased inflammatory disease susceptibility. Limited animal and human research findings imply that exercise may have a beneficial role in preventing and ameliorating such diseases by having an effect on gut immune function and, recently, microbiome characteristics. Emerging data from our laboratory show that different forms of exercise training differentially impact the severity of intestinal inflammation during an inflammatory insult (for example, ulcerative colitis) and may be jointly related to gut immune cell homeostasis and microbiota-immune interactions. The evidence we review and present will provide data in support of rigorous investigations concerning the effects of habitual exercise on gut health and disease.

Gut Microbiota Dysbiosis in Obesity-Linked Metabolic Diseases and Prebiotic Potential of Polyphenol-Rich Extracts

Trillions of microorganisms inhabit the human body, strongly colonizing the gastro-intestinal tract and outnumbering our own cells. High-throughput sequencing techniques and new bioinformatic tools have enabled scientists to extend our knowledge on the relationship between the gut microbiota and host's physiology. Disruption of the ecological equilibrium in the gut (i.e., dysbiosis) has been associated with several pathological processes, including obesity and its related comorbidities, with diet being a strong determinant of gut microbial balance. In this review, we discuss the potential prebiotic effect of polyphenol-rich foods and extracts and how they can reshape the gut microbiota, emphasizing the novel role of the mucin-degrading bacterium Akkermansia muciniphila in their metabolic benefits.

L-Carnitine intake and high trimethylamine N-oxide plasma levels correlate with low aortic lesions in ApoE(-/-) transgenic mice expressing CETP

OBJECTIVE

Dietary l-carnitine can be metabolized by intestinal microbiota to trimethylamine, which is absorbed by the gut and further oxidized to trimethylamine N-oxide (TMAO) in the liver. TMAO plasma levels have been associated with atherosclerosis development in ApoE(-/-) mice. To better understand the mechanisms behind this association, we conducted in vitro and in vivo studies looking at the effect of TMAO on different steps of atherosclerotic disease progression.

METHODS

J774 mouse macrophage cells were used to evaluate the effect of TMAO on foam cell formation. Male ApoE(-/-) mice transfected with human cholesteryl ester transfer protein (hCETP) were fed l-carnitine and/or methimazole, a flavin monooxygenase 3 (FMO3) inhibitor that prevents the formation of TMAO. Following 12 week treatment, l-carnitine and TMAO plasma levels, aortic lesion development, and lipid profiles were determined.

RESULTS

TMAO at concentrations up to 10-fold the Cmax reported in humans did not affect in vitro foam cell formation. In ApoE(-/-)mice expressing hCETP, high doses of l-carnitine resulted in a significant increase in plasma TMAO levels. Surprisingly, and independently from treatment group, TMAO levels inversely correlated with aortic lesion size in both aortic root and thoracic aorta. High TMAO levels were found to significantly correlate with smaller aortic lesion area. Plasma lipid and lipoprotein levels did not change with treatment nor with TMAO levels, suggesting that the observed effects on lesion area were independent from lipid changes.

CONCLUSION

These findings suggest that TMAO slows aortic lesion formation in this mouse model and may have a protective effect against atherosclerosis development in humans.

Asthma

Asthma is the most common inflammatory disease of the lungs. The prevalence of asthma is increasing in many parts of the world that have adopted aspects of the Western lifestyle, and the disease poses a substantial global health and economic burden. Asthma involves both the large-conducting and the small-conducting airways, and is characterized by a combination of inflammation and structural remodelling that might begin in utero. Disease progression occurs in the context of a developmental background in which the postnatal acquisition of asthma is strongly linked with allergic sensitization. Most asthma cases follow a variable course, involving viral-induced wheezing and allergen sensitization, that is associated with various underlying mechanisms (or endotypes) that can differ between individuals. Each set of endotypes, in turn, produces specific asthma characteristics that evolve across the lifecourse of the patient. Strong genetic and environmental drivers of asthma interconnect through novel epigenetic mechanisms that operate prenatally and throughout childhood. Asthma can spontaneously remit or begin de novo in adulthood, and the factors that lead to the emergence and regression of asthma, irrespective of age, are poorly understood. Nonetheless, there is mounting evidence that supports a primary role for structural changes in the airways with asthma acquisition, on which altered innate immune mechanisms and microbiota interactions are superimposed. On the basis of the identification of new causative pathways, the subphenotyping of asthma across the lifecourse of patients is paving the way for more-personalized and precise pathway-specific approaches for the prevention and treatment of asthma, creating the real possibility of total prevention and cure for this chronic inflammatory disease.

Are allergic multimorbidities and IgE polysensitization associated with the persistence or re-occurrence of foetal type 2 signalling? The MeDALL hypothesis

Allergic diseases [asthma, rhinitis and atopic dermatitis (AD)] are complex. They are associated with allergen-specific IgE and nonallergic mechanisms that may coexist in the same patient. In addition, these diseases tend to cluster and patients present concomitant or consecutive diseases (multimorbidity). IgE sensitization should be considered as a quantitative trait. Important clinical and immunological differences exist between mono- and polysensitized subjects. Multimorbidities of allergic diseases share common causal mechanisms that are only partly IgE-mediated. Persistence of allergic diseases over time is associated with multimorbidity and/or IgE polysensitization. The importance of the family history of allergy may decrease with age. This review puts forward the hypothesis that allergic multimorbidities and IgE polysensitization are associated and related to the persistence or re-occurrence of foetal type 2 signalling. Asthma, rhinitis and AD are manifestations of a common systemic immune imbalance (mesodermal origin) with specific patterns of remodelling (ectodermal or endodermal origin). This study proposes a new classification of IgE-mediated allergic diseases that allows the definition of novel phenotypes to (i) better understand genetic and epigenetic mechanisms, (ii) better stratify allergic preschool children for prognosis and (iii) propose novel strategies of treatment and prevention.

Mode of delivery and childhood fractional exhaled nitric oxide, interrupter resistance and asthma: the Generation R study

BACKGROUND

Previous studies suggest that caesarean section may influence the risk of childhood asthma. We examined the associations of different modes of delivery with childhood wheezing patterns, asthma, fractional exhaled nitric oxide (FeNO) and airway interrupter resistance (Rint) up to school age.

METHODS

This study among 6,128 children was embedded in a population-based prospective cohort study. Information on mode of delivery was obtained from midwives and hospital registries. Wheezing patterns from birth onwards and ever physician-diagnosed asthma at age 6 yr were assessed by questionnaires. FeNO and Rint were measured at age 6 yr. We used multivariate polynomial, logistic and linear regression models.

RESULTS

Compared with vaginal delivery, caesarean section was associated with increased risks of early and persistent wheezing up to school age [odds ratios (95% confidence interval): 1.36 (1.06, 1.75) and 1.73 (1.24, 2.40), respectively]. The effect sizes of elective and emergency caesarean section with wheezing outcomes were similar. Only elective caesarean section was associated with a higher FeNO level [sympercent (95% CI): 12.7 (0.6, 24.8)]. We did not observe associations of mode of delivery with asthma or Rint. Also, vacuum- or forceps-assisted vaginal delivery was not associated with any asthma or related outcome.

CONCLUSIONS

Both elective and emergency caesarean sections are associated with increased risks of early and persistent wheezing up to school age. This might be explained by increased airway inflammation reflected by higher FeNO levels.