The evolution of the hygiene hypothesis: the role of early-life exposures to viruses and microbes and their relationship to asthma and allergic diseases. Curr Opin Allergy Clin Immunol. 2014;14:390-396. [PMID: 25102107 DOI: 10.1097/aci.0000000000000101]

Maternal and infant predictors of proinflammatory milk immune activity in Kilimanjaro, Tanzania

OBJECTIVES

The immune system of milk (ISOM) creates a mother-infant immune axis that plays an important role in protecting infants against infectious disease (ID). Tradeoffs in the immune system suggest the potential for both protection and harm, so we conceive of two dimensions via which the ISOM impacts infants: promotion of protective activity and control of activity directed at benign targets. High variability in ISOM activity across mother-infant dyads suggests investment the ISOM may have evolved to be sensitive to maternal and/or infant characteristics. We assessed predictors of appropriate and misdirected proinflammatory ISOM activity in an environment of high ID risk, testing predictions drawn from life history theory and other evolutionary perspectives.

METHODS

We characterized milk in vitro interleukin-6 (IL-6) responses to Salmonella enterica (a target of protective immune activity; N = 96) and Escherichia coli (a benign target; N = 85) among mother-infant dyads in rural Kilimanjaro, Tanzania. We used ordered logistic regression and mixture models to evaluate maternal and infant characteristics as predictors of IL-6 responses.

RESULTS

In all models, IL-6 responses to S. enterica increased with maternal age and decreased with gravidity. In mixture models, IL-6 responses to E. coli declined with maternal age and increased with gravidity. No other considered variables were consistently associated with IL-6 responses.

CONCLUSIONS

The ISOM's capacities for appropriate proinflammatory activity and control of misdirected proinflammatory activity increases with maternal age and decreases with gravidity. These findings are consistent with the hypothesis that the mother-infant immune axis has evolved to respond to maternal life history characteristics.

Global knowledge mapping and emerging research trends in the microbiome and asthma: A bibliometric and visualized analysis using VOSviewer and CiteSpace

Background

Numerous prior studies have extensively highlighted the significance of the microbiome in association with asthma. While several studies have concentrated on the asthma microbiome in previous research, there is currently a lack of publications that employ bibliometric methods to assess this area.

Methods

In this study, the Web of Science Core Collection database was utilized as the data source, and the SCI-EXPANDED index was employed to ensure that the retrieved data were comprehensive and accurate. All original research articles and review articles related to the correlation between asthma and the microbiome were systematically searched from the inception of the database until June 20, 2023. These articles were subsequently visualized and analyzed using VOSviewer and CiteSpace software.

Results

A total of 1366 relevant publications were acquired, indicating a consistent annual increase in global publications in the field. The United States and China emerged as the top two contributors to international publications. Among prolific authors, Susan V. Lynch achieved the highest publication record, with Hans Bisgaard and Jakob Stokholm sharing the second position. The majority of publications concentrated on allergy-related and microbiome areas, with a few comprehensive journals standing out. Journals with 40 or more publications included the Journal of Allergy and Clinical Immunology, Allergy, Frontiers in Immunology, and PLOS One. The top 5 cited journals were the Journal of Allergy and Clinical Immunology, PLOS One, American Journal of Respiratory and Critical Care Medicine, Clinical and Experimental Allergy, and Nature. Upon analyzing keywords, high-frequency terms, such as asthma, gut microbiota, microbiome, children, childhood asthma, allergy, risk, exposure, inflammation, diversity, and chain fatty acids emerged as representative terms in the field.

Conclusion

This study systematically presented a comprehensive overview of the literature regarding the association between asthma and the microbiome over the last two decades. Through a bibliometric perspective, the findings may assist researchers with a better understanding of the essential information in the field.

Lung Involvement in Inflammatory Bowel Diseases: Shared Pathways and Unwanted Connections

Inflammatory bowel diseases (IBDs) are chronic, relapsing inflammatory disorders of the gastrointestinal tract, frequently associated with extraintestinal manifestations (EIMs) that can severely affect IBD patients' quality of life, sometimes even becoming life-threatening. Respiratory diseases have always been considered a rare and subsequently neglected extraintestinal manifestations of IBD. However, increasing evidence has demonstrated that respiratory involvement is frequent in IBD patients, even in the absence of respiratory symptoms. Airway inflammation is the most common milieu of IBD-related involvement, with bronchiectasis being the most common manifestation. Furthermore, significant differences in prevalence and types of involvement are present between Crohn's disease and ulcerative colitis. The same embryological origin of respiratory and gastrointestinal tissue, in addition to exposure to common antigens and cytokine networks, may all play a potential role in the respiratory involvement. Furthermore, other causes such as drug-related toxicity and infections must always be considered. This article aims at reviewing the current evidence on the association between IBD and respiratory diseases. The purpose is to raise awareness of respiratory manifestation among IBD specialists and emphasize the need for identifying respiratory diseases in early stages to promptly treat these conditions, avoid worsening morbidity, and prevent lung damage.

Broncho-Vaxom bacterial lysate prevents asthma via acetate enhancement in mouse model

PURPOSE

Broncho-Vaxom (BV) is known to attenuate allergic airway inflammation and chronic bronchitis in humans, but the underlying mechanism of this gut-mediated immunity remains unclear. This study investigated the effects of an oral BV on gut and systemic short-chain fatty acids (SCFAs) and immune responses.

METHODS

Oral BV was administered daily for 15 days prior to commencing the study in an asthma mouse model. Asthma was induced by ovalbumin (OVA) sensitization followed by a challenge with 1% OVA by inhalation. Asthmatic phenotypes, gut- and systemic- immune responses, and SCFAs in the cecum and blood were then investigated.

RESULTS

Airway hyperresponsiveness, total immunoglobulin E production, and pulmonary inflammation were all significantly suppressed by BV. The interleukin-13 level was also suppressed, whereas TGF-β expression was increased, in the lungs of the BV-treated mice. The regulatory T (Treg) cell numbers were increased in the small intestine, and the acetate level was increased in the cecum and serum after BV treatment. The levels of acetate in the cecum and serum were negatively correlated with airway hyperresponsiveness and with the eosinophil numbers in the BAL fluid of the OVA-induced mice. There was a positive correlation between the acetate levels in the feces and serum and the lung expression of TGF-β in the asthma mice.

CONCLUSIONS

Oral BV administration appears to prevent allergic inflammation by enhancing Treg cell proliferation and acetate production in an asthmatic mouse model.

A Review of the Epigenetic Clock: Emerging Biomarkers for Asthma and Allergic Disease

DNA methylation (DNAm) is a dynamic, age-dependent epigenetic modification that can be used to study interactions between genetic and environmental factors. Environmental exposures during critical periods of growth and development may alter DNAm patterns, leading to increased susceptibility to diseases such as asthma and allergies. One method to study the role of DNAm is the epigenetic clock-an algorithm that uses DNAm levels at select age-informative Cytosine-phosphate-Guanine (CpG) dinucleotides to predict epigenetic age (EA). The difference between EA and calendar age (CA) is termed epigenetic age acceleration (EAA) and reveals information about the biological capacity of an individual. Associations between EAA and disease susceptibility have been demonstrated for a variety of age-related conditions and, more recently, phenotypes such as asthma and allergic diseases, which often begin in childhood and progress throughout the lifespan. In this review, we explore different epigenetic clocks and how they have been applied, particularly as related to childhood asthma. We delve into how in utero and early life exposures (e.g., smoking, air pollution, maternal BMI) result in methylation changes. Furthermore, we explore the potential for EAA to be used as a biomarker for asthma and allergic diseases and identify areas for further study.

When the allergy alarm bells toll: The role of Toll-like receptors in allergic diseases and treatment

Toll-like receptors of the human immune system are specialized pathogen detectors able to link innate and adaptive immune responses. TLR ligands include among others bacteria-, mycoplasma- or virus-derived compounds such as lipids, lipo- and glycoproteins and nucleic acids. Not only are genetic variations in TLR-related genes associated with the pathogenesis of allergic diseases, including asthma and allergic rhinitis, their expression also differs between allergic and non-allergic individuals. Due to a complex interplay of genes, environmental factors, and allergen sources the interpretation of TLRs involved in immunoglobulin E-mediated diseases remains challenging. Therefore, it is imperative to dissect the role of TLRs in allergies. In this review, we discuss i) the expression of TLRs in organs and cell types involved in the allergic immune response, ii) their involvement in modulating allergy-associated or -protective immune responses, and iii) how differential activation of TLRs by environmental factors, such as microbial, viral or air pollutant exposure, results in allergy development. However, we focus on iv) allergen sources interacting with TLRs, and v) how targeting TLRs could be employed in novel therapeutic strategies. Understanding the contributions of TLRs to allergy development allow the identification of knowledge gaps, provide guidance for ongoing research efforts, and built the foundation for future exploitation of TLRs in vaccine design.

Dietary intervention with functional foods modulating gut microbiota for improving the efficacy of COVID-19 vaccines

Dysbiosis of the gut microbiota with aging contributes to a reduction in important cross-feeding bacterial reactions in the gut and immunosenescence, which could contribute to a decrease in vaccine efficacy. Fever, cough, and fatigue are the main signs of coronavirus disease 2019 (COVID-19); however, some patients with COVID-19 present with gastrointestinal symptoms. COVID-19 vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the best measures to reduce SARS-CoV-2 infection rates and the severity of COVID-19. The immunogenicity of COVID-19 vaccines is influenced by the composition of the gut microbiota, and the immune response to COVID-19 vaccines decreases with age. In this review, we discuss gut microbiota dysbiosis and immunosenescence in the older adults, the role of gut microbiota in improving the efficacy of COVID-19 vaccines, and dietary interventions to improve the efficacy of COVID-19 vaccines in the older adults.

The many faces of parasite calreticulin

Calreticulin from parasites and its vertebrate hosts share ~50% identity and many of its functions are equally conserved. However, the existing amino acid differences can affect its biological performance. Calreticulin plays an important role in Ca2+ homeostasis and as a chaperone involved in the correct folding of proteins within the endoplasmic reticulum. Outside the endoplasmic reticulum, calreticulin is involved in several immunological functions such as complement inhibition, enhancement of efferocytosis, and immune upregulation or inhibition. Several parasite calreticulins have been shown to limit immune responses and promote infectivity, while others are strong immunogens and have been used for the development of potential vaccines that limit parasite growth. Furthermore, calreticulin is essential in the dialogue between parasites and hosts, inducing Th1, Th2 or regulatory responses in a species-specific manner. In addition, calreticulin participates as initiator of endoplasmic reticulum stress in tumor cells and promotion of immunogenic cell death and removal by macrophages. Direct anti-tumoral activity has also been reported. The highly immunogenic and pleiotropic nature of parasite calreticulins, either as positive or negative regulators of the immune response, render these proteins as valuable tools to modulate immunopathologies and autoimmune disorders, as well as a potential treatment of neoplasms. Moreover, the disparities in the amino acid composition of parasite calreticulins might provide subtle variations in the mechanisms of action that could provide advantages as therapeutic tools. Here, we review the immunological roles of parasite calreticulins and discuss possible beneficial applications.

Early-life respiratory tract infections and the risk of school-age lower lung function and asthma: a meta-analysis of 150 000 European children

BACKGROUND

Early-life respiratory tract infections might affect chronic obstructive respiratory diseases, but conclusive studies from general populations are lacking. Our objective was to examine if children with early-life respiratory tract infections had increased risks of lower lung function and asthma at school age.

METHODS

We used individual participant data of 150 090 children primarily from the EU Child Cohort Network to examine the associations of upper and lower respiratory tract infections from age 6 months to 5 years with forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC), FEV1/FVC, forced expiratory flow at 75% of FVC (FEF75%) and asthma at a median (range) age of 7 (4-15) years.

RESULTS

Children with early-life lower, not upper, respiratory tract infections had a lower school-age FEV1, FEV1/FVC and FEF75% (z-score range: -0.09 (95% CI -0.14- -0.04) to -0.30 (95% CI -0.36- -0.24)). Children with early-life lower respiratory tract infections had a higher increased risk of school-age asthma than those with upper respiratory tract infections (OR range: 2.10 (95% CI 1.98-2.22) to 6.30 (95% CI 5.64-7.04) and 1.25 (95% CI 1.18-1.32) to 1.55 (95% CI 1.47-1.65), respectively). Adjustment for preceding respiratory tract infections slightly decreased the strength of the effects. Observed associations were similar for those with and without early-life wheezing as a proxy for early-life asthma.

CONCLUSIONS

Our findings suggest that early-life respiratory tract infections affect development of chronic obstructive respiratory diseases in later life, with the strongest effects for lower respiratory tract infections.

Assessing the prevalence and severity of asthma, rhinitis, and eczema among schoolchildren (6-7 and 13-14 years old) in Khuzestan, Iran: a cross-sectional survey

Background

Asthma and allergic complications are the most common chronic disorders in children and adolescents. This study aimed to determine the prevalence and severity of asthma, allergic rhinitis, eczema among schoolchildren, and some related risk factors.

Methods

The cross-sectional study was performed in 2019 and involved 4000 students aged 6–7 years and 4000 students aged 13–14 years (both girls and boys) from urban schools in Khuzestan Province, southwestern Iran. We used the multi-stage sampling method. Data were collected using the Persian version of the International Study of Asthma and Allergies in Childhood (ISAAC) questionnaire.

Results

The prevalence of current wheeze, wheeze ever and asthma ever in the age group of 6–7 years was 3.8, 4.5, and 1.8%, respectively; in the age group of 13–14 years, it was 4.4, 5.9, and 3.4, respectively. In terms of gender, males (4.9, 6.0, and 2.7 percent, respectively) had substantially higher rates of current wheeze, wheeze ever, and asthma ever compared to the girls (2.8, 3.6, and 2.0 percent, respectively) (p < 0.001). The prevalence of rhinitis, Hay fever, and eczema among young people was 5.3%, 3.5%, and 1.0%, respectively. Current wheeze was more common in children with allergic rhinitis in the last 12 months (30.3% vs. 2.7%, p < 0.001), Hay fever (32.8% vs. 0.3%, p < 0.001) and eczema (27.8% vs 3.8%, p < 0.001), compared to children who did not.

Conclusions

The prevalence and severity of asthma symptoms were significantly associated with allergic rhinitis, eczema, and gender.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12887-022-03520-x.

The Complex Link and Disease Between the Gut Microbiome and the Immune System in Infants

The human gut microbiome is important for human health. The development of stable microbial communities in the gastrointestinal tract is closely related to the early growth and development of host immunity. After the birth of a baby, immune cells and the gut microbiome mature in parallel to adapt to the complex gut environment. The gut microbiome is closely linked to the immune system and influences each other. This interaction is associated with various diseases in infants and young children, such as asthma, food allergies, necrotizing colitis, obesity, and inflammatory bowel disease. Thus, the composition of the infant gut microbiome can predict the risk of disease development and progression. At the same time, the composition of the infant gut microbiome can be regulated in many ways and can be used to prevent and treat disease in infants by modulating the composition of the infant gut microbiome. The most important impacts on infant gut microbiota are maternal, including food delivery and feeding. The differences in the gut microbiota of infants reflect the maternal gut microbiota, which in turn reflects the gut microbiota of a given population, which is clinically significant.

Yifei Sanjie Formula Treats Chronic Obstructive Pulmonary Disease by Remodeling Pulmonary Microbiota

Chronic obstructive pulmonary disease (COPD) is one of the most common pulmonary diseases. Evidence suggests that dysbiosis of pulmonary microbiota leads to the COPD pathological process. Yifei Sanjie Formula (YS) is widely used to treat diseases in respiratory systems, yet little is known about its mechanisms. In the present study, we first established the fingerprint of YS as the background for UHPLC-QTOF-MS. Components were detected, including alkaloids, amino acid derivatives, phenylpropanoids, flavonoids, terpenoids, organic acids, phenols, and the like. The therapeutic effect of YS on COPD was evaluated, and the pulmonary function and ventilatory dysfunction (EF50, TV, and MV) were improved after the administration of YS. Further, the influx of lymphocytes was inhibited in pulmonary parenchyma, accompanied by down-regulation of inflammation cytokines via the NLRP3/caspase-1/IL-1β signaling pathway. The severity of pulmonary pathological damage was reversed. Disturbed pulmonary microbiota was discovered to involve an increased relative abundance of Ralstonia and Mycoplasma and a decreased relative abundance of Lactobacillus and Bacteroides in COPD animals. However, the subversive effect was shown. The abundance and diversity of pulmonary microflora were remodeled, especially increasing beneficial genua Lactobacillus and Bacteroides, as well as downregulating pathogenic genua Ralstonia and Mycoplasma in the YS group. Environmental factor correlation analysis showed that growing pulmonary microbiota was positively correlated with the inflammatory factor, referring to Ralstonia and Mycoplasma, as well as negatively correlated with the inflammatory factor, referring to Lactobacillus and Bacteroides. These results suggest that the effects of YS involved remodeling lung microbes and anti-inflammatory signal pathways, revealing that intervention microbiota and an anti-inflammatory may be a potential therapeutic strategy for COPD.

Microbial Dysbiosis Tunes the Immune Response Towards Allergic Disease Outcomes

The hygiene hypothesis has been popularized as an explanation for the rapid increase in allergic disease observed over the past 50 years. Subsequent epidemiological studies have described the protective effects that in utero and early life exposures to an environment high in microbial diversity have in conferring protective benefits against the development of allergic diseases. The rapid advancement in next generation sequencing technology has allowed for analysis of the diverse nature of microbial communities present in the barrier organs and a determination of their role in the induction of allergic disease. Here, we discuss the recent literature describing how colonization of barrier organs during early life by the microbiota influences the development of the adaptive immune system. In parallel, mechanistic studies have delivered insight into the pathogenesis of disease, by demonstrating the comparative effects of protective T regulatory (Treg) cells, with inflammatory T helper 2 (Th2) cells in the development of immune tolerance or induction of an allergic response. More recently, a significant advancement in our understanding into how interactions between the adaptive immune system and microbially derived factors play a central role in the development of allergic disease has emerged. Providing a deeper understanding of the symbiotic relationship between our microbiome and immune system, which explains key observations made by the hygiene hypothesis. By studying how perturbations that drive dysbiosis of the microbiome can cause allergic disease, we stand to benefit by delineating the protective versus pathogenic aspects of human interactions with our microbial companions, allowing us to better harness the use of microbial agents in the design of novel prophylactic and therapeutic strategies.

The Beneficial Role of Probiotic Lactobacillus in Respiratory Diseases

Respiratory diseases cause a high incidence and mortality worldwide. As a natural immunobiotic, Lactobacillus has excellent immunomodulatory ability. Administration of some Lactobacillus species can alleviate the symptoms of respiratory diseases such as respiratory tract infections, asthma, lung cancer and cystic fibrosis in animal studies and clinical trials. The beneficial effect of Lactobacillus on the respiratory tract is strain dependent. Moreover, the efficacy of Lactobacillus may be affected by many factors, such as bacteria dose, timing and host background. Here, we summarized the beneficial effect of administered Lactobacillus on common respiratory diseases with a focus on the mechanism and safety of Lactobacillus in regulating respiratory immunity.

Hygiene Hypothesis Indicators and Prevalence of Antinuclear Antibodies in US Adolescents

Autoimmunity prevalence, as measured by antinuclear antibodies (ANA), is increasing in U.S. adolescents. Improved hygiene and cleaner environments in childhood may reduce exposure to infections and other immune challenges, resulting in improper immune responses to later-life exposures. We examined associations of hygiene hypothesis indicators, including asthma, allergies, and antibodies to infectious agents, with ANA prevalence, measured by HEp-2 immunofluorescence, in adolescents (aged 12-19 years) over a 25-year time span in the National Health and Nutrition Examination Survey (NHANES) (N=2,709), adjusting for age, sex, race/ethnicity, body mass index, education and survey cycle, overall and within individual time periods, using logistic regression. Prevalence of ANA in adolescents increased from 5.0% in 1988-1991 to 12.8% in 2011-2012. ANA were positively associated with diagnosis of asthma in early childhood (OR: 2.07, CI: 1.09-3.99) and the effect estimate for current hay fever was elevated but not statistically significant (OR: 1.55, CI: 0.85-2.84). Fewer than 2% of those with ANA in 1988-1991 had been diagnosed with asthma, compared with 18% in 1999-2000, and 27% in 2003-2004 and 2011-2012. ANA trended negatively with Helicobacter pylori antibodies (OR: 0.49, CI: 0.24-0.99). ANA may be useful as an additional indicator of inadequate immune education in adolescence, a critical period of growth and development.

Cropping Up Crisis at the Nexus Between COVID-19 and Antimicrobial Resistance (AMR) in Africa: A Scoping Review and Synthesis of Early Evidence

In this study, we aim to synthesize some evidence on the impacts that coronavirus disease 2019 (COVID-19) is having on the epidemiology of antimicrobial resistance (AMR) in Africa since it was declared a global pandemic by the WHO in March 2020.

A scoping review was undertaken by collecting and curating relevant resources from peer-reviewed articles and also from the gray literature. Mixed approaches of extracting data (qualitative and quantitative) were employed in synthesizing evidence, as suggested by the Health Evidence Network.

A model constructed based on the synthesis of early evidence available on the effects of factors linked to COVID-19 in impacting the evolution of AMR in Africa predicted that, in cumulative terms, those factors favoring the evolution of AMR outpace those disfavoring it by no less than three folds.

COVID-19 is likely fueling the evolution of AMR almost unhindered in Africa. Due to the recognition of this crisis, concerted efforts for resource mobilization and global cooperation are needed to tackle it.

Tradeoffs in milk immunity affect infant infectious disease risk

Background and objectives

The human immune system has evolved to balance protection against infection with control of immune-mediated damage and tolerance of commensal microbes. Such tradeoffs between protection and harm almost certainly extend to the immune system of milk.

Methodology

Among breastfeeding mother–infant dyads in Kilimanjaro, Tanzania, we characterized in vitro proinflammatory milk immune responses to Salmonella enterica (an infectious agent) and Escherichia coli (a benign target) as the increase in interleukin-6 after 24 h of incubation with each bacterium. We characterized incident infectious diseases among infants through passive monitoring. We used Cox proportional hazards models to describe associations between milk immune activity and infant infectious disease.

Results

Among infants, risk for respiratory infections declined with increasing milk in vitro proinflammatory response to S. enterica (hazard ratio [HR]: 0.68; 95% confidence interval [CI]: 0.54, 0.86; P: 0.001), while risk for gastrointestinal infections increased with increasing milk in vitro proinflammatory response to E. coli (HR: 1.44; 95% CI: 1.05, 1.99; P: 0.022). Milk proinflammatory responses to S. enterica and E. coli were positively correlated (Spearman’s rho: 0.60; P: 0.000).

Conclusions and implications

These findings demonstrate a tradeoff in milk immune activity: the benefits of appropriate proinflammatory activity come at the hazard of misdirected proinflammatory activity. This tradeoff is likely to affect infant health in complex ways, depending on prevailing infectious disease conditions. How mother–infant dyads optimize proinflammatory milk immune activity should be a central question in future ecological–evolutionary studies of the immune system of milk.

Early-life cytomegalovirus infection is associated with gut microbiota perturbations and increased risk of atopy

BACKGROUND

The "old friends" hypothesis posits that reduced exposure to previously ubiquitous microorganisms is one factor involved in the increased rates of allergic diseases. Cytomegalovirus (CMV) may be one of the "old friends" hypothesized to help prevent allergic diseases. We sought to elucidate whether early-life CMV infection is associated with childhood atopy via perturbations of the gut microbiota.

METHODS

Participants were recruited from a population-based birth cohort (CHILD study) and followed prospectively until age 5 years in four Canadian cities. A total of 928 participants provided stool microbiome data, urine for CMV testing, skin prick tests, and questionnaire-based detailed environmental exposures. Cytomegalovirus infection was assessed in the first year of life while the main outcome was defined by persistent sensitization to any allergen at ages 1, 3, and 5 years.

RESULTS

Early CMV infection was associated with increased beta and decreased alpha diversity of the gut microbiota. Both changes in diversity measures and early CMV infection were associated with persistent allergic sensitization at age 5 years (aOR = 2.08; 95% CI: 1, 4.33). Mediation analysis demonstrated that perturbation of gut microbial composition explains 30% of the association.

CONCLUSIONS

Early-life CMV infection is associated with an alteration in the intestinal microbiota, which mediates the effect of the infection on childhood atopy. This work indicates that preventing CMV infection would not put children at increased risk of developing atopy. Rather, a CMV vaccine, in addition to preventing CMV-associated morbidity and mortality, might reduce the risk of childhood allergic diseases.

The influence of constipation on asthma: A real-world, population-based cohort study

BACKGROUND

Among respiratory diseases, asthma is one of the most burdensome disorder worldwide. Growing evidence disclose gut dysbiosis may contribute to asthma via the gut-lung axis. Constipation can lead to alteration of the gut microflora. The clinical impact of constipation on asthma has not been researched. Therefore, we aim to assess the risk of asthma in constipated patients by a nationwide population-based cohort study.

METHODS

We analysed 86 860 constipated patients and 86 860 individuals without constipation between 1999 and 2013 from the Taiwanese National Health Insurance Research Database. Analysis of propensity score was utilised to match age, gender, comorbidities and medications at a ratio of 1:1. Besides, multiple Cox regression analysis was performed to evaluate the adjusted hazard ratio of asthma. Furthermore, sensitivity tests and stratified analysis were conducted.

RESULTS

The incidence of asthma was 10.4 per 1000 person-years in the constipation group, which was higher than the rate of 5.7 per 1000 person-years observed in the non-constipation group. After adjustment for age, gender, urbanisation, comorbidities and medications, constipated patients had a 1.81-fold greater risk of asthma compared with those without constipation (adjusted hazard ratio [aHR]: 1.81, 95% CI: 1.74-1.88). In subgroup analyses, patients aged 20-39 years had a 2.01-fold highest risk of asthma in the constipation cohort (aHR: 2.01, 95% CI: 1.82-2.22). Besides, the severity of constipation is associated with an increased risk of asthma; the aHR was 1.92 (1.84-2.00), 2.07 (1.94-2.21) and 2.10 (1.96-2.25) for ≤ 30 days, 31-120 days and >120 days of laxatives prescription within 1 year after the index date, respectively (P < .001).

CONCLUSION

Constipation relates to a significantly increased risk of asthma. Physicians should be aware of the possibility of asthma in constipated people. Further research is warranted to investigate the possible pathological mechanisms of this association.

Association between vesicoureteral reflux, urinary tract infection and antibiotics exposure in infancy and risk of childhood asthma

Background

The use of antibiotics for treating infection in childhood and their association with increased risk of asthma remain controversial. Infants diagnosed with vesicoureteral reflux (VUR) belong to a unique population who are administered antibiotics for a long time and are susceptible to recurrent UTI. It is interesting to study the risk of asthma in these infants with or without VUR.

Methods

Taiwanese children born between 2000 and 2007 were enrolled in population-based birth cohort study. Participants diagnosed with VUR and UTI within first year were classified into four groups (VUR, UTI, VUR and UTI, and control). We calculated follow-up person-years for each participant from the index date until the asthma diagnosis, their withdrawal from the insurance system (because of death or loss to follow-up), or till the end of 2008. The risk of asthma was compared between the 4 cohorts by using Cox proportional hazards model analysis, adjusted hazard ratio (aHR), and 95% confidence interval (95% CI).

Results

Children diagnosed with VUR (n  =  350), UTI (n  =  15542), VUR and UTI (n  =  1696), and randomly selected controls (n  =  17588) were enrolled. The overall rate of incidence of asthma was found to be 1.64-fold, 1.45-fold, and 1.17-fold higher in the UTI, VUR/UTI, and VUR cohorts than in the controls (5.60, 5.07, and 4.10 vs. 3.17 per 100 person-years), respectively. After adjusting the potential factors, the overall risk of asthma remained the highest in UTI (aHR: 1.74, 95% CI : 1.65 to 1.80) followed by VUR/UTI (aHR: 1.56, 95% CI : 1.40 to 1.75) and VUR cohorts (aHR: 1.25, 95% CI: 0.96 to 1.62). The incidence of asthma was higher in boys than in girls.

Conclusion

The nationwide retrospective cohort study demonstrated that short-term therapeutic dose of antibiotics for UTI in infants with or without VUR has a positive correlation with the prevalence of childhood asthma. Significant risk of childhood asthma was not observed when VUR cohort was exposed to long-term low-dose of prophylactic antibiotics.

Omouma: a prospective mother and child cohort aiming to identify early biomarkers of pregnancy complications in women living in Qatar

BACKGROUND

Pregnancy is governed by multiple molecular and cellular processes, which might influence pregnancy health and outcomes. Failure to predict and understand the cause of pregnancy complications, adverse pregnancy outcomes, infant's morbidity and mortality, have limited effective interventions. Integrative multi-omics technologies provide an unbiased platform to explore the complex molecular interactions with an unprecedented depth. The objective of the present protocol is to build a longitudinal mother-baby cohort and use multi-omics technologies to help identify predictive biomarkers of adverse pregnancy outcomes, early life determinants and their effect on child health.

METHODS/DESIGN

One thousand pregnant women with a viable pregnancy in the first trimester (6-14 weeks of gestation) will be recruited from Sidra Medicine hospital. All the study participants will be monitored every trimester, at delivery, and one-year post-partum. Serial high-frequency sampling, including blood, stool, urine, saliva, skin, and vaginal swabs (mother only) from the pregnant women and their babies, will be collected. Maternal and neonatal health, including mental health and perinatal growth, will be recorded using a combination of questionnaires, interviews, and medical records. Downstream sample processing including microbial profiling, vaginal immune response, blood transcriptomics, epigenomics, and metabolomics will be performed.

DISCUSSION

It is expected that the present study will provide valuable insights into predicting pregnancy complications and neonatal health outcomes. Those include whether specific microbial and/or epigenomics signatures, immune profiles are associated with a healthy pregnancy and/or complicated pregnancy and poor neonatal health outcome. Moreover, this non-interventional cohort will also serve as a baseline dataset to understand how familial, socioeconomic, environmental and lifestyle factors interact with genetic determinants to influence health outcomes later in life. These findings will hold promise for the diagnosis and precision-medicine interventions.

Do Children With Constipation Have Increased Risk of Asthma? Real-World Data From a Nationwide Population-Based Cohort Study

Background: Asthma is one of the most burdensome childhood disorders. Growing evidence disclose intestinal dysbiosis may contribute to asthma via the gut-lung axis. Constipation can lead to alteration of the gut microbiota. The clinical impact of constipation on asthma has not been researched. Therefore, we aim to assess whether pediatric constipation influence the risk of developing asthma by a nationwide population-based cohort study. Methods: We analyzed 10,363 constipated patients and 10,363 individuals without constipation between 1999 and 2013 from Taiwan's National Health Insurance Research Database. Analysis of propensity score was utilized to match age, sex, comorbidities, and medications at a ratio of 1:1. In addition, multiple Cox regression analysis was performed to evaluate the adjusted hazard ratio of asthma. Furthermore, sensitivity tests and a stratified analysis were performed. Results: After adjustment for age, sex, comorbidities, and medications, constipated patients had a 2.36-fold greater risk of asthma compared to those without constipation [adjusted hazard ratio (aHR): 2.36, 95% C.I. 2.04-2.73, p < 0.001]. Furthermore, the severity of constipation is associated with an increased risk of asthma; the adjusted hazard ratio was 2.25, 2.85, and 3.44 within < 3, 3-12, and ≥12 times of laxatives prescription within 1 year, respectively (p < 0.001). Conclusion: Constipation was correlated with a significantly increased risk of asthma. Pediatricians should be aware of the possibility of asthma in constipated patients. Further research is warranted to investigate the possible pathological mechanisms of this association.

Perinatal environment shapes microbiota colonization and infant growth: impact on host response and intestinal function

BACKGROUND

Early microbial colonization triggers processes that result in intestinal maturation and immune priming. Perinatal factors, especially those associated with birth, including both mode and place of delivery are critical to shaping the infant gut microbiota with potential health consequences.

METHODS

Gut microbiota profile of 180 healthy infants (n = 23 born at home and n = 157 born in hospital, 41.7% via cesarean section [CS]) was analyzed by 16S rRNA gene sequencing at birth, 7 days, and 1 month of life. Breastfeeding habits and infant clinical data, including length, weight, and antibiotic exposure, were collected up to 18 months of life. Long-term personalized in vitro models of the intestinal epithelium and innate immune system were used to assess the link between gut microbiota composition, intestinal function, and immune response.

RESULTS

Microbiota profiles were shaped by the place and mode of delivery, and they had a distinct biological impact on the immune response and intestinal function in epithelial/immune cell models. Bacteroidetes and Bifidobacterium genus were decreased in C-section infants, who showed higher z-scores BMI and W/L during the first 18 months of life. Intestinal simulated epithelium had a stronger epithelial barrier function and intestinal maturation, alongside a higher immunological response (TLR4 route activation and pro-inflammatory cytokine release), when exposed to home-birth fecal supernatants, compared with CS. Distinct host response could be associated with different microbiota profiles.

CONCLUSIONS

Mode and place of birth influence the neonatal gut microbiota, likely shaping its interplay with the host through the maturation of the intestinal epithelium, regulation of the intestinal epithelial barrier, and control of the innate immune system during early life, which can affect the phenotypic responses linked to metabolic processes in infants.

TRIAL REGISTRATION

NCT03552939 . Video Abstract.

Complete Genome Sequence of Lactococcus lactis subsp. lactis G121, an Isolate with Allergy-Protective Features Derived from a Farming Environment

Early childhood exposure to a farming environment has been found to be protective against asthma and other atopic disorders. Here, we report the complete genome sequence of Lactococcus lactis subsp. lactis G121, which was isolated from the kitchen of a farm in Bavaria (Germany) and is recognized for its allergy-protective properties. It could be assembled into one circular chromosome, three circular plasmids, and one linear plasmid.

The Gut Microbiota and Respiratory Diseases: New Evidence

Human body surfaces, such as the skin, intestines, and respiratory and urogenital tracts, are colonized by a large number of microorganisms, including bacteria, fungi, and viruses, with the gut being the most densely and extensively colonized organ. The microbiome plays an essential role in immune system development and tissue homeostasis. Gut microbiota dysbiosis not only modulates the immune responses of the gastrointestinal (GI) tract but also impacts the immunity of distal organs, such as the lung, further affecting lung health and respiratory diseases. Here, we review the recent evidence of the correlations and underlying mechanisms of the relationship between the gut microbiota and common respiratory diseases, including asthma, chronic obstructive pulmonary disease (COPD), cystic fibrosis (CF), lung cancer, and respiratory infection, and probiotic development as a therapeutic intervention for these diseases.

Children From the Age of Three Show a Developmental Switch in T-Cell Differentiation

Every sixth child suffers from hypertrophy of the adenoid, a secondary lymphoid organ, at least once in childhood. Little is known about the impact of pathogen-provocation vs. developmental impact on T-cell responses after 1 year of age. Therefore, developmental and infection-driven influences on the formation of T-cell-compartments and -multifunctionality in adenoids were analyzed taking into account patient's history of age and inflammatory processes. Here, we show that in adenoids of 102 infants and children similar frequencies of naïve, effector, and memory T-cells were accumulated, whereby history of suffering from subsequent infection symptoms resulted in lower frequencies of CD4⁺ and CD8⁺ T-cells co-expressing several cytokines. While patients suffering from sole nasal obstruction had balanced Th1- and Th17-compartments, Th1 dominated in patients with concomitant upper airway infections. In addition, analysis of cytokine co-expressing CD4⁺ and CD8⁺ T-cells showed that children at the age of three or older differed significantly from those being 1- or 2-years old, implicating a developmental switch in T-cell differentiation at that age. Yet, dissecting age and infectious history of the patients revealed that while CD8⁺ T-cell differentiation seems to be triggered by development, CD4⁺ T-cell functionality is partly impaired by infections. However, this functionality recovers by the age of 3 years. Thus, 3 years of age seems to be a critical period in an infant's life to develop robust T-cell compartments of higher quality. These findings identify important areas for future research and distinguish an age period in early childhood when to consider adjusting the choice of treatment of infections.

Seeking Windows of Opportunity to Shape Lifelong Immune Health: A Network-Based Strategy to Predict and Prioritize Markers of Early Life Immune Modulation

A healthy immune status is strongly conditioned during early life stages. Insights into the molecular drivers of early life immune development and function are prerequisite to identify strategies to enhance immune health. Even though several starting points for targeted immune modulation have been identified and are being developed into prophylactic or therapeutic approaches, there is no regulatory guidance on how to assess the risk and benefit balance of such interventions. Six early life immune causal networks, each compromising a different time period in early life (the 1st, 2nd, 3rd trimester of gestations, birth, newborn, and infant period), were generated. Thereto information was extracted and structured from early life literature using the automated text mining and machine learning tool: Integrated Network and Dynamical Reasoning Assembler (INDRA). The tool identified relevant entities (e.g., genes/proteins/metabolites/processes/diseases), extracted causal relationships among these entities, and assembled them into early life-immune causal networks. These causal early life immune networks were denoised using GeneMania, enriched with data from the gene-disease association database DisGeNET and Gene Ontology resource tools (GO/GO-SLIM), inferred missing relationships and added expert knowledge to generate information-dense early life immune networks. Analysis of the six early life immune networks by PageRank, not only confirmed the central role of the "commonly used immune markers" (e.g., chemokines, interleukins, IFN, TNF, TGFB, and other immune activation regulators (e.g., CD55, FOXP3, GATA3, CD79A, C4BPA), but also identified less obvious candidates (e.g., CYP1A2, FOXK2, NELFCD, RENBP). Comparison of the different early life periods resulted in the prediction of 11 key early life genes overlapping all early life periods (TNF, IL6, IL10, CD4, FOXP3, IL4, NELFCD, CD79A, IL5, RENBP, and IFNG), and also genes that were only described in certain early life period(s). Concluding, here we describe a network-based approach that provides a science-based and systematical method to explore the functional development of the early life immune system through time. This systems approach aids the generation of a testing strategy for the safety and efficacy of early life immune modulation by predicting the key candidate markers during different phases of early life immune development.

Examining pathogenic concepts of autoimmune hepatitis for cues to future investigations and interventions

BACKGROUND

Multiple pathogenic mechanisms have been implicated in autoimmune hepatitis, but they have not fully explained susceptibility, triggering events, and maintenance or escalation of the disease. Furthermore, they have not identified a critical defect that can be targeted. The goals of this review are to examine the diverse pathogenic mechanisms that have been considered in autoimmune hepatitis, indicate investigational opportunities to validate their contribution, and suggest interventions that might evolve to modify their impact. English abstracts were identified in PubMed by multiple search terms. Full length articles were selected for review, and secondary and tertiary bibliographies were developed. Genetic and epigenetic factors can affect susceptibility by influencing the expression of immune regulatory genes. Thymic dysfunction, possibly related to deficient production of programmed cell death protein-1, can allow autoreactive T cells to escape deletion, and alterations in the intestinal microbiome may help overcome immune tolerance and affect gender bias. Environmental factors may trigger the disease or induce epigenetic changes in gene function. Molecular mimicry, epitope spread, bystander activation, neo-antigen production, lymphocytic polyspecificity, and disturbances in immune inhibitory mechanisms may maintain or escalate the disease. Interventions that modify epigenetic effects on gene expression, alter intestinal dysbiosis, eliminate deleterious environmental factors, and target critical pathogenic mechanisms are therapeutic possibilities that might reduce risk, individualize management, and improve outcome. In conclusion, diverse pathogenic mechanisms have been implicated in autoimmune hepatitis, and they may identify a critical factor or sequence that can be validated and used to direct future management and preventive strategies.

Role of timing of exposure to pets and dampness or mould on asthma and sensitization in adolescence

BACKGROUND

Pet and dampness or mould exposure are considered risk factors for asthma and sensitization. It is unclear whether timing of exposure to these factors is differentially associated with asthma risk and sensitization in adolescence.

OBJECTIVE

We investigated the role of timing of pet and dampness or mould exposure in asthma and sensitization in adolescence. Understanding this role is essential to build targeted prevention strategies.

METHODS

We used data from 1871 participants of the Dutch Prevention and Incidence of Asthma and Mite Allergy (PIAMA) cohort. Residential exposure to pets, dampness or mould was assessed by repeated parental questionnaires. We used asthma data from the 17-year questionnaire and sensitization data from the 16-year medical examination. We characterized timing using longitudinal exposure patterns from pregnancy till age 17 using longitudinal latent class growth modelling. We used logistic regression models to analyse associations of exposure patterns with asthma at age 17 and sensitization at age 16.

RESULTS

For none of the time windows, exposure to pets and dampness or mould was associated with asthma at age 17, but a lower sensitization risk at age 16 was suggested, for example the odds ratio (95% confidence interval) for sensitization was 0.63 (0.35-1.11) and 0.69 (0.44-1.08) for early life and persistently high pet exposure, respectively, compared with very low exposure. An inverse association was also suggested for sensitization and moderate early childhood dampness or mould exposure (0.71 [0.42-1.19]).

CONCLUSION AND CLINICAL RELEVANCE

Different timing of pet and dampness or mould exposure was not associated with asthma, but lower risk of sensitization in adolescence was suggested, which could be partly attributable to reversed causation. Current findings are not sufficient to recommend pet avoidance to prevent allergic disease. More prospective studies are needed to obtain insights that can be used in clinical practice.

Respiratory viral infection in early life and development of asthma in childhood: A protocol for systematic review and meta-analysis

BACKGROUND

Respiratory viruses are the leading cause of early life wheezing that may contribute to the development of childhood asthma leading to increasing morbidity and socioeconomic burden. The aim of this review is to identify whether respiratory viral infections during first year of life were associated with development of childhood asthma.

METHODS

We will search major scientific databases (MEDLINE, CINAHL, Web of Science, Cochrane Library, and ClinicalTrials.gov) using truncated and phrase-searched keywords and relevant subject headings. Observational studies including case-control studies, cohort studies, and randomized control trails published in English will be included in this review. Case reports, qualitative studies, and narrative overviews will be excluded. Exposure will be defined as laboratory-confirmed viral respiratory tract infection in the first year of life and outcome will be defined as development of asthma between ages 5 and 18 years. Effect sizes in bivariate and multivariate analyses will be presented as odds or prevalence ratios. We will explore for heterogeneity of the standard errors across the studies, and if appropriate, we will perform a meta-analysis using a random-effects model to present a summary estimate of the odds or prevalence ratios.

RESULTS

This review will assess whether respiratory viral infections during first year of life increases the risk of childhood asthma development.

CONCLUSIONS

This systematic review will evaluate published literature, assessing the link between early life viral infection and childhood asthma. Pooled data may provide evidence that infantile respiratory viral infection results in higher incidence of recurrent wheezing and asthma, thereby stimulating further research into the cost-effectiveness of pharmaceutical interventions such as vaccines and nonpharmaceutical interventions such as hand-washing and respiratory hygiene promotion to young children. Implementing the results of such research may then reduce the burden of acute viral respiratory infections and subsequent recurrent wheezing and asthma.

SYSTEMATIC REVIEW REGISTRATION

This systematic review has been registered on PROSPERO (CRD42018105519).

Factors associated with asthma expression in adolescents

Objective:

To evaluate risk factors associated with asthma symptoms in adolescents in the 13- to 14-year age bracket.

Methods:

This was a cross-sectional study involving adolescents enrolled in randomly selected public schools in the city of Belo Horizonte, Brazil, and conducted with the use of the International Study of Asthma and Allergies in Childhood (ISAAC) questionnaire and its supplementary module for risk factor assessment. The ISAAC questionnaire was completed by the students themselves, whereas the supplementary questionnaire was completed by their parents or legal guardians. Variables showing p ≤ 0.25 in the univariate analysis were included in the multivariate analysis. Stepwise regression with backward elimination was used for variable selection.

Results:

We evaluated 375 adolescents, 124 (33.1%) of whom had asthma symptoms. The final multivariate analysis model revealed that asthma symptoms were associated with birth weight < 2,500 g (p < 0.001), day care center or nursery attendance (p < 0.002), maternal history of asthma (p < 0.001), contact with animals during the first year of life (p < 0.027), current contact with animals outside the home (dogs, cats, or farm animals; p < 0.005), and more than 20 cigarettes per day smoked by parents or other household members (p < 0.02).

Conclusions:

Exposure to animals in and outside the home is associated with asthma symptoms, as is environmental tobacco smoke exposure. Families, health professionals, and administrators of health care facilities should take that into account in order to prevent asthma and reduce asthma morbidity.

Probiotics in Disease Prevention and Treatment

Few treatments for human diseases have received as much investigation in the past 20 years as probiotics. In 2017, English-language meta-analyses totaling 52 studies determined the effect of probiotics on conditions ranging from necrotizing enterocolitis and colic in infants to constipation, irritable bowel syndrome, and hepatic encephalopathy in adults. The strongest evidence in favor of probiotics lies in the prevention or treatment of 5 disorders: necrotizing enterocolitis, acute infectious diarrhea, acute respiratory tract infections, antibiotic-associated diarrhea, and infant colic. Probiotic mechanisms of action include the inhibition of bacterial adhesion; enhanced mucosal barrier function; modulation of the innate and adaptive immune systems (including induction of tolerogenic dendritic cells and regulatory T cells); secretion of bioactive metabolites; and regulation of the enteric and central nervous systems. Future research is needed to identify the optimal probiotic and dose for specific diseases, to address whether the addition of prebiotics (to form synbiotics) would enhance activity, and to determine if defined microbial communities would provide benefit exceeding that of single-species probiotics.

Co-occurrence of Asthma and the Inflammatory Bowel Diseases: A Systematic Review and Meta-analysis

Background

Inflammatory bowel diseases (IBD) and asthma share genetic and environmental risk factors. Consequently, several observational studies have explored an association between IBD and asthma. We systematically reviewed and summarized the literature on the co-occurrence of asthma and IBD.

Methods

MEDLINE and EMBASE (to April 2017) were searched to identify observational studies on the association between asthma and IBD. Relative risks (RR) were pooled using random effects models. Heterogeneity was assessed using the I² and Cochran Q statistics. Meta-regression based on study design, source of patients (population-based vs. tertiary-care center) and study location was conducted to explain between-study heterogeneity.

Results

Eighteen studies were identified (15 Crohn’s disease, 15 ulcerative colitis (UC)). Asthma was associated with both Crohn’s disease (pooled RR 1.30, 95% confidence interval (CI) 1.16–1.47, I² = 88%) and UC (RR 1.34, 95% CI 1.24–1.44, I² = 93%). The study design and source of patients and study location explained between-study heterogeneity in Crohn’s disease, but not UC.

Conclusion

Asthma is associated with both Crohn’s disease and UC. Additional research is needed to determine if one disease influences the risk of developing the other or if the frequent co-occurrence of these diseases result from shared genetic, environmental, and microbial risk factors.

Microbiome and Allergic Diseases

Allergic diseases, such as respiratory, cutaneous, and food allergy, have dramatically increased in prevalence over the last few decades. Recent research points to a central role of the microbiome, which is highly influenced by multiple environmental and dietary factors. It is well established that the microbiome can modulate the immune response, from cellular development to organ and tissue formation exerting its effects through multiple interactions with both the innate and acquired branches of the immune system. It has been described at some extent changes in environment and nutrition produce dysbiosis in the gut but also in the skin, and lung microbiome, inducing qualitative and quantitative changes in composition and metabolic activity. Here, we review the potential role of the skin, respiratory, and gastrointestinal tract (GIT) microbiomes in allergic diseases. In the GIT, the microbiome has been proven to be important in developing either effector or tolerant responses to different antigens by balancing the activities of Th1 and Th2 cells. In the lung, the microbiome may play a role in driving asthma endotype polarization, by adjusting the balance between Th2 and Th17 patterns. Bacterial dysbiosis is associated with chronic inflammatory disorders of the skin, such as atopic dermatitis and psoriasis. Thus, the microbiome can be considered a therapeutical target for treating inflammatory diseases, such as allergy. Despite some limitations, interventions with probiotics, prebiotics, and/or synbiotics seem promising for the development of a preventive therapy by restoring altered microbiome functionality, or as an adjuvant in specific immunotherapy.

Multiobjective grammar-based genetic programming applied to the study of asthma and allergy epidemiology

Background

Asthma and allergies prevalence increased in recent decades, being a serious global health problem. They are complex diseases with strong contextual influence, so that the use of advanced machine learning tools such as genetic programming could be important for the understanding the causal mechanisms explaining those conditions. Here, we applied a multiobjective grammar-based genetic programming (MGGP) to a dataset composed by 1047 subjects. The dataset contains information on the environmental, psychosocial, socioeconomics, nutritional and infectious factors collected from participating children. The objective of this work is to generate models that explain the occurrence of asthma, and two markers of allergy: presence of IgE antibody against common allergens, and skin prick test positivity for common allergens (SPT).

Results

The average of the accuracies of the models for asthma higher in MGGP than C4.5. IgE were higher in MGGP than in both, logistic regression and C4.5. MGGP had levels of accuracy similar to RF, but unlike RF, MGGP was able to generate models that were easy to interpret.

Conclusions

MGGP has shown that infections, psychosocial, nutritional, hygiene, and socioeconomic factors may be related in such an intricate way, that could be hardly detected using traditional regression based epidemiological techniques. The algorithm MGGP was implemented in c ++ and is available on repository: http://bitbucket.org/ciml-ufjf/ciml-lib.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2233-z) contains supplementary material, which is available to authorized users.

Dual Role of Toll-like Receptors in Human and Experimental Asthma Models

Asthma is a chronic airway inflammatory disease that is influenced by the interplay between genetic factors and exposure to environmental allergens, microbes, or microbial products where toll-like receptors (TLRs) play a pivotal role. TLRs recognize a wide range of microbial or endogenous molecules as well as airborne environmental allergens and act as adjuvants that influence positively or negatively allergic sensitization. TLRs are qualitatively and differentially expressed on hematopoietic and non-hematopoietic stromal or structural airway cells that when activated by TLRs agonists exert an immune-modulatory role in asthma development. Therefore, understanding mechanisms and pathways by which TLRs orchestrate asthma outcomes may offer new strategies to control the disease. Here, we aim to review and critically discuss the role of TLRs in human asthma and murine models of allergic airway inflammation, highlighting the complexity of TLRs function in development, exacerbation, or control of airway allergic inflammation.

Asthma Is Associated With Subsequent Development of Inflammatory Bowel Disease: A Population-based Case-Control Study

BACKGROUND & AIMS

Asthma and the inflammatory bowel diseases (IBD) each arise through complex interactions between genetic and environmental factors, and share many environmental risk factors. We examined the association between asthma and Crohn's disease or ulcerative colitis.

METHODS

We performed a population-based case-control study using health administrative data from the province of Alberta, Canada. The odds of a diagnosis of asthma preceding the diagnosis of either Crohn's disease (N = 3087) or ulcerative colitis (N = 2377) were compared with the odds of diagnosis of asthma among persons without IBD (N = 402,800) using logistic regression. Effect measure modification by age at diagnosis of IBD (16 years or less, 17-40 years, or older than 40 years) was tested using a likelihood ratio test.

RESULTS

A diagnosis of asthma was associated with increased odds of incident Crohn's disease (adjusted odds ratio [OR], 1.45; 95% confidence interval [CI], 1.31-1.60). No effect measure modification was observed for age at diagnosis for Crohn's disease (P = .42). However, we observed effect measure modification by age at diagnosis for ulcerative colitis (P = .0103), with an adjusted OR of 1.49 (95% CI, 1.08-2.07) among individuals diagnosed at an age of 16 years or less (OR) and an adjusted OR of 1.57 (95% CI, 1.31-1.89) among individuals diagnosed at an age older than 40 years. However, there was no association between asthma and ulcerative colitis among individuals diagnosed between ages 17 and 40 (adjusted OR, 1.05; 95% CI, 0.86-1.26).

CONCLUSIONS

In a population-based case-control study, we associated asthma with Crohn's disease, and with early and late-onset ulcerative colitis.

Differences in the Nasopharyngeal Microbiome During Acute Respiratory Tract Infection With Human Rhinovirus and Respiratory Syncytial Virus in Infancy

Respiratory viruses alter the nasopharyngeal microbiome and may be associated with a distinct microbial signature. To test this hypothesis, we compared the nasopharyngeal microbiome of 135 previously healthy infants with acute respiratory infection due to human rhinovirus (HRV; n = 52) or respiratory syncytial virus (RSV; n = 83). The nasopharyngeal microbiome was assessed by sequencing the V4 region of the 16S ribosomal RNA. Respiratory viruses were identified by quantitative reverse-transcription polymerase chain reaction. We found significant differences in the overall taxonomic composition and abundance of certain bacterial genera between infants infected with HRV and those infected with RSV. Our results suggest that respiratory tract viral infections are associated with different nasopharyngeal microbial profiles.

Immunological considerations regarding parental concerns on pediatric immunizations

Despite the fundamental role of vaccines in the decline of infant mortality, parents may decide to decline vaccination for their own children. Many factors may influence this decision, such as the belief that the infant immune system is weakened by vaccines, and concerns have been raised about the number of vaccines and the early age at which they are administered. Studies focused on the infant immune system and its reaction to immunizations, summarized in this review, show that vaccines can overcome those suboptimal features of infant immune system that render them more at risk of infections and of their severe manifestations. In addition, many vaccines have been shown to improve heterologous innate and adaptive immunity resulting in lower mortality rates for fully vaccinated children. Thus, multiple vaccinations are necessary and not dangerous, as infants can respond to several antigens as well as when responding to single stimuli. Current immunization schedules have been developed and tested to avoid vaccine interference, improve benefits and reduce side effects compared to single administrations. The infant immune system is therefore capable, early after birth, of managing several antigenic challenges and exploits them to prompt its development.

The Maternal Diet, Gut Bacteria, and Bacterial Metabolites during Pregnancy Influence Offspring Asthma

This review focuses on the current evidence that maternal dietary and gut bacterial exposures during pregnancy influence the developing fetal immune system and subsequent offspring asthma. Part 1 addresses exposure to a farm environment, antibiotics, and prebiotic and probiotic supplementation that together indicate the importance of bacterial experience in immune programming and offspring asthma. Part 2 outlines proposed mechanisms to explain these associations including bacterial exposure of the fetoplacental unit; immunoglobulin-related transplacental transport of gut bacterial components; cytokine signaling producing fetomaternal immune alignment; and immune programming via metabolites produced by gut bacteria. Part 3 focuses on the interplay between diet, gut bacteria, and bacterial metabolites. Maternal diet influences fecal bacterial composition, with dietary microbiota-accessible carbohydrates (MACs) selecting short-chain fatty acid (SCFA)-producing bacteria. Current evidence from mouse models indicates an association between increased maternal dietary MACs, SCFA exposure during pregnancy, and reduced offspring asthma that is, at least in part, mediated by the induction of regulatory T lymphocytes in the fetal lung. Part 4 discusses considerations for future studies investigating maternal diet-by-microbiome determinants of offspring asthma including the challenge of measuring dietary MAC intake; limitations of the existing measures of the gut microbiome composition and metabolic activity; measures of SCFA exposure; and the complexities of childhood respiratory health assessment.

Associations of gestational and early life exposures to ambient air pollution with childhood atopic eczema in Shanghai, China

Whether ambient air pollution is associated with childhood atopic eczema is controversial. In this paper, we selected 3358 preschool children who had not altered residences since pregnancy from a cross-sectional study during 2011-2012 in Shanghai, China, and obtained parent-reported data regarding childhood atopic eczema using an improved ISAAC questionnaire. We recorded daily concentrations of SO₂, NO₂, and PM₁₀ throughout the child's lifetime (2006-2012), and calculated period-averaged concentrations for each district where the child lived to represent the child's exposure levels of these pollutants during different periods. In the multiple logistic regression analyses adjusted for potential confounders as well as for the other pollutants in the same periods, childhood atopic eczema was significantly associated with increments of NO₂ in the approximate interquartile range (20μg/m³) during gestational period (adjusted OR, 95% CI for eczema lifetime-ever: 1.80, 1.29-2.49; for eczema in the year prior to the survey: 2.32, 1.57-3.43) and during the first year of life (2.00, 1.40-2.84; 2.16, 1.43-3.28). Exposure to elevated NO₂ in the first two years, three years and total lifetime, as well as exposure to mixtures containing NO₂ in each of these periods, were consistently associated with increased likelihood of childhood eczema. The highest odds ratios were found between exposure to a mixture of SO₂ and NO₂ during total lifetime (increment: 35μg/m³) and childhood eczema (adjusted OR, 95% CI: 2.80, 1.75-4.48; 3.50, 1.98-6.19). No significant associations were found between childhood eczema and ambient SO₂ and PM₁₀ individually or in mixtures. This study indicates that gestational and lifetime exposures to ambient NO₂ are risk factors for atopic eczema in childhood. Exposure to ambient SO₂ and PM₁₀ may enhance the effect of NO₂ exposure on childhood eczema.

Early-life antibiotic use and subsequent diagnosis of food allergy and allergic diseases

BACKGROUND

Antibiotic use in early life has been linked to disruptions in the microbiome. Such changes can disturb immune system development. Differences have been observed in the microbiota of children with and without allergies, but there have been few studies on antibiotic use and allergic disease.

OBJECTIVE

We evaluated associations of early-life antibiotic use with subsequent occurrence of food allergy and other allergies in childhood using electronic health record data.

METHODS

We used longitudinal data on 30 060 children up to age 7 years from Geisinger Clinic's electronic health record to conduct a sex- and age-matched case-control study to evaluate the association between antibiotic use and milk allergy, non-milk food allergies, and other allergies. For each outcome, we estimated conditional logistic regression models adjusting for race/ethnicity, history of Medical Assistance, and mode of birth delivery. Models were repeated separately for penicillins, cephalosporins and macrolides.

RESULTS

There were 484 milk allergy cases, 598 non-milk food allergy cases and 3652 other allergy cases. Children with three or more antibiotic orders had a greater odds of milk allergy (Odds Ratio; 95% Confidence interval) (1.78; 1.28-2.48), non-milk food allergy (1.65; 1.27-2.14), and other allergies (3.07; 2.72-3.46) compared with children with no antibiotic orders. Associations were strongest at younger ages and differed by antibiotic class.

CONCLUSIONS AND CLINICAL RELEVANCE

We observed associations between antibiotic orders and allergic diseases, providing evidence of a potentially modifiable clinical practice associated with paediatric allergic disease. Differences by antibiotic class should be further explored, as this knowledge could inform paediatric treatment decisions.

Linking microbiota and respiratory disease

An increasing body of evidence indicates the relevance of microbiota for pulmonary health and disease. Independent investigations recently demonstrated that the lung harbors a resident microbiota. Therefore, it is intriguing that a lung microbiota can shape pulmonary immunity and epithelial barrier functions. Here, we discuss the ways how the composition of the microbial community in the lung may influence pulmonary health and vice versa, factors that determine community composition. Prominent microbiota at other body sites such as the intestinal one may also contribute to pulmonary health and disease. However, it is difficult to discriminate between influences of lung vs. gut microbiota due to systemic mutuality between both communities. With focuses on asthma and respiratory infections, we discuss how microbiota of lung and gut can determine pulmonary immunity and barrier functions.

Regulation of Autoimmunity by the Microbiome

Intestinal microbes have profound effects on inflammatory autoimmunity in sites distant from the gut. The mechanisms whereby this happens are only now beginning to be understood and may include such diverse effects as innate stimulation of migrating immune cells and effects of circulating bacterial metabolites. Our studies add to this the demonstration that microbiota may provide a source of cross-reactive antigenic material that activates autoreactive lymphocytes within the gut environment. In a spontaneous model of autoimmune uveitis, T lymphocytes specific to a retinal autoantigen are activated through their specific antigen receptor in the gut and acquire the ability to fuel inflammatory autoimmunity in the eye. In view of the huge diversity of commensals, it is conceivable that they may provide surrogate antigens for activation of autoreactive lymphocytes(s) of other tissue specificities, and might therefore be involved in the etiology of autoimmune diseases more frequently than is currently appreciated.

Draft Genome Sequence and Complete Plasmid Sequence of Acinetobacter lwoffii F78, an Isolate with Strong Allergy-Protective Properties

The hygiene hypothesis states that the tremendous increase in atopic diseases correlates significantly with less contact to microbes in childhood. Here, we report the draft genome sequence of Acinetobacter lwoffii F78, a rural cowshed isolate with strong allergy-protective properties that contains an 8,579-bp plasmid.