Microbiome influences on allergy in mice and humans

Environmental Risk Factors, Protective Factors, and Biomarkers for Allergic Rhinitis: A Systematic Umbrella Review of the Evidence

Many potential environmental risk factors, protective factors, and biomarkers of AR have been published, but so far, the strength and consistency of their evidence are unclear. We conducted a comprehensive review of environmental risk, protective factors, and biomarkers for AR to establish the evidence hierarchy. We systematically searched Embase, PubMed, Cochrane Library, and Web of Science electronic database from inception to December 31, 2022. We calculated summary effect estimate (odds ratio (OR), relative risk (RR), hazard ratio (HR), and standardized mean difference (SMD)), 95% confidence interval, random effects p value, I2 statistic, 95% prediction interval, small study effects, and excess significance biases, and stratification of the level of evidence. Methodological quality was assessed by AMSTAR 2 (A Measurement Tool to Assess Systematic Reviews 2). We retrieved 4478 articles, of which 43 met the inclusion criteria. The 43 eligible articles identified 31 potential environmental risk factors (10,806,206 total population, two study not reported), 11 potential environmental protective factors (823,883 total population), and 34 potential biomarkers (158,716 total population) for meta-analyses. The credibility of evidence was convincing (class I) for tic disorders (OR = 2.89, 95% CI 2.11-3.95); and highly suggestive (class II) for early-life antibiotic use (OR = 3.73, 95% CI 3.06-4.55), exposure to indoor dampness (OR = 1.49, 95% CI 1.27-1.75), acetaminophen exposure (OR = 1.54, 95% CI 1.41-1.69), childhood acid suppressant use (OR = 1.40, 95% CI 1.23-1.59), exposure to indoor mold (OR = 1.66, 95% CI 1.26-2.18), coronavirus disease 2019 (OR = 0.11, 95% CI 0.06-0.22), and prolonged breastfeeding (OR = 0.72, 95% CI 0.65-0.79). This study is registered in PROSPERO (CRD42022384320).

Preterm Delivery: Microbial Dysbiosis, Gut Inflammation and Hyperpermeability

Preterm birth is one of the main health problems encountered in the neonatal period, especially because it is also the first cause of death in the critical 1st month of life and the second in children under 5 years of age. Not only preterm birth entails short term health risks due to low weight and underdeveloped organs, but also increases the risk of suffering from non-transmissible diseases in the long term. To date, it is known that medical conditions and lifestyle factors could increase the risk of preterm birth, but the molecular mechanisms that control this process remain unclear. Luteolysis, increased inflammation or oxidative stress have been described as possible triggers for preterm birth and, in some cases, the cause of dysbiosis in preterm neonates. Several murine models have been developed to shed light into the mechanistic of preterm birth but, for the most part, are inflammation-based labor induction models and the offspring health readouts are mainly limited to survival and weight. Using a set of SWISS-CD1 mice born prematurely we analyzed inflammation and gut permeability parameters compared with term pups at weaning age. Overall, preterm mice presented higher systemic inflammation and gastrointestinal tract permeability. In this perspective article, we discuss the recent discoveries on preterm birth and the necessity of non-inflammatory murine models to really understand these phenotypes and be able to design strategies to prevent the sequels of this traumatic event in neonates.

Gram-negative microbiota is related to acute exacerbation in children with asthma

BACKGROUND

The upper-airway microbiota may be associated with the pathogenesis of asthma and useful for predicting acute exacerbation. However, the relationship between the lower-airway microbiota and acute exacerbation in children with asthma is not well understood. We evaluated the characteristics of the airway microbiome using induced sputum from children with asthma exacerbation and compared the microbiota-related differences of inflammatory cytokines with those in children with asthma.

METHODS

We analysed the microbiome using induced sputum during acute exacerbation of asthma in children. We identified microbial candidates that were prominent in children with asthma exacerbation and compared them with those in children with stable asthma using various analytical methods. The microbial candidates were analysed to determine their association with inflammatory cytokines. We also developed a predictive functional profile using PICRUSt.

RESULTS

A total of 95 children with allergic sensitisation including 22 with asthma exacerbation, 67 with stable asthma, and 6 controls were evaluated. We selected 26 microbial candidates whose abundances were significantly increased, decreased, or correlated during acute exacerbation in children with asthma. Among the microbial candidates, Campylobacter, Capnocytophaga, Haemophilus, and Porphyromonas were associated with inflammatory cytokines including macrophage inflammatory protein (MIP)-1β, programmed death-ligand 1, and granzyme B. Both Campylobacter and MIP-1β levels were correlated with sputum eosinophils. Increased lipopolysaccharide biosynthesis and decreased glycan degradation were observed in children with asthma exacerbation.

CONCLUSION

Gram-negative microbes in the lower airway were related to acute exacerbation in children with asthma. These microbes and associated cytokines may play a role in exacerbating asthma in children.

Probiotic mixture reduces gut inflammation and microbial dysbiosis in children with atopic dermatitis

BACKGROUND

Recent data suggested that dysbiosis of the gut microbiome is associated with childhood allergic diseases. Oral administration of probiotic formulations may improve the severity of atopic dermatitis (AD) by restoring imbalanced gut microbiota and reducing intestinal inflammation in children.

OBJECTIVES

The aim of this study was to investigate the effects of a probiotic mixture on the clinical severity of AD, gut inflammatory markers and alterations in microbiome dysbiosis in children with AD.

METHODS

A total of 25 subjects were enrolled in this study and administered with a mixture of probiotic strains consisting of Lactobacilli and Bifidobacteria for 4 weeks. The clinical efficacy of the probiotic mixture was assessed using SCORAD index and TEWL. Faecal calprotectin levels were measured as a marker for intestinal inflammation. The composition and diversity of the gut microbiome were analysed using 16S rRNA pyrosequencing.

RESULTS

The SCORAD (38.9 ± 17.2 vs 29.0 ± 15.4, P < 0.001) and TEWL (58.3 ± 12.5 vs 27.3 ± 8.7 g/m² /h, P = 0.028) were significantly decreased after 4 weeks administration of the probiotic mixture. The faecal calprotectin level (121.5 [27.7-292.9] vs 37.0 μg/g [12.6-108.9 μg/g], P = 0.038) was significantly decreased. The α-diversity and composition of the gut microbiome were not significantly changed, but β-diversity was increased after 4 weeks.

CONCLUSIONS

The oral administration of the probiotic mixture was effective in reducing clinical severity and intestinal inflammation in children with AD. Gut microbial diversity was slightly increased after administration of the probiotic mixture. The results of this study suggest that a probiotic mixture can alleviate AD by decreasing inflammation and modulating the gut microbiota in children with AD.

Association between acid-suppressive drug use and atopic dermatitis in patients with upper gastrointestinal diseases: A population-based retrospective cohort study

WHAT IS KNOWN AND OBJECTIVE

Proton-pump inhibitors (PPIs) and histamine-2-receptor antagonists (H2RAs) are two of the most widely used acid-suppressive drugs (ASDs). Some studies have reported that prenatal ASD exposure may increase the risk of asthma and other allergic diseases. This study investigated the effects of ASDs on the risk of atopic dermatitis in patients with upper gastrointestinal diseases.

METHODS

This population-based retrospective cohort study used data of 289,850 patients with at least two diagnoses of upper gastrointestinal diseases (UGIDs) between 1 January 2001 and 31 December 2005, from Taiwan's National Health Insurance Research Database. The AD risks among ASD users and nonusers were compared. Differences in sociodemographic characteristics and potential covariates were examined. AD hazard ratios were estimated, and groups were compared using Cox proportional hazards regression analysis after adjustment for age, sex and other covariates.

RESULTS AND DISCUSSION

In total, 109,980 patients were included. The adjusted hazard ratio (HR) of AD risk in ASD users relative to that in nonusers was 1.52 (95% confidence interval [CI]: 1.40-1.64, p < 0.001). For a dose-effect sub-analysis, patients were divided into four groups based on their defined daily dose. ASDs dose-dependently affected the AD risk (p for trend <0.01). Furthermore, the adjusted HR of the AD risk among ASD nonusers was 2.30 (95% CI: 2.06-2.57) relative to that in the comparison group (ASD nonusers without UGIDs). Among patients with UGIDs, ASD users had a higher AD risk than ASD nonusers. A subgroup analysis revealed only H2RA use was associated with an increased AD risk (adjusted HR 1.70, 95% CI: 1.53-1.89, p < 0.001).

WHAT IS NEW AND CONCLUSIONS

These results indicate that the use of H2RAs was associated with an increased risk of AD among patients with UGIDs, and the increase in risk appeared to be dose-dependent. ASDs should be used only in situations where clear clinical benefits can be obtained.

Increasing allergy: are antibiotics the elephant in the room?

Antibiotics cause dramatic changes to the human microbiome. The composition of the microbiome has been associated with changes in the immune system and these changes are beginning to be linked to immune diseases. Thus, antibiotics have been implicated as a significant contributor to the continual rise of allergies and autoimmune disease in developed countries. This recognition will hopefully result in the development of post-antibiotic therapies that restore a healthy microbiome and reduce immune system disorders.

Precision Medicine in Childhood Asthma: Omic Studies of Treatment Response

Asthma is a heterogeneous and multifactorial respiratory disease with an important impact on childhood. Difficult-to-treat asthma is not uncommon among children, and it causes a high burden to the patient, caregivers, and society. This review aims to summarize the recent findings on pediatric asthma treatment response revealed by different omic approaches conducted in 2018–2019. A total of 13 studies were performed during this period to assess the role of genomics, epigenomics, transcriptomics, metabolomics, and the microbiome in the response to short-acting beta agonists, inhaled corticosteroids, and leukotriene receptor antagonists. These studies have identified novel associations of genetic markers, epigenetic modifications, metabolites, bacteria, and molecular mechanisms involved in asthma treatment response. This knowledge will allow us establishing molecular biomarkers that could be integrated with clinical information to improve the management of children with asthma.

The Role of Home Environments in Allergic Disease

Allergic diseases are surprisingly common, chronic health conditions. The primary location where the vast majority of people are exposed to allergens and other substances is in their home. This means it is important to understand home environments and how a home's systems function and interact-and that how we occupy these spaces plays a crucial role in both environmental exposure and management of allergic disease. This review provides an overview of what is understood about home environmental exposure and its impact on our health, and proposes a systematic process for using a patient's environmental history to develop individualized, manageable and cost-effective recommendations. Once occupant-related information has been gathered, a home environmental exposure assessment should be performed focused on identifying the relationships between any identified sources of contaminants and the housing systems, and conditions that may be contributing to exposure. The results and recommendations from this assessment can then be used to guide exposure-reduction efforts by patients and/or their caregivers in an effort to improve disease management. In this review, we'll discuss three different types of home interventions-active, which must be routinely performed by the patient and/or caregiver, passive, which are interventions that work without routine, direct interaction from the homeowner, and behavioral changes in how the home environment is cleaned and maintained for long-term reduction of allergens. In this review, and others evaluated for this discussion, a significant number of home environmental assessment and intervention programs were shown to be cost effective, with the majority of programs showing a net positive return on investment. It is important to recognize that to be cost effective, the level and intensity of services offered through home visit programs need be stratified, based on the estimated health risks of the patient, in order to tailor the assessment and target the interventions to a patient's needs while maximizing cost effectiveness.

Dynamic construction of gut microbiota may influence allergic diseases of infants in Southwest China

BACKGROUND

Gut microbes have been suggested as the possible targets in the management of allergic diseases. However, the way in which these microbes influence allergic diseases remain unclear. Forty-seven full-term newborns were selected from a 1000-infant birth cohort. Among them were 23 allergic infants, whereas 24 infants were healthy without allergic symptoms at 1 year of age. Two hundred and sixty-four fecal samples were collected at 7 time points following their birth. These fecal samples were microbiologically analyzed using 16S rRNA gene sequencing. The dynamic processes involved in gut microbiota diversity and composition in the tested infants were constructed.

RESULTS

Healthy infants demonstrated more statistical differences in longitudinal changes in the alpha diversity of their microbiota at the time points compared with day 0 (meconium) than did allergic infants. Analysis of beta diversity showed that the fecal microbiota of days 0 and 2 comprised different communities in healthy infants, and that there were three separate communities in the fecal microbiota of day 0 of the healthy infants, those of day 2 of the healthy infants, and those of days 0-2 of the allergic infants. The relative abundance of dominant gut microbiota at phylum level varied at different time points in the healthy and diseased groups. Bifidobacterium, Escherichia-Shigella, Streptococcus, Clostridium_sensu_stricto_1, Akkermansia and Erysipelatoclostridium were significantly different between the healthy and diseased groups at a different time points.

CONCLUSION

The dynamic construction processes of gut microbiota during early life might be associated with the occurrence of long-term allergic diseases, with the first month following birth potentially being the most critical.

Glycoconjugates of Gram-negative bacteria and parasitic protozoa - are they similar in orchestrating the innate immune response?

Innate immunity is an evolutionarily ancient form of host defense that serves to limit infection. The invading microorganisms are detected by the innate immune system through germline-encoded PRRs. Different classes of PRRs, including TLRs and cytoplasmic receptors, recognize distinct microbial components known collectively as PAMPs. Ligation of PAMPs with receptors triggers intracellular signaling cascades, activating defense mechanisms. Despite the fact that Gram-negative bacteria and parasitic protozoa are phylogenetically distant organisms, they express glycoconjugates, namely bacterial LPS and protozoan GPI-anchored glycolipids, which share many structural and functional similarities. By activating/deactivating MAPK signaling and NF-κB, these ligands trigger general pro-/anti-inflammatory responses depending on the related patterns. They also use conservative strategies to subvert cell-autonomous defense systems of specialized immune cells. Signals triggered by Gram-negative bacteria and parasitic protozoa can interfere with host homeostasis and, depending on the type of microorganism, lead to hypersensitivity or silencing of the immune response. Activation of professional immune cells, through a ligand which triggers the opposite effect (antagonist versus agonist) appears to be a promising solution to restoring the immune balance.

Effects of the 1975 Japanese diet on the gut microbiota in younger adults

Japan is known for its longevity worldwide; the Japanese diet is thought to contribute to this longevity. However, the Japanese diet has become westernized over the past years, with a parallel increase in the incidence of lifestyle diseases. Thus, whether the modern Japanese diet is still healthy requires investigation. A diet with characteristics of the 1975 Japanese diet (JD) was previously shown to have beneficial effects on mice and humans. In this study, we examined whether intestinal bacteria are involved in the health benefits of this diet by analyzing changes in the composition of the fecal microbiota between humans who ingested the JD and those consuming a modern Japanese diet (MD). We also examined correlations between intestinal bacteria and biological parameters. A randomized controlled trial was performed to determine the effects of the 1975 JD compared to those of the MD. Subjects aged 20-29 years were randomly assigned to the JD (n=11) and MD (n=10) groups. Each subject consumed their respective diet three times per day for 28 days, and changes in intestinal bacteria before to after this period were evaluated. Four genera (unclassified Lachnospiraceae, Parabacteroides, Sutterella and unclassified Rikenellaceae) were significantly changed upon intake of the JD. Based on correlation analysis, relationships were found between changes in these genera and decreases in fat%; fat mass; and levels of blood glutamic oxaloacetic transaminase, blood triacylglycerols and hemoglobin A1c. These results suggest that changes in intestinal bacteria are involved in the health benefits of the JD.

Allergen Immunization Induces Major Changes in Microbiota Composition and Short-Chain Fatty Acid Production in Different Gut Segments in a Mouse Model of Lupine Food Allergy

BACKGROUND

The incidence of food allergies in western countries has increased in recent decades.

OBJECTIVES

To study the association between gut bacterial microbiota composition, short-chain fatty acids (SCFAs) and food allergy in a mouse model.

METHODS

After oral immunizations with the human food allergen lupine with the adjuvant cholera toxin (CT) (or buffer in controls), sensitization and anaphylactic responses were determined. Gastrointestinal content was collected from the distal ileum, cecum, colon, and fecal pellets, and the bacterial diversity and composition was determined by deep sequencing of the 16S rRNA gene. SCFAs in gastrointestinal content supernatants were determined by gas chromatography.

RESULTS

The microbiota signatures were profoundly affected by allergen immunization. Ten operational taxonomic units (OTUs) were significantly different between immunized and control animals for at least one of the intestinal segments; eight of these OTUs belonged to the Clostridia class. Although consistent across all four gut segments, the colon showed the highest number of OTUs significantly associated with allergic immunization. SCFA levels in the cecum were also altered by immunization.

CONCLUSIONS

Allergen immunization with CT in the present food allergy model induced profound changes in the microbiome composition and SCFA production. The result suggests that the colon may be the most sensitive gut segment for investigating changes in the gut microbiome.

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.

Association Between Use of Acid-Suppressive Medications and Antibiotics During Infancy and Allergic Diseases in Early Childhood

IMPORTANCE

Allergic diseases are prevalent in childhood. Early exposure to medications that can alter the microbiome, including acid-suppressive medications and antibiotics, may influence the likelihood of allergy.

OBJECTIVE

To determine whether there is an association between the use of acid-suppressive medications or antibiotics in the first 6 months of infancy and development of allergic diseases in early childhood.

DESIGN, SETTING, AND PARTICIPANTS

A retrospective cohort study was conducted in 792 130 children who were Department of Defense TRICARE beneficiaries with a birth medical record in the Military Health System database between October 1, 2001, and September 30, 2013, with continued enrollment from within 35 days of birth until at least age 1 year. Children who had an initial birth stay of greater than 7 days or were diagnosed with any of the outcome allergic conditions within the first 6 months of life were excluded from the study. Data analysis was performed from April 15, 2015, to January 4, 2018.

EXPOSURES

Exposures were defined as having any dispensed prescription for a histamine-2 receptor antagonist (H2RA), proton pump inhibitor (PPI), or antibiotic.

MAIN OUTCOMES AND MEASURES

The main outcome was allergic disease, defined as the presence of food allergy, anaphylaxis, asthma, atopic dermatitis, allergic rhinitis, allergic conjunctivitis, urticaria, contact dermatitis, medication allergy, or other allergy.

RESULTS

Of 792 130 children (395 215 [49.9%] girls) included for analysis, 60 209 (7.6%) were prescribed an H2RA, 13 687 (1.7%) were prescribed a PPI, and 131 708 (16.6%) were prescribed an antibiotic during the first 6 months of life. Data for each child were available for a median of 4.6 years. Adjusted hazard ratios (aHRs) in children prescribed H2RAs and PPIs, respectively, were 2.18 (95% CI, 2.04-2.33) and 2.59 (95% CI, 2.25-3.00) for food allergy, 1.70 (95% CI, 1.60-1.80) and 1.84 (95% CI, 1.56-2.17) for medication allergy, 1.51 (95% CI, 1.38-1.66) and 1.45 (95% CI, 1.22-1.73) for anaphylaxis, 1.50 (95% CI, 1.46-1.54) and 1.44 (95% CI, 1.36-1.52) for allergic rhinitis, and 1.25 (95% CI, 1.21-1.29) and 1.41 (95% CI, 1.31-1.52) for asthma. The aHRs after antibiotic prescription in the first 6 months of life were 2.09 (95% CI, 2.05-2.13) for asthma, 1.75 (95% CI, 1.72-1.78) for allergic rhinitis, 1.51 (95% CI, 1.38-1.66) for anaphylaxis, and 1.42 (95% CI, 1.34-1.50) for allergic conjunctivitis.

CONCLUSIONS AND RELEVANCE

This study found associations between the use of acid-suppressive medications and antibiotics during the first 6 months of infancy and subsequent development of allergic disease. Acid-suppressive medications and antibiotics should be used during infancy only in situations of clear clinical benefit.

Development of allergic immunity in early life

The growth and maturity of the peripheral immune system and subsequent development of pulmonary immunity in early life is dictated by host, environmental and microbial factors. Dysregulation during the critical window of immune development in the postnatal years results in disease which impacts on lifelong lung health. Asthma is a common disease in childhood and is often preceded by wheezing illnesses during the preschool years. However, the mechanisms underlying development of wheeze and how and why only some children progress to asthma is unknown. Human studies to date have generally focused on peripheral immune development, with little assessment of local tissue pathology in young children. Moreover, mechanisms underlying the interactions between inflammation and tissue repair at mucosal surfaces in early life remain unknown. Disappointingly, mechanistic studies in mice have predominantly used adult models. This review will consider the aspects of the neonatal immune system which might contribute to the development of early life wheezing disorders and asthma, and discuss the external environmental factors which may influence this process.

Finding a needle in a haystack: Bacteroides fragilis polysaccharide A as the archetypical symbiosis factor

Starting from birth, all animals develop a symbiotic relationship with their resident microorganisms that benefits both the microbe and the host. Recent advances in technology have substantially improved our ability to direct research toward the identification of important microbial species that affect host physiology. The identification of specific commensal molecules from these microbes and their mechanisms of action is still in its early stages. Polysaccharide A (PSA) of Bacteroides fragilis is the archetypical example of a commensal molecule that can modulate the host immune system in health and disease. This zwitterionic polysaccharide has a critical impact on the development of the mammalian immune system and also on the stimulation of interleukin 10-producing CD4⁺ T cells; consequently, PSA confers benefits to the host with regard to experimental autoimmune, inflammatory, and infectious diseases. In this review, we summarize the current understanding of the immunomodulatory effects of B. fragilis PSA and discuss these effects as a novel immunological paradigm. In particular, we discuss recent advances in our understanding of the unique functional mechanisms of this molecule and its therapeutic potential, and we review the recent literature in the field of microbiome research aimed at discovering new commensal products and their immunomodulatory potential.

Kinetic changes of intestinal microbiota in the course of intestinal sensitization

Food allergy (FA) is an adverse immune response to certain innocent food. It is estimated about 2% to 6% of the general population suffer from FA. Symptoms of a food allergic reaction may involve the gastrointestinal tract or/and other organs. The gut microbiota plays a critical role in diet-induced health problems. Whether the changes in the composition of the intestinal microbiota regulate allergic responses to food remains poorly understood. Thus, we created an FA animal model, sequenced the V4-V5 regions of 16S rRNA genes to characterize the genera abundance of gut microbiota. The results showed that mice under FA condition showed different gut bacterial structures. Diverse distribution of the bacterial species was identified between FA and control groups. FA altered the components of intestinal Microbiota in mice. The dysbiosis of the gut metagenome correlated with the development of the FA.

Development of a Stable Lung Microbiome in Healthy Neonatal Mice

The lower respiratory tract has been previously considered sterile in a healthy state, but advances in culture-independent techniques for microbial identification and characterization have revealed that the lung harbors a diverse microbiome. Although research on the lung microbiome is increasing and important questions were already addressed, longitudinal studies aiming to describe developmental stages of the microbial communities from the early neonatal period to adulthood are lacking. Thus, little is known about the early-life development of the lung microbiome and the impact of external factors during these stages. In this study, we applied a barcoding approach based on high-throughput sequencing of 16S ribosomal RNA gene amplicon libraries to determine age-dependent differences in the bacterial fraction of the murine lung microbiome and to assess potential influences of differing "environmental microbiomes" (simulated by the application of used litter material to the cages). We could clearly show that the diversity of the bacterial community harbored in the murine lung increases with age. Interestingly, bacteria belonging to the genera Delftia and Rhodococcus formed an age-independent core microbiome. The addition of the used litter material influenced the lung microbiota of young mice but did not significantly alter the community composition of adult animals. Our findings elucidate the dynamic nature of the early-life lung microbiota and its stabilization with age. Further, this study indicates that even slight environmental changes modulate the bacterial community composition of the lung microbiome in early life, whereas the lung microbes of adults demonstrate higher resilience towards environmental variations.

Correlation of Severity of Functional Gastrointestinal Disease Symptoms with that of Asthma and Chronic Obstructive Pulmonary Disease: A Multicenter Study

Introduction

There is a growing clinical awareness about the influence of gut-lung axis on lung injury and coexisting manifestations of disease processes in both the intestine and lungs. Patients of chronic lung diseases such as chronic obstructive pulmonary disease (COPD) and asthma very often present with coexistent gut symptoms. In the present study, we have tried to establish the correlation of severity of pulmonary pathology of COPD and asthma patients with functional gastrointestinal (GI) symptoms of the patients.

Materials and Methods

This is a prospective, questionnaire-based study comprising patients with asthma and COPD. After following strict inclusion and exclusion criteria, a total of 200 patients (100 patients of bronchial asthma and 100 patients of COPD) were included in the study. Functional GI symptom questionnaire [Annexure 1-Bowel Disease Questionnaire] is based on ROME III diagnostic criteria. On the basis of GOLD (Global Initiative for Obstructive Lung Disease) guidelines, COPD patients were divided into 4 categories (mild - GOLD 1, moderate - GOLD2, severe - GOLD3 and very severe - GOLD4). Asthma patients were divided into three categories (well controlled, partly controlled, uncontrolled) on the basis of GINA (Global Initiative for Asthma) guidelines.

Results

Highest percentage of patients with maximum GI symptoms was found in "GOLD-4" group among COPD patients and "uncontrolled" group among asthma patients. Highest percentage of patients with least GI symptoms was found in "GOLD-1" group among COPD patients and "well controlled" group among asthma patients.

Conclusion

We can conclude from our study that the phenomenon of gut-lung axis not only exists but also the severity of symptoms of one system (gut) carries a high degree of concordance with severity of other (lung).

Fungal Microbiota in Chronic Airway Inflammatory Disease and Emerging Relationships with the Host Immune Response

The respiratory tract is a complex system that is inhabited by niche-specific communities of microbes including bacteria, fungi, and viruses. These complex microbial assemblages are in constant contact with the mucosal immune system and play a critical role in airway health and immune homeostasis. Changes in the composition and diversity of airway microbiota are frequently observed in patients with chronic inflammatory diseases including chronic rhinosinusitis (CRS), cystic fibrosis, allergy, and asthma. While the bacterial microbiome of the upper and lower airways has been the focus of many recent studies, the contribution of fungal microbiota to inflammation is an emerging research interest. Within the context of allergic airway disease, fungal products are important allergens and fungi are potent inducers of inflammation. In addition, murine models have provided experimental evidence that fungal microbiota in peripheral organs, notably the gastrointestinal (GI) tract, influence pulmonary health. In this review, we explore the role of the respiratory and GI microbial communities in chronic airway inflammatory disease development with a specific focus on fungal microbiome interactions with the airway immune system and fungal-bacterial interactions that likely contribute to inflammatory disease. These findings are discussed in the context of clinical and immunological features of fungal-mediated disease in CRS, allergy, and asthmatic patients. While this field is still nascent, emerging evidence suggests that dysbiotic fungal and bacterial microbiota interact to drive or exacerbate chronic airway inflammatory disease.

The Fungal Mycobiota: Small Numbers, Large Impacts

Fungi are an underappreciated component of the human gut microbiota. In this issue of Cell Host & Microbe, Wheeler et al. (2016) demonstrate that fungal dysbiosis induced by antifungal treatment or inoculation with typically rare fungi results in exaggerated immune responses, suggesting that fungal colonizers play key roles in immune homeostasis.

Emerging evidence of the role of gut microbiota in the development of allergic diseases

PURPOSE OF REVIEW

The purpose is to review recent studies examining the role of gut microbiota in allergic diseases and asthma.

RECENT FINDINGS

Work in experimental models gives further evidence that a disturbed gut microbiota influences the propensity to develop allergic manifestations, and that changing the gut microbiota by dietary means (high fiber/acetate or prebiotics) in pregnancy may reduce the risk of allergic airways disease and food allergy in the offspring, respectively. The gut microbiome in established allergic disease and prior to disease onset has also been assessed in clinical trials. One study demonstrated a strong association between high abundance of Faecalibacterium prausnitzii and decreased levels of butyrate and propionate, and established eczema. Lower relative abundance of Ruminococcaceae appears to be implicated in food sensitization and to precede the development of atopic eczema. Decreased relative abundance of Lachnospira, Veillonella, Faecalibacterium, and Rothia in early infancy was reported to be associated with increased asthma risk. Inoculation of germ-free mice with these genera decreased airway inflammation in their offspring thereby proposing a causal role of bacteria in preventing allergic airways disease.

SUMMARY

Gut microbiome research is an actively developing field. Although candidate bacterial taxa have been reported it still remains unclear which bacteria (or other microbes), in which numbers and combinations, and when during the gut colonization process may prevent allergic diseases and asthma. There is still a call for standardized approaches that will enable direct comparison of different studies.

Oral Probiotics Alter Healthy Feline Respiratory Microbiota

Probiotics have been advocated as a novel therapeutic approach to respiratory disease, but knowledge of how oral administration of probiotics influences the respiratory microbiota is needed. Using 16S rRNA amplicon sequencing of bacterial DNA our objective was to determine whether oral probiotics changed the composition of the upper and lower airway, rectal, and blood microbiota. We hypothesized that oral probiotics would modulate the respiratory microbiota in healthy cats, demonstrated by the detection and/or increased relative abundance of the probiotic bacterial species and altered composition of the microbial population in the respiratory tract. Six healthy young research cats had oropharyngeal (OP), bronchoalveolar lavage fluid (BALF), rectal, and blood samples collected at baseline and 4 weeks after receiving oral probiotics. 16S rRNA gene amplicon libraries were sequenced, and coverage, richness, and relative abundance of representative operational taxonomic units (OTUs) were determined. Hierarchical and principal component analyses (PCA) demonstrated relatedness of samples. Mean microbial richness significantly increased only in the upper and lower airways. The number of probiotic OTUs (out of 5 total) that significantly increased in relative abundance vs. baseline was 5 in OP, 3 in BAL and 2 in feces. Using hierarchical clustering, BALF and blood samples grouped together after probiotic administration, and PERMANOVA supported that these two sites underwent significant changes in microbial composition. PERMANOVA revealed that OP and rectal samples had microbial population compositions that did not significantly change. These findings were visualized via PCA, which revealed distinct microbiomes in each site; samples clustered more tightly at baseline and had more variation after probiotic administration. This is the first study describing the effect of oral probiotics on the respiratory microbiota via detection of probiotic species in the airways. Finding bacterial species present in the oral probiotics in the upper and lower airways provides pilot data suggesting that oral probiotics could serve as a tool to target dysbiosis occurring in inflammatory airway diseases such as feline asthma, a disease in which cats serve as an important comparative and translational model for humans.

Toward precision medicine and health: Opportunities and challenges in allergic diseases

Precision medicine (also called personalized, stratified, or P4 medicine) can be defined as the tailoring of preventive measures and medical treatments to the characteristics of each patient to obtain the best clinical outcome for each person while ideally also enhancing the cost-effectiveness of such interventions for patients and society. Clearly, the best clinical outcome for allergic diseases is not to get them in the first place. To emphasize the importance of disease prevention, a critical component of precision medicine can be referred to as precision health, which is defined herein as the use of all available information pertaining to specific subjects (including family history, individual genetic and other biometric information, and exposures to risk factors for developing or exacerbating disease), as well as features of their environments, to sustain and enhance health and prevent the development of disease. In this article I will provide a personal perspective on how the precision health-precision medicine approach can be applied to the related goals of preventing the development of allergic disorders and providing the most effective diagnosis, disease monitoring, and care for those with these prevalent diseases. I will also mention some of the existing and potential challenges to achieving these ambitious goals.

Immune responses to fungal aeroallergen in Heligmosomoides polygyrus-infected mice vary by age

Parasite infections in the developing world have been considered to promote resistance to immune-mediated diseases such as asthma. Mouse studies have shown that helminths and their products reduce the development of allergic asthma. Since epidemiologic studies that show similar protection are in relation to geohelminth infections that occur in early life, we hypothesized that the parasite-mediated protection against asthma may differ by age. Mice infected with Heligmosomoides polygyrus at 3-weeks of age had similar asthma phenotype compared to mice infected at 28-weeks of age wherein airway eosinophilia was unaltered but tissue inflammation and GC metaplasia were reduced. In contrast, mice infected at 18-weeks of age had elevated macrophagic airway inflammation with accompanying tissue pathology. The presence of γδ T cells and T_reg cells in the airways was also regulated by age at worm infection. Our findings demonstrate the importance of age in immune responses that may regulate gut and lung diseases.

The Host Microbiome Regulates and Maintains Human Health: A Primer and Perspective for Non-Microbiologists

Humans consider themselves discrete autonomous organisms, but recent research is rapidly strengthening the appreciation that associated microorganisms make essential contributions to human health and well being. Each person is inhabited and also surrounded by his/her own signature microbial cloud. A low diversity of microorganisms is associated with a plethora of diseases, including allergy, diabetes, obesity, arthritis, inflammatory bowel diseases, and even neuropsychiatric disorders. Thus, an interaction of microorganisms with the host immune system is required for a healthy body. Exposure to microorganisms from the moment we are born and appropriate microbiome assembly during childhood are essential for establishing an active immune system necessary to prevent disease later in life. Exposure to microorganisms educates the immune system, induces adaptive immunity, and initiates memory B and T cells that are essential to combat various pathogens. The correct microbial-based education of immune cells may be critical in preventing the development of autoimmune diseases and cancer. This review provides a broad overview of the importance of the host microbiome and accumulating knowledge of how it regulates and maintains a healthy human system. Cancer Res; 77(8); 1783-812. ©2017 AACR.

Safety of Bifidobacterium animalis Subsp. Lactis (B. lactis) Strain BB-12-Supplemented Yogurt in Healthy Children

OBJECTIVES

Probiotics are live microorganisms that may provide health benefits to the individual when consumed in sufficient quantities. For studies conducted on health or disease endpoints on probiotics in the United States, the Food and Administration has required those studies to be conducted as investigational new drugs. This phase I, double-blinded, randomized, controlled safety study represents the first requirement of this pathway. The purpose of the study was to determine the safety of Bifidobacterium animalis subsp. lactis (B lactis) strain BB-12 (BB-12)-supplemented yogurt when consumed by a generally healthy group of children. The secondary aim was to assess the effect of BB-12-supplemented yogurt on the gut microbiota of the children.

METHODS

Sixty children ages 1 to 5 years were randomly assigned to consume 4 ounces of either BB-12-supplemented yogurt or nonsupplemented control yogurt daily for 10 days. The primary outcome was to assess safety and tolerability, as determined by the number of reported adverse events.

RESULTS

A total of 186 nonserious adverse events were reported, with no significant differences between the control and BB-12 groups. No significant changes due to probiotic treatment were observed in the gut microbiota of the study cohort.

CONCLUSIONS

BB-12-supplemented yogurt is safe and well-tolerated when consumed by healthy children. The present study will form the basis for future randomized clinical trials investigating the potential effects of BB-12-supplemented yogurt in different disease states.

Factors shaping the composition of the cutaneous microbiota

From birth, we are constantly exposed to bacteria, fungi and viruses, some of which are capable of transiently or permanently inhabiting our different body parts as our microbiota. The majority of our microbial interactions occur during and after birth, and several different factors, including age, sex, genetic constitution, environmental conditions and lifestyle, have been suggested to shape the composition of this microbial community. Propionibacterium acnes is one of the most dominant lipophilic microbes of the postadolescent, sebum-rich human skin regions. Currently, the role of this bacterium in the pathogenesis of the most common inflammatory skin disease, acne vulgaris, is a topic of intense scientific debate. Recent results suggest that Westernization strongly increases the dominance of the Propionibacterium genus in human skin compared with natural populations living more traditional lifestyles. According to the disappearing microbiota hypothesis proposed by Martin Blaser, such alterations in the composition of our microbiota are the possible consequences of socioeconomic and lifestyle changes occurring after the industrial revolution. Evanescence of species that are important elements of the human ecosystem might lead to the overgrowth and subsequent dominance of others because of the lack of ecological competition. Such changes can disturb the fine-tuned balance of the human body and, accordingly, our microbes developed through a long co-evolutionary process. These processes might lead to the transformation of a seemingly harmless species into an opportunistic pathogen through bacterial dysbiosis. This might have happened in the case of P. acnes in acne pathogenesis.

Lung-gut cross-talk: evidence, mechanisms and implications for the mucosal inflammatory diseases

The mucosal immune system (including airway, intestinal, oral and cervical epithelium) is an integrated network of tissues, cells and effector molecules that protect the host from environmental insults and infections at mucous membrane surfaces. Dysregulation of immunity at mucosal surfaces is thought to be responsible for the alarming global increase in mucosal inflammatory diseases such as those affecting the gastrointestinal (Crohn's disease, ulcerative colitis and irritable bowel syndrome) and respiratory (asthma, allergy and chronic obstructive pulmonary disorder) system. Although immune regulation has been well-studied in isolated mucosal sites, the extent of the immune interaction between anatomically distant mucosal sites has been mostly circumstantial and the focus of much debate. With novel technology and more precise tools to examine histological and functional changes in tissues, today there is increased appreciation of the 'common mucosal immunological system' originally proposed by Bienenstock nearly 40 years ago. Evidence is amounting which shows that stimulation of one mucosal compartment can directly and significantly impact distant mucosal site, however the mechanisms are unknown. Today, we are only beginning to understand the complexity of relationships and communications that exist between different mucosal compartments. A holistic approach to studying the mucosal immune system as an integrated global organ is imperative for future advances in understanding mucosal immunology and for future treatment of chronic diseases. In this review, we particularly focus on the latest evidence and the mechanisms operational in driving the lung-gut cross-talk.

'The Microbiome and the Pathophysiology of Asthma'

Asthma is a chronic respiratory disease whose prevalence is increasing in the western world. Recently research has begun to focus on the role the microbiome plays in asthma pathogenesis in the hope of further understanding this respiratory disorder. Considered sterile until recently, the lungs have revealed themselves to contain a unique microbiota. A shift towards molecular methods for the quantification and sequencing of microbial DNA has revealed that the airways harbour a unique microbiota with apparent, reproducible differences present between healthy and diseased lungs. There is a hope that in classifying the microbial load of the asthmatic airway an insight may be afforded as to the possible role pulmonary microbes may have in propagating an asthmatic airway response. This could potentially pave the way for new therapeutic strategies for the treatment of chronic lung conditions such as asthma.

Environmental Factors Associated with Altered Gut Microbiota in Children with Eczema: A Systematic Review

Eczema is a common skin condition that impairs children's daily life activities and quality of life. Previous research shows that gut microbiome composition plays an important role in the development of eczema. The present review summarizes evidence on environmental factors related to altered gut microbiota in children with eczema. We searched Medline, PubMed, Embase, and the Cochrane database of Systematic Reviews through October 2015. The search strategy focused on articles published in peer-reviewed, English-language journals with no publication year limit. Only original studies and review articles that reported environmental factors on gut microbiome specific to eczema were included in this review. We selected six studies (total 1990 participants) for full review and identified that the composition of gut microbiota specific to eczema could be influenced by the following environmental factors: length of gestation, mode of delivery, type of feeding, method of treatment, number of older siblings, and other lifestyle factors. There has been inconsistent empirical evidence as to the modulatory effects of gut microbiota on immunological functions in children with eczema. Further research on the environmental-host-microbial interaction is needed to develop a strong base of knowledge for the development and implementation of prevention strategies and policies for eczema.

A bug's view of allergic airways disease

The increase in allergic airways disease has been linked to modern urbanization and lifestyle. Recent evidence suggests that the associated reduction in microbial exposure, reduction in dietary fibre intake and increased antibiotic use may cause early dysbiosis in infancy, which predisposes to immune dysregulation and allergic airways disease later in life. This implies that there may be a window of opportunity for primary prevention strategies aimed to protect or restore the microbiome early in life and thereby decrease the risk of developing allergic airways disease. Alternatively, strategies that correct dysbiosis may aid in the treatment of established allergic airways disease.

Childhood allergies and asthma: New insights on environmental exposures and local immunity at the lung barrier

While certain bacteria and respiratory viruses promote local inflammation and disease onset, a more diverse colonization of the different species in the (gut) microbiome may be linked to more regulatory responses and protection against asthma and allergies. These processes are also influenced in part by food intake, both targeting the composition of the gut microbiome and influencing the immune system via metabolites. Early life environmental microbial exposure also contributes to protection against asthma and allergy and is linked with an early activation of the innate immune system and the development of regulatory immune responses. Although greater mechanistic insight is needed, it is tempting to speculate that part of the environmental effect can be explained by modulation of the microbiome composition at mucosal surfaces, epithelial barrier function and/or local immunity. A review of the latest studies is provided.

Immunological Consequences of Intestinal Fungal Dysbiosis

Compared to bacteria, the role of fungi within the intestinal microbiota is poorly understood. In this study we investigated whether the presence of a "healthy" fungal community in the gut is important for modulating immune function. Prolonged oral treatment of mice with antifungal drugs resulted in increased disease severity in acute and chronic models of colitis, and also exacerbated the development of allergic airway disease. Microbiota profiling revealed restructuring of fungal and bacterial communities. Specifically, representation of Candida spp. was reduced, while Aspergillus, Wallemia, and Epicoccum spp. were increased. Oral supplementation with a mixture of three fungi found to expand during antifungal treatment (Aspergillus amstelodami, Epicoccum nigrum, and Wallemia sebi) was sufficient to recapitulate the exacerbating effects of antifungal drugs on allergic airway disease. Taken together, these results indicate that disruption of commensal fungal populations can influence local and peripheral immune responses and enhance relevant disease states.

Antibiotic-Induced Changes in the Intestinal Microbiota and Disease

The gut microbiota is a key player in many physiological and pathological processes occurring in humans. Recent investigations suggest that the efficacy of some clinical approaches depends on the action of commensal bacteria. Antibiotics are invaluable weapons to fight infectious diseases. However, by altering the composition and functions of the microbiota, they can also produce long-lasting deleterious effects for the host. The emergence of multidrug-resistant pathogens raises concerns about the common, and at times inappropriate, use of antimicrobial agents. Here we review the most recently discovered connections between host pathophysiology, microbiota, and antibiotics highlighting technological platforms, mechanistic insights, and clinical strategies to enhance resistance to diseases by preserving the beneficial functions of the microbiota.

Diet, microbiota, and dysbiosis: a 'recipe' for colorectal cancer

The food we consume feeds not only us, but also a vast and diverse community of microbiota within our gastrointestinal tract. In a process of symbiotic co-evolution, the gut microbiota became essential for the maintenance of the health and integrity of our colon. The advent of next-generation DNA sequencing technology and metabolic profiling have, in the recent years, revealed the remarkable complexity of microbial diversity and function, and that the microbiota produce a wide variety of bioactive products that are not only active at the mucosal surface, but also absorbed and circulated throughout the body, influencing distant organ health and function. As a result, several microbiota compositional patterns and their associations with both health and disease states have been identified. Importantly, a disturbed microbiota-host relationship, termed dysbiosis, is now recognized to be the root cause for a growing list of diseases, including colorectal cancer (CRC). There is mounting in vitro and in vivo evidence to suggest that diet selects for the microbiota composition and several health promoting and deleterious effects of diet are, in fact, mediated by the microbiota. Recent findings of the feasibility of dietary fiber to boost the colonic microbial synthesis of anti-proliferative and counter carcinogenic metabolites, particularly butyrate, underscores the prerequisite of dietary modification as a key measure to curb the pandemic of CRC in westernized countries. Better understanding of the diet-microbiota interplay and large-scale studies to evaluate the efficacy of dietary modification and gut microbiota modulation in reversing dysbiosis and restoring health could offer novel preventative and/or therapeutic strategies against westernized diseases, which are now considered the chief threat to public health.