Infant gut microbiota and the hygiene hypothesis of allergic disease: impact of household pets and siblings on microbiota composition and diversity

The case in favour of probiotics before, during and after pregnancy: insights from the first 1,500 days

Successful human reproduction requires microbial homeostasis in the female reproductive tract, and colonisation of the newborn with beneficial microbes. In order to prevent several complications associated with dysbiosis, the administration of probiotics is more often being considered. The objective of the enclosed review was to examine the rationale for probiotic utility before and during pregnancy and in the early phase of infant life. The conclusions emerged from a panel of researchers who met during the International Scientific Association for Probiotics and Prebiotics (ISAPP) workshop held in Washington, DC, USA in 2015. The group concluded based upon the current literature, that a case can be made for the use of a specific sets of probiotic organisms during the first 1,500 days of life, with the goal of a healthy pregnancy to term, and a healthy start to life with lowered risk of infections and inflammatory events. The key to successfully translating these recommendations to practice is that products be made available and affordable to women in developed and developing countries.

Sources of airborne microorganisms in the built environment

Each day people are exposed to millions of bioaerosols, including whole microorganisms, which can have both beneficial and detrimental effects. The next chapter in understanding the airborne microbiome of the built environment is characterizing the various sources of airborne microorganisms and the relative contribution of each. We have identified the following eight major categories of sources of airborne bacteria, viruses, and fungi in the built environment: humans; pets; plants; plumbing systems; heating, ventilation, and air-conditioning systems; mold; dust resuspension; and the outdoor environment. Certain species are associated with certain sources, but the full potential of source characterization and source apportionment has not yet been realized. Ideally, future studies will quantify detailed emission rates of microorganisms from each source and will identify the relative contribution of each source to the indoor air microbiome. This information could then be used to probe fundamental relationships between specific sources and human health, to design interventions to improve building health and human health, or even to provide evidence for forensic investigations.

Gut Microbiome and the Development of Food Allergy and Allergic Disease

The impact of gut microbiome on human development, nutritional needs, and disease has become evident with advances in the ability to study these complex communities of microorganisms, and there is growing appreciation for the role of the microbiome in immune regulation. Several studies have examined associations between changes in the commensal microbiota and the development of asthma, allergic rhinitis, and asthma, but far less have evaluated the impact of the microbiome on the development of food allergy. This article reviews the human gastrointestinal microbiome, focusing on the theory and evidence for its role in the development of IgE-mediated food allergy and other allergic diseases.

The relationship between the season of birth and early-onset food allergies in children

BACKGROUND

This study examined the relationship between the season of birth (SoB) and other factors with the development of FA.

METHODS

A multicenter, cross-sectional pilot study recruited 1197 patients with FA. The main study recruited 440 incident cases (FA group) definitively diagnosed as FA at 0-1 year of age. In both studies, the frequency of autumn-winter births (AWBs) in FA patients was compared to the regional control population. In the main study, we analyzed the differences in the SoB and other factors between patients in the FA group and those in the non-FA group (n = 332) in allergy clinics.

RESULTS

The pilot study showed that the frequency of AWB (57.6%) in the FA patients was significantly higher than that of the regional control population (50.4%, OR, 1.34; p < 0.001). The main study also showed the dominance of AWB (62.7%) in the FA group in comparison with that in the regional control population (50.2%, OR, 1.70; p < 0.001). Preterm birth (OR, 0.43; p = 0.027) and the presence of two or more elder siblings (OR, 0.27; p = 0.012) were significantly associated with a lower frequency of FA than those of non-FA. AWB (RR, 1.21; p = 0.020) and preterm birth (RR, 0.55; p = 0.017) were significantly associated with a number of trigger foods. The SoB effect was observed in FA patients irrespective of the presence of infantile eczema.

CONCLUSIONS

AWB was predominant in the patients with newly diagnosed food allergies.

Microbial influences on hormesis, oncogenesis, and therapy: A review of the literature

Utilization of environmental stimuli for growth is the main factor contributing to the evolution of prokaryotes and eukaryotes, independently and mutualistically. Epigenetics describes an organism's ability to vary expression of certain genes based on their environmental stimuli. The diverse degree of dose-dependent responses based on their variances in expressed genetic profiles makes it difficult to ascertain whether hormesis or oncogenesis has or is occurring. In the medical field this is shown where survival curves used in determining radiotherapeutic doses have substantial uncertainties, some as large as 50% (Barendsen, 1990). Many in-vitro radiobiological studies have been limited by not taking into consideration the innate presence of microbes in biological systems, which have either grown symbiotically or pathogenically. Present in-vitro studies neglect to take into consideration the varied responses that commensal and opportunistic pathogens will have when exposed to the same stimuli and how such responses could act as stimuli for their macro/microenvironment. As a result many theories such as radiation carcinogenesis explain microscopic events but fail to describe macroscopic events (Cohen, 1995). As such, this review shows how microorganisms have the ability to perturb risks of cancer and enhance hormesis after irradiation. It will also look at bacterial significance in the microenvironment of the tumor before and during treatment. In addition, bacterial systemic communication after irradiation and the host's immune responses to infection could explain many of the phenomena associated with bystander effects. Therefore, the present literature review considers the paradigms of hormesis and oncogenesis in order to find a rationale that ties them all together. This relationship was thus characterized to be the microbiome.

Microbiomes: unifying animal and plant systems through the lens of community ecology theory

The field of microbiome research is arguably one of the fastest growing in biology. Bacteria feature prominently in studies on animal health, but fungi appear to be the more prominent functional symbionts for plants. Despite the similarities in the ecological organization and evolutionary importance of animal-bacterial and plant-fungal microbiomes, there is a general failure across disciplines to integrate the advances made in each system. Researchers studying bacterial symbionts in animals benefit from greater access to efficient sequencing pipelines and taxonomic reference databases, perhaps due to high medical and veterinary interest. However, researchers studying plant-fungal symbionts benefit from the relative tractability of fungi under laboratory conditions and ease of cultivation. Thus each system has strengths to offer, but both suffer from the lack of a common conceptual framework. We argue that community ecology best illuminates complex species interactions across space and time. In this synthesis we compare and contrast the animal-bacterial and plant-fungal microbiomes using six core theories in community ecology (i.e., succession, community assembly, metacommunities, multi-trophic interactions, disturbance, restoration). The examples and questions raised are meant to spark discussion amongst biologists and lead to the integration of these two systems, as well as more informative, manipulatory experiments on microbiomes research.

Identification of early environmental risk factors for irritable bowel syndrome and dyspepsia

BACKGROUND

The role of childhood environment including exposure to infection via siblings and pets in irritable bowel syndrome (IBS) and dyspepsia is relatively unknown. We assessed proxy measures of microbial exposure in early childhood to assess if these are associated with IBS and functional dyspepsia in later life.

METHODS

Participants (n = 767, response rate = 53%) were a random population sample from Sydney, Australia who previously responded to a validated survey. IBS and functional dyspepsia were defined using Rome III criteria. Early environmental risk factors assessed included type of birth delivery, premature birth, breastfeeding, bedroom sharing, and pet exposure (the latter two then combined as early hygiene factors) up to 5 years of age. Post infectious IBS (PI-IBS) was assessed by development of IBS following gastroenteritis.

KEY RESULTS

In this sample, in adult life 17% developed IBS (of which 20% had PI-IBS) and 12% functional dyspepsia. Development of IBS was associated with childhood factors-a shorter duration of breastfeeding (odds ratios [OR] = 0.87, 95% CI: 0.78-0.97, p = 0.01), sharing a bedroom (OR = 1.89, 95% CI: 1.73-3.08, p = 0.01), exposure to a herbivore pet (OR = 1.65 (1.10, 2.48), p = 0.02), and hygiene factors (OR = 4.39; 95% CI: 1.89-10.21, p = 0.001). The sole factor associated with functional dyspepsia was exposure to a herbivore pet (1.79; 95% CI: 1.19-2.87, p = 0.02).

CONCLUSIONS & INFERENCES

Childhood environment factors, particularly bedroom sharing and pet exposure, combined with subsequent risk of microbial exposure are a risk factor for IBS in later life. These associations however need confirmation to rule out any risk of a type I error.

Having older siblings is associated with gut microbiota development during early childhood

Background

Evidence suggests that early life infections, presence of older siblings and furred pets in the household affect the risk of developing allergic diseases through altered microbial exposure. Recently, low gut microbial diversity during infancy has also been linked with later development of allergies. We investigated whether presence of older siblings, furred pets and early life infections affected gut microbial communities at 9 and 18 months of age and whether these differences were associated with the cumulative prevalence of atopic symptoms of eczema and asthmatic bronchitis at 3 years of age. Bacterial compositions and diversity indices were determined in fecal samples collected from 114 infants in the SKOT I cohort at age 9 and 18 months by 16S rRNA gene sequencing. These were compared to the presence of older siblings, furred pets and early life infections and the cumulative prevalence of diagnosed asthmatic bronchitis and self-reported eczema at 3 years of age.

Results

The number of older siblings correlated positively with bacterial diversity (p = 0.030), diversity of the phyla Firmicutes (p = 0.013) and Bacteroidetes (p = 0.004) and bacterial richness (p = 0.006) at 18 months. Further, having older siblings was associated with increased relative abundance of several bacterial taxa at both 9 and 18 months of age. Compared to the effect of having siblings, presence of household furred pets and early life infections had less pronounced effects on the gut microbiota. Gut microbiota characteristics were not significantly associated with cumulative occurrence of eczema and asthmatic bronchitis during the first 3 years of life.

Conclusions

Presence of older siblings is associated with increased gut microbial diversity and richness during early childhood, which could contribute to the substantiation of the hygiene hypothesis. However, no associations were found between gut microbiota and atopic symptoms of eczema and asthmatic bronchitis during early childhood and thus further studies are required to elucidate whether sibling-associated gut microbial changes influence development of allergies later in childhood.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-015-0477-6) contains supplementary material, which is available to authorized users.

Prevalence of oral Candida in the first year of life

Colonisation of the gastrointestinal tract is influenced by primary microbial exposure and bioactive factors in breastmilk. The aim was to explore the prevalence of oral Candida in the first year of life in relation to selected exposures. Oral Candida was studied in 100 healthy infants at 4 and 8 weeks, 3, 6 and 12 months of age and related to delivery mode, birth weight, infant health and feeding, antibiotics, antimycotics, steroids and probiotics in mother and infant, living conditions, maternal smoking and infections The association between lactoferrin and antisecretory factor in breastmilk and maternal serum haemoglobin, transferrin, and ferritin levels in relation to oral Candida was also explored. About 11% to 15% of the infants had oral Candida at the respective age. Colonisation was fairly stable until 6 months of age. There was no conclusive impact of the investigated exposures at entry. Infants with a furry pet at home had a lower frequency of Candida at 3 months, (P < 0.05) whereas all but one colonised infant had older siblings at 12 months (P < 0.01). Lactoferrin in breastmilk was negatively associated with colonisation at 6 months of age. It is concluded that 11 to 15% had oral Candida. Exposure to furry pets and siblings impacted oral Candida.

Metagenomic surveys of gut microbiota

Gut microbiota of higher vertebrates is host-specific. The number and diversity of the organisms residing within the gut ecosystem are defined by physiological and environmental factors, such as host genotype, habitat, and diet. Recently, culture-independent sequencing techniques have added a new dimension to the study of gut microbiota and the challenge to analyze the large volume of sequencing data is increasingly addressed by the development of novel computational tools and methods. Interestingly, gut microbiota maintains a constant relative abundance at operational taxonomic unit (OTU) levels and altered bacterial abundance has been associated with complex diseases such as symptomatic atherosclerosis, type 2 diabetes, obesity, and colorectal cancer. Therefore, the study of gut microbial population has emerged as an important field of research in order to ultimately achieve better health. In addition, there is a spontaneous, non-linear, and dynamic interaction among different bacterial species residing in the gut. Thus, predicting the influence of perturbed microbe–microbe interaction network on health can aid in developing novel therapeutics. Here, we summarize the population abundance of gut microbiota and its variation in different clinical states, computational tools available to analyze the pyrosequencing data, and gut microbe–microbe interaction networks.

Gut microbiota and the development of pediatric diseases

The human gut harbors a huge number of microbes, which are collectively named "microbiota." The dynamic composition of the human gut microbiota is determined by multiple factors, including mode of delivery, diet, environment, and antibiotics. A healthy gut microbiota is helpful to the host in many aspects, including providing nutrients, protection from pathogens, and maturation of immune responses. Dysbiosis plays important roles in various diseases in infancy and later life: necrotizing enterocolitis, inflammatory bowel disease, obesity, and atopic diseases are some examples. Studies of functional metagenomics by newly developed techniques, such as next-generation sequencing, will not only elucidate the molecular mechanisms underlying gut microbiota-host interactions but will also provide new possibilities for disease prevention and treatment.

Pyrosequencing analysis reveals changes in intestinal microbiota of healthy adults who received a daily dose of immunomodulatory probiotic strains

The colon microbiota plays a crucial role in human gastrointestinal health. Current attempts to manipulate the colon microbiota composition are aimed at finding remedies for various diseases. We have recently described the immunomodulatory effects of three probiotic strains (Lactobacillus rhamnosus CNCM I-4036, Lactobacillus paracasei CNCM I-4034, and Bifidobacterium breve CNCM I-4035). The goal of the present study was to analyze the compositions of the fecal microbiota of healthy adults who received one of these strains using high-throughput 16S ribosomal RNA gene sequencing. Bacteroides was the most abundant genus in the groups that received L. rhamnosus CNCM I-4036 or L. paracasei CNCM I-4034. The Shannon indices were significantly increased in these two groups. Our results also revealed a significant increase in the Lactobacillus genus after the intervention with L. rhamnosus CNCM I-4036. The initially different colon microbiota became homogeneous in the subjects who received L. rhamnosus CNCM I-4036. While some orders that were initially present disappeared after the administration of L. rhamnosus CNCM I-4036, other orders, such as Sphingobacteriales, Nitrospirales, Desulfobacterales, Thiotrichales, and Synergistetes, were detected after the intervention. In summary, our results show that the intake of these three bacterial strains induced changes in the colon microbiota.

The evolution of the hygiene hypothesis: the role of early-life exposures to viruses and microbes and their relationship to asthma and allergic diseases

PURPOSE OF REVIEW

Understanding the mechanisms involved in the development of asthma and allergic diseases is expanding, due in part to sequencing advances that have led to the identification of new viral strains such as human rhinovirus strain C (HRV-C) and the human microbiome project.

RECENT FINDINGS

Recent studies have identified new ways in which viral and microbial exposures in early life interact with host genetic background/variants to modify the risk for developing asthma and allergic diseases. Recent research suggests that HRV-C is the main pathogenic agent associated with infant wheeze, hospitalizations and likely the subsequent development of asthma. Pulmonary He MRI suggests that HRV infection in early childhood and subsequent immune responses initiate airway remodeling. Numerous studies of the microbiome indicate that intestinal and airway microbiome diversity and composition contribute to the cause of asthma and allergic diseases.

SUMMARY

Susceptibility to asthma and allergic diseases is complex and involves genetic variants and environmental exposures (bacteria, viruses, smoking, and pet ownership), alteration of our microbiome and potentially large-scale manipulation of the environment over the past century.

Unraveling the Hygiene Hypothesis of helminthes and autoimmunity: origins, pathophysiology, and clinical applications

BACKGROUND

The Hygiene Hypothesis (HH) attributes the dramatic increase in autoimmune and allergic diseases observed in recent decades in Western countries to the reduced exposure to diverse immunoregulatory infectious agents. This theory has since largely been supported by strong epidemiological and experimental evidence.

DISCUSSION

The analysis of these data along with the evolution of the Western world's microbiome enable us to obtain greater insight into microorganisms involved in the HH, as well as their regulatory mechanisms on the immune system. Helminthes and their derivatives were shown to have a protective role. Helminthes' broad immunomodulatory properties have already begun to be exploited in clinical trials of autoimmune diseases, including inflammatory bowel disease, multiple sclerosis, rheumatoid arthritis, and type-1 diabetes.

SUMMARY

In this review, we will dissect the microbial actors thought to be involved in the HH as well as their immunomodulatory mechanisms as emphasized by experimental studies, with a particular attention on parasites. Thereafter, we will review the early clinical trials using helminthes' derivatives focusing on autoimmune diseases.

The gastrointestinal microbiota and colorectal cancer

The human gut is home to a complex and diverse microbiota that contributes to the overall homeostasis of the host. Increasingly, the intestinal microbiota is recognized as an important player in human illness such as colorectal cancer (CRC), inflammatory bowel diseases, and obesity. CRC in itself is one of the major causes of cancer mortality in the Western world. The mechanisms by which bacteria contribute to CRC are complex and not fully understood, but increasing evidence suggests a link between the intestinal microbiota and CRC as well as diet and inflammation, which are believed to play a role in carcinogenesis. It is thought that the gut microbiota interact with dietary factors to promote chronic inflammation and CRC through direct influence on host cell physiology, cellular homeostasis, energy regulation, and/or metabolism of xenobiotics. This review provides an overview on the role of commensal gut microbiota in the development of human CRC and explores its association with diet and inflammation.

Factors associated with atopy in toddlers: a case-control study

In this case-control study the association between the approaches used to feed infants, together with known family and environmental factors, and the occurrence of atopic illness in toddlers between the ages of 4 months to 3 years in Hong Kong was examined. A total of 206 subjects were recruited from April to June of 2014. The results obtained by binary logistic regression indicated that atopy is associated with boys (OR 2.072, CI 1.089-3.941), the maternal use of antibiotics in utero or while breast feeding (OR 2.276, CI 1.151-4.504), the later commencement of mixed feeding (OR 2.497, CI 1.025-6.082), breast feeding exclusively for 3 months (OR 1.972, CI 1.009-3.857), and having a mother who was diagnosed with eczema (OR 4.510, CI 1.764-11.530). Although an exclusive reliance on breast feeding has been shown to be predictive of atopy among toddlers, the positive qualities of breast milk cannot be ignored. A further study of the contents and nutritional values of breast milk is warranted.

Early-life risk factors for chronic nonrespiratory diseases

We have witnessed a change in disease patterns contributing to the global burden of disease, with a shift from early childhood deaths due to the classic infectious communicable diseases to years lived with disability from chronic noncommunicable diseases. In both developing and developed countries, the years lived with disability attributable to chronic disease have increased: cardiovascular diseases by 17.7%; chronic respiratory disease by 8.5%; neurological conditions by 12.2%; diabetes by 30.0%; and mental and behavioural disorders by 5.0% over the past 20 years. Recognition of the contribution made by adverse environmental exposures in early life to noncommunicable diseases in later life is increasing. These early-life exposures appear to contribute to both chronic respiratory and chronic nonrespiratory diseases. In this State of the Art article, we aim to examine early-life environmental exposures that have an epidemiological association with chronic nonrespiratory diseases, such as obesity and type II diabetes, cardiovascular disease, and neurocognitive and behavioural problems. We will highlight the potential overlap in environmental risks with respiratory diseases, and point out knowledge gaps and research opportunities.

Modulation of fecal Clostridiales bacteria and butyrate by probiotic intervention with Lactobacillus paracasei DG varies among healthy adults

BACKGROUND

The modulation of gut microbiota is considered to be the first target to establish probiotic efficacy in a healthy population.

OBJECTIVE

This study was conducted to determine the impact of a probiotic on the intestinal microbial ecology of healthy volunteers.

METHODS

High-throughput 16S ribosomal RNA gene sequencing was used to characterize the fecal microbiota in healthy adults (23-55 y old) of both sexes, before and after 4 wk of daily consumption of a capsule containing at least 24 billion viable Lactobacillus paracasei DG cells, according to a randomized, double-blind, crossover placebo-controlled design.

RESULTS

Probiotic intake induced an increase in Proteobacteria (P = 0.006) and in the Clostridiales genus Coprococcus (P = 0.009), whereas the Clostridiales genus Blautia (P = 0.036) was decreased; a trend of reduction was also observed for Anaerostipes (P = 0.05) and Clostridium (P = 0.06). We also found that the probiotic effect depended on the initial butyrate concentration. In fact, participants with butyrate >100 mmol/kg of wet feces had a mean butyrate reduction of 49 ± 21% and a concomitant decrease in the sum of 6 Clostridiales genera, namely Faecalibacterium, Blautia, Anaerostipes, Pseudobutyrivibrio, Clostridium, and Butyrivibrio (P = 0.021), after the probiotic intervention. In contrast, in participants with initial butyrate concentrations <25 mmol/kg of wet feces, the probiotic contributed to a 329 ± 255% (mean ± SD) increment in butyrate concomitantly with an ∼55% decrease in Ruminococcus (P = 0.016) and a 150% increase in an abundantly represented unclassified Bacteroidales genus (P = 0.05).

CONCLUSIONS

The intake of L. paracasei DG increased the Blautia:Coprococcus ratio, which, according to the literature, can potentially confer a health benefit on the host. The probiotic impact on the microbiota and on short-chain fatty acids, however, seems to strictly depend on the initial characteristics of the intestinal microbial ecosystem. In particular, fecal butyrate concentrations could represent an important biomarker for identifying subjects who may benefit from probiotic treatment. This trial was registered at www.controlled-trials.com/isrctn as ISRCTN56945491.

Reprint of: Perinatal and early childhood environmental factors influencing allergic asthma immunopathogenesis

BACKGROUND

The prevalence of asthma has increased dramatically over the past several decades. While hereditary factors are highly important, the rapid rise outstrips the pace of genomic variation. Great emphasis has been placed on potential modifiable early life exposures leading to childhood asthma.

METHODS

We reviewed the recent medical literature for important studies discussing the role of the perinatal and early childhood exposures and the inception of childhood asthma.

RESULTS AND DISCUSSION

Early life exposure to allergens (house dust mite (HDM), furred pets, cockroach, rodent and mold), air pollution (nitrogen dioxide (NO2), ozone (O3), volatile organic compounds (VOCs), and particulate matter (PM)) and viral respiratory tract infections (Respiratory syncytial virus (RSV) and human rhinovirus (hRV)) has been implicated in the development of asthma in high risk children. Conversely, exposure to microbial diversity in the perinatal period may diminish the development of atopy and asthma symptoms.

Prevention of asthma: where are we in the 21st century?

Asthma is the most common chronic disease of childhood and, in the latter part of the 20th century, reached epidemic proportions. Asthma is generally believed to result from gene-environment interactions. There is consensus that a 'window of opportunity' exists during pregnancy and early in life when environmental factors may influence its development. We review multiple environmental, biologic and sociologic factors that may be important in the development of asthma. Meta-analyses of studies have demonstrated that multifaceted interventions are required in order to develop asthma prevention. Multifaceted allergen reduction studies have shown clinical benefits. Asthma represents a dysfunctional interaction with our genes and the environment to which they are exposed, especially in fetal and early infant life. The increasing prevalence of asthma also may be an indication of increased population risk for the development of other chronic non-communicable autoimmune diseases. This review will focus on the factors which may be important in the primary prevention of asthma. Better understanding of the complex gene-environment interactions involved in the development of asthma will provide insight into personalized interventions for asthma prevention.

Perinatal and early childhood environmental factors influencing allergic asthma immunopathogenesis

BACKGROUND

The prevalence of asthma has increased dramatically over the past several decades. While hereditary factors are highly important, the rapid rise outstrips the pace of genomic variation. Great emphasis has been placed on potential modifiable early life exposures leading to childhood asthma.

METHODS

We reviewed the recent medical literature for important studies discussing the role of the perinatal and early childhood exposures and the inception of childhood asthma.

RESULTS AND DISCUSSION

Early life exposure to allergens (house dust mite (HDM), furred pets, cockroach, rodent and mold), air pollution (nitrogen dioxide (NO(2)), ozone (O(3)), volatile organic compounds (VOCs), and particulate matter (PM)) and viral respiratory tract infections (Respiratory syncytial virus (RSV) and human rhinovirus (hRV)) has been implicated in the development of asthma in high risk children. Conversely, exposure to microbial diversity in the perinatal period may diminish the development of atopy and asthma symptoms.

Associations between bacterial communities of house dust and infant gut

The human gut is host to a diverse and abundant community of bacteria that influence health and disease susceptibility. This community develops in infancy, and its composition is strongly influenced by environmental factors, notably perinatal anthropogenic exposures such as delivery mode (Cesarean vs. vaginal) and feeding method (breast vs. formula); however, the built environment as a possible source of exposure has not been considered. Here we report on a preliminary investigation of the associations between bacteria in house dust and the nascent fecal microbiota from 20 subjects from the Canadian Healthy Infant Longitudinal Development (CHILD) Study using high-throughput sequence analysis of portions of the 16S rRNA gene. Despite significant differences between the dust and fecal microbiota revealed by Nonmetric Multidimensional Scaling (NMDS) analysis, permutation analysis confirmed that 14 bacterial OTUs representing the classes Actinobacteria (3), Bacilli (3), Clostridia (6) and Gammaproteobacteria (2) co-occurred at a significantly higher frequency in matched dust-stool pairs than in randomly permuted pairs, indicating an association between these dust and stool communities. These associations could indicate a role for the indoor environment in shaping the nascent gut microbiota, but future studies will be needed to confirm that our findings do not solely reflect a reverse pathway. Although pet ownership was strongly associated with the presence of certain genera in the dust for dogs (Agrococcus, Carnobacterium, Exiguobacterium, Herbaspirillum, Leifsonia and Neisseria) and cats (Escherichia), no clear patterns were observed in the NMDS-resolved stool community profiles as a function of pet ownership.

Gut microbiota and allergic disease: new findings

PURPOSE OF REVIEW

Disturbed gut colonization patterns are proposed to be associated with the development of allergic disease.

RECENT FINDINGS

Studies using new systems biology methods confirm previous findings that early environmental exposures, for example cesarean delivery, are associated with disturbed gut colonization patterns and reduced microbial diversity. Low microbial diversity in infancy is also observed to precede onset of allergic disease. In a large population-based cohort study, probiotic consumption in pregnancy was associated with reduced risk of eczema and rhinoconjunctivitis in the child, but not asthma. The association between probiotics and rhinoconjunctivitis appeared stronger if both mother and child (from 6 months) consumed probiotics. Follow-up data from primary prevention studies with probiotics do not support a role for probiotics in asthma prevention. In meta-analyses, both prebiotics (high-risk infants only) and probiotics modestly reduce the eczema risk, but no other allergic manifestations. Their use is not generally recommended for prevention, or treatment, of allergic disease.

SUMMARY

Gut microbial patterns are associated with susceptibility to allergic disease, but the incomplete understanding of what constitutes a healthy gut microbiota that promotes tolerance, remains a challenge. Further understanding of gut microbial functions may pave the way for more effective allergy prevention and treatment strategies.

New insights into the hygiene hypothesis in allergic diseases: mediation of sibling and birth mode effects by the gut microbiota

There is convincing evidence from both human and animal studies suggesting that the infant intestinal microbiota plays an important role in regulating immune responses associated with the development of allergic diseases. To date there are, however, still no definite bacterial taxa or particular subsets of the microbiota that have been consistently associated with allergic diseases, which is mainly attributable to the methodological dissimilarities between studies. As such there is a need to apply different methodological concepts to enhance a deeper and more refined understanding of the relationship between the gut microbiota and allergies. Within our recent studies we reported that colonization by clostridia in early infancy increased the risk of atopic dermatitis. Using subsequent mediation analysis, we demonstrated that birth mode and having older siblings strongly impacted the infant microbiota which in turn affected the risk of atopic dermatitis. The results of these mediation analyses contributed stronger evidence for a causal link of birth mode and birth order on allergy risk through modulation of the microbiota composition.

The relationship between advances in understanding the microbiome and the maturing hygiene hypothesis

Expanding knowledge about an interaction of the bacterial colonization with pathogenic and non-pathogenic bacteria and the human immune system leads to speculation on potential effects on health and disease. Recent advances in sequencing technologies and new bioinformatic possibilities now allow investigating the microbes that colonize the human gut, skin and airways in more detail. In light of the hygiene hypothesis, the impact of the microbial composition of individuals with allergic sensitization and/or atopic diseases, i.e., allergic asthma or atopic eczema, were investigated in several clinical trials. Altered diversity of gut microbiota during infancy as well as colonization with specific pathogenic and apathogenic bacteria has been linked with an elevated risk for allergy. There are ongoing attempts to establish intervention strategies aimed at modifying initial colonization patterns in early life. While results from animal models, in-vitro data and epidemiological studies encourage the concept of a relationship between the microbiome and the development of allergic diseases, the transfer of these findings to intervention strategies still seems to be a major challenge.

Prenatal dog-keeping practices vary by race: speculations on implications for disparities in childhood health and disease

OBJECTIVE

There is consistent evidence demonstrating that pet-keeping, particularly of dogs, is beneficial to human health. We explored relationships between maternal race and prenatal dog-keeping, accounting for measures of socioeconomic status that could affect the choice of owning a pet, in a demographically diverse, unselected birth cohort.

DESIGN

Self-reported data on mothers' race, socioeconomic characteristics and dog-keeping practices were obtained during prenatal interviews and analyzed cross-sectionally. Robust methods of covariate balancing via propensity score analysis were utilized to examine if race (Black vs White), independent of other participant traits, influenced prenatal dog-keeping.

SETTING

A birth cohort study conducted in a health care system in metropolitan Detroit, Michigan between September 2003 and November 2007.

PARTICIPANTS

1065 pregnant women (n=775 or 72.8% Black), between ages 21 and 45, receiving prenatal care.

MAIN OUTCOME MEASURES

Participant's self-report of race/ethnicity and prenatal dog-keeping, which was defined as her owning or caring for > or =1 dog for more than 1 week at her home since learning of her pregnancy, regardless of whether the dog was kept inside or outside of her home.

RESULTS

In total, 294 women (27.6%) reported prenatal dog-keeping. Prenatal dog-keeping was significantly lower among Black women as compared to White women (20.9% vs 45.5%, P<.001), and remained significantly different even after propensity score analysis was applied.

CONCLUSION

Findings suggest that there are persistent racial differences in dog-keeping not fully explained by measures of socioeconomic status. Racial differences in prenatal dog-keeping may contribute to childhood health disparities.

Food allergy diagnosis and therapy: where are we now?

Food allergy is a growing worldwide epidemic that adversely effects up to 10% of the population. Causes and risk factors remain unclear and diagnostic methods are imprecise. There is currently no accepted treatment for food allergy. Therefore, there is an imminent need for greater understanding of food allergies, revised diagnostics and development of safe, effective therapies. Oral immunotherapy provides a particularly promising avenue, but is still highly experimental and not ready for clinical use.