Cesarean section changes neonatal gut colonization

Pathogens, microbiome and the host: emergence of the ecological Koch's postulates

Even though tremendous progress has been made in the last decades to elucidate the mechanisms of intestinal homeostasis, dysbiosis and disease, we are only at the beginning of understanding the complexity of the gut ecosystem and the underlying interaction networks. We are also only starting to unravel the mechanisms that pathogens have evolved to overcome the barriers imposed by the microbiota and host to exploit the system to their own benefit. Recent work in these domains clearly indicates that the 'traditional Koch's postulates', which state that a given pathogen leads to a distinct disease, are not valid for all 'infectious' diseases, but that a more complete and complex interpretation of Koch's postulates is needed in order to understand and explain them. This review summarises the current understanding of what defines a healthy gut ecosystem and highlights recent progress in uncovering the interplay between the host, its microbiota and invading intestinal pathogens. Based on these recent findings, we propose a new interpretation of Koch's postulates that we term 'ecological Koch's postulates'.

Caesarean delivery, childhood asthma, and effect modification by sex: An observational study and meta-analysis

BACKGROUND

Numerous studies indicate caesarean delivery is associated with childhood asthma. Sex-specific associations were reported in four of these studies, and in all four studies, the estimated association between caesarean delivery and asthma was of greater magnitude among girls, although most report a lack of evidence of multiplicative interaction.

METHODS

We assessed potential effect modification by sex, on the additive and multiplicative scales, of the association between caesarean delivery and asthma by ages 2 through 6 in up to 17 075 racially diverse children from a retrospective birth cohort, the Kaiser Air Pollution and Pediatric Asthma (KAPPA) Study. We also conducted a random-effects meta-analysis, combining our sex-stratified results (using the odds ratio for compatibility with previous studies) with previously published results.

RESULTS

Adjusted risk differences for caesarean delivery and asthma in the KAPPA cohort were higher among girls than boys at every follow-up age. By age 5, caesarean delivery was associated with an absolute 3.8% (95% confidence interval [CI] 0.4%, 7.3%) higher asthma risk among girls and a 1.9% (95% CI -1.7, 5.4) higher risk among boys. The summary odds ratio from the meta-analysis for caesarean delivery and asthma among girls was 1.26 (95% CI 1.14, 1.39) and 1.08 (95% CI 0.98, 1.20) among boys (P = 0.036).

CONCLUSIONS

Higher, but imprecise, estimates for females across five studies should motivate investigators to estimate sex-specific associations for caesarean delivery and asthma and to explore biological mechanisms or sex-dependent biases that could explain this possible heterogeneity.

The gut microbiome: Relationships with disease and opportunities for therapy

This review provides an overview of the influence of the gut microbiome on host health with a focus on immunomodulation and discusses strategies for manipulating the gut microbiome for the management or prevention of chronic inflammatory conditions.

Over the past decade, our view of human-associated microbes has expanded beyond that of a few species toward an appreciation of the diverse and niche-specialized microbial communities that develop in the human host with chronological age. The largest reservoir of microbes exists in the distal gastrointestinal tract, both in the lumen, where microbes facilitate primary and secondary metabolism, and on mucosal surfaces, where they interact with host immune cell populations. While local microbial-driven immunomodulation in the gut is well described, more recent studies have demonstrated a role for the gut microbiome in influencing remote organs and mucosal and hematopoietic immune function. Unsurprisingly, therefore, perturbation to the composition and function of the gut microbiota has been associated with chronic diseases ranging from gastrointestinal inflammatory and metabolic conditions to neurological, cardiovascular, and respiratory illnesses. Considerable effort is currently focused on understanding the natural history of microbiome development in humans in the context of health outcomes, in parallel with improving our knowledge of microbiome–host molecular interactions. These efforts ultimately aim to develop effective approaches to rehabilitate perturbed human microbial ecosystems as a means to restore health or prevent disease. This review details the role of the gut microbiome in modulating host health with a focus on immunomodulation and discusses strategies for manipulating the gut microbiome for the management or prevention of chronic inflammatory conditions.

Lifestyle Factors Affecting the Gut Microbiota's Relationship with Type 1 Diabetes

PURPOSE OF REVIEW

The incidence of type 1 diabetes (T1D) is rising drastically for the past decades at a rate that cannot be explained by genetic changes alone. Environmental changes are considered to be the main drivers of this change. Recently, the gut microbiota has been suggested as a missing link between known environmental disease modulators and T1D promotion. Lifestyle factors have changed over time and have altered the gut microbiota-host interaction affecting T1D development. The purpose of this review is to discuss recent data emphasizing the modulatory potential of early lifestyle factors on gut microbiota and to elucidate their implication for T1D.

RECENT FINDINGS

Recent findings show that lifestyle factors, especially those that affect the early establishment of gut homeostasis and the education of the immune system, are crucial disease modulators. Changing lifestyle factors affecting the early establishment of gut homeostasis are suggested to be key drivers of the rising T1D incidence.

The effect of selected risk factors, including the mode of delivery, on the development of allergic rhinitis and bronchial asthma

Introduction

Cesarean section affects the process of colonization by bacteria transferred from the mother’s skin and hospital bacteria, which in turn contributes to development of allergic conditions.

Aim

To assess selected risk factors, including the mode of delivery, parity, and the role of genetic factors for the development of allergic rhinitis and bronchial asthma.

Material and methods

The study was conducted in 18,617 respondents aged 6–7, 13–14, and 20–44 years who completed the ECRHS II and ISSAC questionnaires. Thirty percent of the study population underwent complementary assessments in the form of skin-prick tests, serum IgE levels, lung function tests, and peak nasal inspiratory flow (PNIF). The study is a part of the Epidemiology of Allergic Disorders in Poland (ECAP) study conducted in 8 areas in Poland (Warsaw, Lublin, Bialystok, Gdansk, Poznan, Wroclaw, Katowice, Krakow, and two rural areas – Zamosc and Krasnystaw counties).

Results

Respondents diagnosed with allergic rhinitis were at a significantly higher risk of inheriting the allergic condition if their mother (OR = 2.17; 95% CI: 1.98–2.39, p = 2.00 × 10^–16) or father (OR = 2.20; 95% CI: 1.96–2.47; p = 2.00 × 10^–16) suffers from this allergy. Conversely, in the group diagnosed with bronchial asthma, the highest risk of an inherited allergy was observed in situations where maternal (OR = 2.00; 95% CI: 1.57–2.55; p = 1.69 × 10^–5) or paternal (OR = 1.94; 95% CI: 1.42–2.66; p = 3.61 × 10^–5) grandparent was affected. Moreover, the risk of developing allergic rhinitis depended on the mode of delivery: i.e. it was higher for a Cesarean section (OR = 1.20; 95% CI: 1.01–1.43; p = 0.04) than vaginal delivery (OR = 0.88; 95% CI: 0.78–0.99; p = 0.03). The higher the number of siblings, the lower the risk of allergic rhinitis.

Conclusions

Allergy risk factors, especially those predisposing to allergic rhinitis, include not only genetic factors but also the mode of delivery: vaginal delivery or Cesarean section.

Epidemiology and Risk Factors of Infection in Early Childhood

BACKGROUND

There is a large, unexplained variation in the frequency of childhood infections. We described incidence and risk factors of infections in early childhood.

METHODS

Simple infections were captured during the first 3 years of life in the Copenhagen Prospective Studies on Asthma in Childhood 2000 birth cohort. Environmental exposures were analyzed by quasi-Poisson regression and sparse principal component analysis.

RESULTS

The 334 children experienced a median of 14 (range 2-43) infectious episodes at ages 0 to 3 years. The overall rate of infections was associated with the number of children in the day care (adjusted incidence rate ratio [aIRR] 1.09 [1.2-1.16]) and the m² per child in the day care (aIRR 0.96 [0.92-0.99]). Upper respiratory infections were also associated with the number of children in the day care (aIRR 1.11 [1.03-1.20]) and the m² per child in the day care (aIRR 0.95 [0.91-0.99]), whereas lower respiratory infections were associated with caesarean section (aIRR 1.49 [1.12-1.99]), maternal smoking (aIRR 1.66 [1.18-2.33]), older siblings (aIRR 1.54 [1.19-2.01]), and the age at entry to day care (aIRR 0.77 [0.65-0.91]). The sparse principal component analysis revealed a risk factor profile driven by tobacco exposure, social circumstances, and domestic pets, but could only be used to explain 8.4% of the infection burden.

CONCLUSIONS

Children experienced around 14 infections during the first 3 years of life, but incidences varied greatly. Environmental exposures only explained a small fraction of the variation, suggesting host factors as major determinants of infectious burden.

The importance of the microbiome in pediatrics and pediatric infectious diseases

PURPOSE OF REVIEW

Emerging research on the pediatric microbiome implicates the importance of the microbiome on the development of the immune system, nervous system, and growth. Changes to the microbiome during infancy are associated with the development of chronic illnesses such as asthma and inflammatory bowel disease. Additionally, the microbiome provides protection against certain pathogens, affects vaccine responses, and alters drug metabolism. This review highlights what is known about the microbiome, the establishment of a healthy microbiome and the significance that changes to the microbiome composition have on growth and health of children and adolescents.

RECENT FINDINGS

Vaginal delivery, breastfeeding, maternal health, and nutrition help shape a healthy microbiome. Caesarian delivery, formula feeding, and antibiotic use perturb the microbiome and are associated with the development of type II diabetes, asthma, allergic diseases, and obesity later in life. Specific interventions using pre and probiotics in multiple settings are under investigation with limited success.

SUMMARY

A better understanding of the microbiome and the interaction with the immune system may help guide interventions to alter the microbiome toward a state of lifelong health.

Maturation of the gut microbiome and risk of asthma in childhood

The composition of the human gut microbiome matures within the first years of life. It has been hypothesized that microbial compositions in this period can cause immune dysregulations and potentially cause asthma. Here we show, by associating gut microbial composition from 16S rRNA gene amplicon sequencing during the first year of life with subsequent risk of asthma in 690 participants, that 1-year-old children with an immature microbial composition have an increased risk of asthma at age 5 years. This association is only apparent among children born to asthmatic mothers, suggesting that lacking microbial stimulation during the first year of life can trigger their inherited asthma risk. Conversely, adequate maturation of the gut microbiome in this period may protect these pre-disposed children.

Colonization of commensal bacteria is thought to impact immune development, especially in the earliest years of life. Here, the authors show, by analyzing the development of the gut microbiome of 690 children, that microbial composition at the age of 1 year is associated with asthma diagnosed in the first 5 years of life.

Advances in mechanisms of allergic disease in 2016

This review highlights advances in mechanisms of allergic disease, particularly type 2 innate lymphoid cells; T_H2 lymphocytes; eicosanoid regulation of inflammation; extracellular vesicles in allergic responses; IL-33; microbiome properties, especially as they relate to mucosal barrier function; and a series of findings concerning the allergic inflammatory cells eosinophils, basophils, and mast cells. During the last year, mechanistic advances occurred in understanding type 2 innate lymphoid cells, particularly related to their response to ozone, involvement with experimental food allergy responses, and regulation by IL-33. Novel ways of regulating T_H2 cells through epigenetic regulation of GATA-3 through sirtuin-1, a class III histone deacetylase, were published. The understanding of eicosanoid regulation of inflammation increased and focused on additional properties of phospholipase A₂ and the role of prostaglandin D₂ and its receptors and inhibitory prostaglandin E₂ pathways. Mechanisms through which extracellular vesicles are released and contribute to allergic responses were reported. There was a deeper appreciation of mucosal barrier function, the epithelial alarmin IL-33, and the microbiome. Finally, there were advances concerning allergic inflammatory cells (mast cells, basophils, and eosinophils) that will undoubtedly have an effect on disease understanding and new therapeutic strategies.

Does the maternal vaginal microbiota play a role in seeding the microbiota of neonatal gut and nose?

The acquisition and early maturation of infant microbiota is not well understood despite its likely influence on later health. We investigated the contribution of the maternal microbiota to the microbiota of infant gut and nose in the context of mode of delivery and feeding. Using 16S rRNA sequencing and specific qPCR, we profiled microbiota of 42 mother-infant pairs from the GUSTO birth cohort, at body sites including maternal vagina, rectum and skin; and infant stool and nose. In our study, overlap between maternal vaginal microbiota and infant faecal microbiota was minimal, while the similarity between maternal rectal microbiota and infant microbiota was more pronounced. However, an infant's nasal and gut microbiota were no more similar to that of its own mother, than to that of unrelated mothers. These findings were independent of delivery mode. We conclude that the transfer of maternal vaginal microbes play a minor role in seeding infant stool microbiota. Transfer of maternal rectal microbiota could play a larger role in seeding infant stool microbiota, but approaches other than the generally used analyses of community similarity measures are likely to be needed to quantify bacterial transmission. We confirmed the clear difference between microbiota of infants born by Caesarean section compared to vaginally delivered infants and the impact of feeding mode on infant gut microbiota. Only vaginally delivered, fully breastfed infants had gut microbiota dominated by Bifidobacteria. Our data suggest that reduced transfer of maternal vaginal microbial is not the main mechanism underlying the differential infant microbiota composition associated with Caesarean delivery. The sources of a large proportion of infant microbiota could not be identified in maternal microbiota, and the sources of seeding of infant gut and nasal microbiota remain to be elucidated.

Early-life origin of intestinal inflammatory disorders

A growing body of evidence supports the concept of perinatal programming through which the perinatal environment affects the development of the fetus and infant, thereby modifying the risk profile for disease later in life. Increasing attention is focusing on the role of the early environment in the development of chronic intestinal disorders. Epidemiological studies have highlighted the link between perinatal factors, such as breastfeeding, cesarean delivery, and antibiotic use, and an increased risk for inflammatory bowel disease and/or celiac disease. These links are consistent with the concept of perinatal programming of intestinal inflammatory disorders. Animal models have shown that the early-life environment affects the development of the gastrointestinal tract, but further experimental studies are needed to confirm the long-term effects of the perinatal environment on susceptibility to chronic intestinal disorders later in life. Changes in the development and composition of the intestinal microbiota as well as epigenetic changes are emerging as key mechanisms through which the perinatal environment determines susceptibility to intestinal inflammatory disorders.

Contributions of the intestinal microbiome in lung immunity

The intestine is a critical site of immune cell development that not only controls intestinal immunity but extra-intestinal immunity as well. Recent findings have highlighted important roles for gut microbiota in shaping lung inflammation. Here, we discuss interactions between the microbiota and immune system including T cells, protective effects of microbiota on lung infections, the role of diet in shaping the composition of gut microbiota and susceptibility to asthma, epidemiologic evidence implicating antibiotic use and microbiota in asthma and clinical trials investigating probiotics as potential treatments for atopy and asthma. The systemic effects of gut microbiota are partially attributed to their generating metabolites including short chain fatty acids, which can suppress lung inflammation through the activation of G protein-coupled receptors. Thus, studying the interactions between microbiota and immune cells can lead to the identification of therapeutic targets for chronic lower respiratory diseases.

Epidemiology and clinical relevance of Staphylococcus aureus intestinal carriage: a systematic review and meta-analysis

INTRODUCTION

Recent data highlight the importance of screening more than one site for improving the detection of S. aureus colonization. Intestinal carriage is frequently under-investigated and its clinical impact ought to be defined a better way. Areas covered: This review and meta-analysis provide an updated overview of prevalence, characteristics and clinical significance of S. aureus intestinal carriage in different populations, both for methicillin-susceptible and -resistant S. aureus strains. Expert commentary: Intestinal S. aureus carriage is documented with higher prevalence in children and in patients with S. aureus skin and soft tissue infections. This site of colonization was shown to be associated with a high risk of dissemination in the environment and with S. aureus infection. Intestinal carriage is frequently retrieved in nasal carriers, reflecting probably an association with a high bacterial load. Exclusive intestinal carriage present in one third of intestinal carriers can be associated with infection. Comparative genotyping analysis of different strains from nasal and extra-nasal sites of carriage, including the intestinal ones, in the same individuals, would allow a better comprehension of the pathophysiology of S. aureus endogenous infection. It could also permit to improve the prevention of these infections by decolonization of sites implicated in infection genesis.

Cesarean Delivery and Body Mass Index at 6 Months and Into Childhood

BACKGROUND AND OBJECTIVES

The prevalence of cesarean delivery (CD) is rising worldwide, and so is childhood obesity. Studies have shown associations between these factors. We examined the development of BMI from birth through childhood to determine whether CDs were associated with differences in growth and obesity.

METHODS

Term children from the birth cohorts Copenhagen Prospective Studies on Asthma in Childhood₂₀₀₀ (COPSAC₂₀₀₀) and COPSAC₂₀₁₀ were included. Height, length, and weight measurements were collected prospectively until 5 years in COPSAC₂₀₁₀ and until 13 years in COPSAC₂₀₀₀. Dual-energy x-ray absorptiometry (DXA) scans were performed at 3.5 and 7 years. Information on relevant covariates were verified during clinical visits. Analyses were adjusted for covariates associating with CD.

RESULTS

In COPSAC₂₀₁₀, 20% (N = 138/673) of the children were delivered by CD; 49% were girls. In COPSAC₂₀₀₀, 19% (N = 76/393) were delivered by CD; 51% were girls. Children delivered by CD had a higher mean BMI at 6 months compared with those delivered vaginally: COPSAC₂₀₁₀ β-coefficient, .41 (95% confidence interval [CI], .12 to .69), P = .01; COPSAC₂₀₀₀ β-coefficient, .16 (95% CI, -.11 to .68), P = .16; and meta-analysis β-coefficient, .37 (95% CI, .14 to .60), P = .002. There were no differences in BMI trajectory between the 2 groups by 5 and 13 years, nor cross-sectional BMI at 5 and 13 years, nor in fat percentages from DXA scans.

CONCLUSIONS

Children delivered by CD had a higher BMI at 6 months of age, but this difference did not track into later childhood. Our study does not support the hypothesis that CD leads to later overweight.

Delivery and feeding mode affects fecal calprotectin levels in infants <7months old

BACKGROUND

Elevated fecal calprotectin (FC) is a non-invasive marker of inflammation indicating bowel disease. However, healthy infants have displayed high FC levels, with large variation. We sought to determine what factors might affect FC levels in children <6months old.

METHODS

We recruited 133 healthy infants aged 0-6months from four Korean day care centers. Stool samples were analyzed by immunosorbent assay. All infants completed a questionnaire related to clinical characteristics including birth and feeding history.

RESULTS

The mean FC concentration of all of participants was 237.40μg/g (range 11.5-1330.6μg/g). FC levels between 0 and 6months reduced with increasing age and the differences were statistically significant. The mean FC value according to feeding mode was 354.67μg/g for those fed breast milk and 149.44μg/g for those fed formula milk (p<0.001). Mean FC values were 319.69μg/g vs. 130.97μg/g for normal spontaneous vaginal delivery (NSVD) vs. caesarean section births, respectively (p<0.001). In addition, delivery mode affected the FC level at 0-6months regardless of feeding mode.

CONCLUSION

The FC levels of infants aged 0-6months reduced with age and were higher than the normal levels observed in healthy older infants. The FC value at <7months was higher in infants who were fed breast milk and born by NSVD.

Antibiotics in Pregnancy Increase Children's Risk of Otitis Media and Ventilation Tubes

OBJECTIVES

To study the association between antibiotic intake in pregnancy and the development of otitis media and placement of ventilation tubes (VTs) in the offspring under the hypothesis that antibiotics in pregnancy may alter the offspring's propensity for disease.

STUDY DESIGN

Data from the 700 children in the Copenhagen Prospective Studies on Asthma in Childhood 2010 unselected birth cohort study were used. Information on maternal antibiotic use and other exposures during pregnancy was collected prospectively from interviews and validated in national registries. Otitis media episodes were registered in a prospective diary for 3 years. Information regarding children's VTs was obtained from national registries.

RESULTS

There were 514 children who had diary information and were included in the analysis regarding otitis media episodes. For VTs analysis, 699 children were included. Thirty-seven percent of the mothers received antibiotics during pregnancy, and this was associated with increased risk of otitis media (adjusted hazard ratio 1.30; 95% CI 1.04-1.63; P = .02). The risk of receiving VTs was especially associated with third trimester antibiotics (adjusted hazard ratio 1.60; 95% CI 1.08-2.36, P = .02). The risk of otitis media increased with increasing number of treatments (per-level adjusted hazard ratio 1.20; 95% CI 1.04-1.40; P = .02), but for VTs this association was not significant after adjustment.

CONCLUSION

Maternal use of antibiotics during pregnancy is associated with an increased risk of otitis media and VT insertions in the offspring. Antibiotics late in pregnancy mainly contributed to these effects, pointing toward potential transmission of an unfavorable microbiome from mother to child.

The infant gut bacterial microbiota and risk of pediatric asthma and allergic diseases

Among the many areas being revolutionized by the recent introduction of culture-independent microbial identification techniques is investigation of the relationship between close contact with large animals, antibiotics, breast feeding, mode of birth, and other exposures during infancy as related to a reduced risk of asthma and allergic disease. These exposures were originally clustered under the "Hygiene Hypothesis" which has evolved into the "Microbiota Hypothesis". This review begins by summarizing epidemiologic studies suggesting that the common feature of these allergy risk-related exposures is their influence on the founding and early development of a child's gut microbiota. Next, studies using culture-independent techniques are presented showing that children who have experienced the exposures of interest have altered gut microbiota. Finally, selected mouse and human studies are presented which begin to corroborate the protective exposures identified in epidemiologic studies by elucidating mechanisms through which microbes can alter immune development and function. These microbially driven immune alterations demonstrate that microbial exposures in many cases could alter the risk of subsequent allergic disease and asthma. Hopefully, a better understanding of how microbes influence allergic disease will lead to safe and effective methods for reducing the prevalence of all forms of allergic disease.

The microbiome in asthma

PURPOSE OF REVIEW

Asthma is a complex and heterogeneous disease with strong genetic and environmental components that manifests within a variety of clinical features and diverse patterns of immune responses. Asthma prevalence has dramatically increased over the last decade in Westernized societies, thereby suggesting a key function of environmental factors in disease promotion and development.

RECENT FINDINGS

'Early-life' microbial exposure and bacterial colonization are crucial for the maturation and the education of the immune system. The commensal flora is also critical in order to maintain immune homeostasis at the mucosal surfaces and may consequently play an important function in allergic disease development. Recent evidence demonstrates that asthma influences and is also impacted by the composition and function of the human intestinal and respiratory microbiome.

SUMMARY

In this review, we summarize the most recent findings on how asthma development is connected with respiratory and intestinal microbial dysbiosis. We highlight and discuss recent research that reveals the existence of a 'gut-lung' microbial axis and its impact on asthma development. We also analyze how 'early-life' microbial exposure affects the immune response and the consequences for asthma development.

Microbiome and its impact on gastrointestinal atopy

The prevalence of allergic conditions has continuously increased in the last few decades in Westernized countries. A dysbiotic gut microbiome may play an important role in the development of allergic diseases. Genetic, environmental, and dietary factors may alter the commensal microbiota leading to inflammatory dysregulation of homeostasis. Murine and human studies have begun to elucidate the role of the microbiota in the pathogenesis of atopic diseases including asthma, atopic dermatitis, and food allergies. However, the role of the microbiome in most eosinophilic gastrointestinal diseases (EGIDs) is not yet known. This review provides an overview of what is currently known about the development of tolerance from both molecular and clinical standpoints. We also look at the gut-specific microbiome and its role in atopic conditions with the hope of applying this knowledge to the understanding, prevention, and treatment of EGIDs, particularly EoE.