Microbial Exposure In Early Life Research Articles

Laboratory mice with a wild microbiota generate strong allergic immune responses.

Allergic disorders are caused by a combination of hereditary and environmental factors. The hygiene hypothesis postulates that early-life microbial exposures impede the development of subsequent allergic disease. Recently developed "wildling" mice are genetically identical to standard laboratory specific pathogen-free (SPF) mice but are housed under seminatural conditions and have rich microbial exposures from birth. Thus, by comparing conventional SPF mice with wildlings, we can uncouple the impact of lifelong microbial exposures from genetic factors on the allergic immune response. We found that wildlings developed larger populations of antigen-experienced T cells than conventional SPF mice, which included interleukin-10-producing CD4 T cells specific for commensal Lactobacilli strains and allergy-promoting T helper 2 (TH2) cells. In models of airway exposure to house dust mite (HDM), recombinant interleukin-33, or Alternaria alternata, wildlings developed strong allergic inflammation, characterized by eosinophil recruitment, goblet cell metaplasia, and antigen-specific immunoglobulin G1 (IgG1) and IgE responses. Wildlings developed robust de novo TH2 cell responses to incoming allergens, whereas preexisting TH2 cells could also be recruited into the allergic immune response in a cytokine-driven and TCR-independent fashion. Thus, wildling mice, which experience diverse and lifelong microbial exposures, were not protected from developing pathological allergic immune responses. Instead, wildlings mounted robust allergic responses to incoming allergens, shedding new light on the hygiene hypothesis.

Early-life interactions between the microbiota and immune system: impact on immune system development and atopic disease.

Prenatal and early postnatal life represent key periods of immune system development. In addition to genetics and host biology, environment has a large and irreversible role in the immune maturation and health of an infant. One key player in this process is the gut microbiota, a diverse community of microorganisms that colonizes the human intestine. The diet, environment and medical interventions experienced by an infant determine the establishment and progression of the intestinal microbiota, which interacts with and trains the developing immune system. Several chronic immune-mediated diseases have been linked to an altered gut microbiota during early infancy. The recent rise in allergic disease incidence has been explained by the 'hygiene hypothesis', which states that societal changes in developed countries have led to reduced early-life microbial exposures, negatively impacting immunity. Although human cohort studies across the globe have established a correlation between early-life microbiota composition and atopy, mechanistic links and specific host-microorganism interactions are still being uncovered. Here, we detail the progression of immune system and microbiota maturation in early life, highlight the mechanistic links between microbes and the immune system, and summarize the role of early-life host-microorganism interactions in allergic disease development.

Association of indoor dust microbiota with cognitive function and behavior in preschool-aged children

BackgroundChildhood cognitive development depends on neuroimmune interactions. Immunomodulation by early-life microbial exposure may influence neuropsychological function. In this study, we investigate the association between residential indoor microbiota and cognition and behavior among preschoolers.ResultsIndoor-settled dust bacterial and fungal characteristics were assessed using 16S and ITS amplicon sequencing (microbial diversity) and qPCR measurements (microbial loads). Child behavior was assessed using four scales: peer relationship, emotional, conduct, and hyperactivity was assessed by the Strengths and Difficulties Questionnaire (SDQ). Cognitive function was assessed using four tasks of the Cambridge Neuropsychological Test Automated Battery (CANTAB) software. The first two tasks were designed to assess attention and psychomotor speed (Motor Screening (MOT) and Big/Little Circle (BLC)) and the last two to evaluate the child’s visual recognition/working memory (Spatial Span (SSP) and Delayed Matching to Sample (DMS)). Among the 172 included children (age 4–6 years), we observed a 51% (95%CI;75%;9%) lower odds of children scoring not normal for hyperactivity and a decrease of 3.20% (95%CI, −6.01%; −0.30%) in BLC response time, for every IQR increase in fungal Shannon diversity. Contrarily, microbial loads were directly associated with SDQ scales and response time. For example, a 2-fold increase in Gram-positive bacterial load was associated with 70% (95%CI 18%; 156%) higher odds of scoring not normal for hyperactivity and an increase of 5.17% (95%CI 0.87%; 9.65%) in DMS response time.ConclusionsOur findings show that early-life exposure to diverse indoor fungal communities is associated with better behavioral and cognitive outcomes, whereas higher indoor microbial load was associated with worse outcomes.-hh8RCLyRPCU1iX3VFx5YbVideo

Gut microbiota promotes stem cell differentiation through macrophage and mesenchymal niches in early postnatal development

Intestinal stem cell maturation and development coincide with gut microbiota exposure after birth. Here, we investigated how early life microbial exposure, and disruption of this process, impacts the intestinal stem cell niche and development. Single-cell transcriptional analysis revealed impaired stem cell differentiation into Paneth cells and macrophage specification upon antibiotic treatment in early life. Mouse genetic and organoid co-culture experiments demonstrated that a CD206+ subset of intestinal macrophages secreted Wnt ligands, which maintained the mesenchymal niche cells important for Paneth cell differentiation. Antibiotics and reduced numbers of Paneth cells are associated with the deadly infant disease, necrotizing enterocolitis (NEC). We showed that colonization with Lactobacillus or transfer of CD206+ macrophages promoted Paneth cell differentiation and reduced NEC severity. Together, our work defines the gut microbiota-mediated regulation of stem cell niches during early postnatal development.

Early microbial exposure shapes adult immunity by altering CD8+ T cell development

Microbial exposure during development can elicit long-lasting effects on the health of an individual. However, how microbial exposure in early life leads to permanent changes in the immune system is unknown. Here, we show that the microbial environment alters the set point for immune susceptibility by altering the developmental architecture of the CD8+ T cell compartment. In particular, early microbial exposure results in the preferential expansion of highly responsive fetal-derived CD8+ T cells that persist into adulthood and provide the host with enhanced immune protection against intracellular pathogens. Interestingly, microbial education of fetal-derived CD8+ T cells occurs during thymic development rather than in the periphery and involves the acquisition of a more effector-like epigenetic program. Collectively, our results provide a conceptual framework for understanding how microbial colonization in early life leads to lifelong changes in the immune system.

The Role of the Gut Microbiome in Cow's Milk Allergy: A Clinical Approach.

Cow's milk allergy (CMA) is the most prevalent food allergy (FA) in infancy and early childhood and can be present with various clinical phenotypes. The significant increase in FA rates recorded in recent decades has been associated with environmental and lifestyle changes that limit microbial exposure in early life and induce changes in gut microbiome composition. Gut microbiome is a diverse community of microbes that colonize the gastrointestinal tract (GIT) and perform beneficial functions for the host. This complex ecosystem interacts with the immune system and has a pivotal role in the development of oral tolerance to food antigens. Emerging evidence indicates that alterations of the gut microbiome (dysbiosis) in early life cause immune dysregulation and render the host susceptible to immune-mediated diseases later in life. Therefore, the colonization of the gut by "healthy" microbes that occurs in the first years of life determines the lifelong health of the host. Here, we present current data on the possible role of the gut microbiome in the development of CMA. Furthermore, we discuss how gut microbiome modification might be a potential strategy for CMA prevention and treatment.

The Ecoimmunology of Health and Disease: The Hygiene Hypothesis and Plasticity in Human Immune Function

The original hygiene hypothesis proposed that certain diseases derive from low levels of early-life microbial exposure. Since then, the hypothesis has been applied to numerous inflammatory, autoimmune, and allergic conditions. The changes in hygiene linked to these diseases include numerous changes in biotic exposure and lifestyle. To this end, some scholars have called for abandonment of the term or have suggested alternate labels, e.g., the old friends hypothesis. However, neither of these terms encompasses the complexity of plasticity in immune response and host–parasite/commensal interactions that influence these conditions. Here, I review this complexity, with particular regard to the factors affecting immunological strategies, the development of tolerance, immune dysfunction, and ecological interactions among organisms. I discuss the biotic factors that affect immune plasticity and how these interact with abiotic factors such as nutrition, as well as how transgenerational exposures may affect immune plasticity. Finally, I review the general features of diseases linked to biotic exposures.

Early life microbial exposures shape the Crassostrea gigas immune system for lifelong and intergenerational disease protection

BackgroundThe interaction of organisms with their surrounding microbial communities influences many biological processes, a notable example of which is the shaping of the immune system in early life. In the Pacific oyster, Crassostrea gigas, the role of the environmental microbial community on immune system maturation — and, importantly, protection from infectious disease — is still an open question.ResultsHere, we demonstrate that early life microbial exposure durably improves oyster survival when challenged with the pathogen causing Pacific oyster mortality syndrome (POMS), both in the exposed generation and in the subsequent one. Combining microbiota, transcriptomic, genetic, and epigenetic analyses, we show that the microbial exposure induced changes in epigenetic marks and a reprogramming of immune gene expression leading to long-term and intergenerational immune protection against POMS.ConclusionsWe anticipate that this protection likely extends to additional pathogens and may prove to be an important new strategy for safeguarding oyster aquaculture efforts from infectious disease. tag the videobyte/videoabstract in this section5X1-nepGVFkCxreirqFTHAVideo

246-LB: Neonatal Microbes Stimulate Beta-Cell Development

Newborns are exposed to environmental microbes that colonize the gut and increase in diversity during childhood to establish the resident microbiota. Concurrently, insulin-producing β-cells enter a postnatal window of proliferation and maturation. We found that germ-free animal models exhibit significant reductions in β-cell mass compared to their microbe-carrying counterparts, revealing a role for microbes in the establishment of these cells. By mining this unique source, we uncovered mechanisms of bacterially driven β-cell development. Neonatal mice given strategically timed doses of broad-spectrum antibiotics incurred lasting reductions in β-cell mass, revealing a critical period of microbial influence on β-cells. Though reconstituted with a normal microbiota after antibiotic treatment, as adults these animals had reduced glucose tolerance and insulin secretion, and were more susceptible to metabolic disease. Treatment of neonatal mice with selective antibiotics resulted in variations in β-cell mass, blood glucose, and insulin levels, suggesting unique bacterial taxa or products influence these traits. Sequencing revealed that distinct microbes were enriched within each antibiotic treatment, allowing us to identify candidate bacterial taxa that we show are sufficient to stimulate β-cell expansion and restore insulin function. Further, we have identified multiple islet associated cell types that respond to these microbial cues. Previously, we identified the bacterial protein, BefA, that directly stimulates β-cell proliferation, and we anticipate finding additional bacterial modulators of this important tissue. Reduced microbiota diversity can be predictive of diabetes in susceptible children, suggesting that early life microbial exposures are critical to prevent disease. Our results indicate loss of specific bacteria may result in reduced insulin production capacity prior to autoimmunity. If we can reinstate these lost microbes, we may be able to bolster the β-cell population against loss. Disclosure J. H. Hill: None. K. Guillemin: None. C. L. Murtaugh: None. J. Round: None. Funding Junior Diabetes Research Foundation (3-PDF-2019-747-A-N)

The role of LPS and CpG in the farm effect against allergies, and beyond.

The prevalence of allergic disease has increased significantly over the past decades. Although allergies are inherently multifactorial and heterogenous; environmental, maternal, and early-life microbial exposures could strongly modify disease risk. The effects of environmental microbiota are illustrated by the “farm effect”, showing protection against asthma when children grow up on traditional farms. Recent studies have further revealed an important role for early-life exposure to a microbe-rich environment imposing lung and gut microbiome maturation and immune education, preventing allergic disease in childhood. Advances are made in the field of immunology and microbiome research, which identified entire microbial taxa, as well as specific microbial metabolites and bacterial products associated with reducing disease risk. Here we discuss the cross-talk between the microbiota and the pathogenesis of allergic disease, including bacterial products as lipopolysaccharide and CpG, in the farm effect.

Impact of maternal antibodies and microbiota development on the immunogenicity of oral rotavirus vaccine in African, Indian, and European infants

Identifying risk factors for impaired oral rotavirus vaccine (ORV) efficacy in low-income countries may lead to improvements in vaccine design and delivery. In this prospective cohort study, we measure maternal rotavirus antibodies, environmental enteric dysfunction (EED), and bacterial gut microbiota development among infants receiving two doses of Rotarix in India (n = 307), Malawi (n = 119), and the UK (n = 60), using standardised methods across cohorts. We observe ORV shedding and seroconversion rates to be significantly lower in Malawi and India than the UK. Maternal rotavirus-specific antibodies in serum and breastmilk are negatively correlated with ORV response in India and Malawi, mediated partly by a reduction in ORV shedding. In the UK, ORV shedding is not inhibited despite comparable maternal antibody levels to the other cohorts. In both India and Malawi, increased microbiota diversity is negatively correlated with ORV immunogenicity, suggesting that high early-life microbial exposure may contribute to impaired vaccine efficacy.

Delivery Mode and Gut Microbial Changes Correlate With an Increased Risk of Childhood Asthma

Children born via cesarean delivery have higher rates of childhood asthma. In this study, researchers examined associations between mode of delivery and the gut microbiome and tested for relationships between these changes and asthma risk.In this study, 700 children enrolled in the Copenhagen Prospective Studies on Asthma in Childhood 2010 birth cohort were included. Of these children, 151 were born via cesarean delivery, and 549 were born by vaginal delivery.In this study, researchers used a nested case-control design. All children had at least 1 fecal sample collected before 1 year of age (1 week, 1 month, and/or 1 year), analyzed by using 16S rRNA sequencing. A sparse partial least squares model was used to identify correlations between cesarean delivery and gut microbial composition at each time point. A “cesarean microbial score” was calculated for each time point, and a Kaplan-Meyer estimate was used to identify the cumulative asthma risk on the basis of delivery method and cesarean microbial score.Cesarean delivery was associated with significant increases in asthma prevalence at age 6 (odds ratio: 2.45). Cesarean delivery was also associated with marked differences in gut microbiota at 1 week and 1 month of age that became less significant by 1 year. The relationship between cesarean delivery and asthma depended on the microbiome composition at the age of 1 year. Of the children delivered by cesarean, only those who still had a significant cesarian microbiota signature at 1 year of age had higher rates of asthma at age 6 (odds ratio: 1.37).Cesarean delivery was associated with increased asthma risk but only in children who still had a cesarean gut microbial signature at 1 year of age.There is increasing evidence that early-life microbial exposures drive immune maturation and the risk of allergic diseases and asthma. With this study, the authors help to explain how delivery method influences asthma risk. In the results, it is indicated that cesarean delivery prevents the transfer of bacteria that produce short chain fatty acids in the gut to promote immune system regulation. With this observation, it is suggested that replacing these “missing bacteria” or their metabolites could reduce the risk for allergies and asthma in children born by cesarean delivery.

Evaluation of the Antibacterial Potential of Essential Oil and Extract of Apium graveolens L. as an Environmentally Friendly Technology Against Helicobacter pylori

The hygiene hypothesis links the environmental and microbial exposure in early life to the prevalence of atopy, allergy, and asthma. Helicobacter pylori infection is typically acquired in childhood and the acquisition is associated with poor household hygiene. In this study, the current knowledge on the activity of essential oils and extract of Apium graveolens L. (celery seeds) and their derivatives against H. pylori was reviewed. Celery seeds were prepared at the Pharmaceutical Farm (Babol, Mazandaran) of Iran. The essential oils were extracted by a Clevenger approach and analyzed using GC-MS, and maceration method was used to prepare the extract. H. pylori bacteria were isolated by the cultivation of gastric biopsy removed from the patient who had gastric ulcer. The antibacterial activities of both essential oils and extract against H. pylori were evaluated by agar dilution method, and the corresponding MIC (minimum inhibitory concentration) and MBC (minimum bactericidal concentration) values were determined for each sample. The results showed that the main components in celery seed essential oils were α-pinene (20.25%), β-pinene (16.62%), and Sabinene (7.81%). Among different samples, essential oils of celery seed exhibited better effect on H. pylori with MIC value of 1.56 mg/mL and MBC value of 3.12 mg/mL. Methanol and water extracts of celery seed showed MIC values of 0.38 mg/mL and 0.78 mg/mL and MBC values of 1.56 mg/mL and 6.25 mg/ mL, respectively (P≤0.005). The results of this study indicated that all the samples had antibacterial effect against H. pylori due to antibacterial components.

Early Life Microbial Exposure and Immunity Training Effects on Asthma Development and Progression.

Asthma is the most common inflammatory disease affecting the lungs, which can be caused by intrauterine or postnatal insults depending on the exposure to environmental factors. During early life, the exposure to different risk factors can influence the microbiome leading to undesired changes to the immune system. The modulations of the immunity, caused by dysbiosis during development, can increase the susceptibility to allergic diseases. On the other hand, immune training approaches during pregnancy can prevent allergic inflammatory diseases of the airways. In this review, we focus on evidence of risk factors in early life that can alter the development of lung immunity associated with dysbiosis, that leads to asthma and affect childhood and adult life. Furthermore, we discuss new ideas for potential prevention strategies that can be applied during pregnancy and postnatal period.

Early Microbial-Immune Interactions and Innate Immune Training of the Respiratory System during Health and Disease.

Over the past two decades, several studies have positioned early-life microbial exposure as a key factor for protection or susceptibility to respiratory diseases. Birth cohorts have identified a strong link between neonatal bacterial colonization of the nasal airway and gut with the risk for respiratory infections and childhood asthma. Translational studies have provided companion mechanistic insights on how viral and bacterial exposures in early life affect immune development at the respiratory mucosal barrier. In this review, we summarize and discuss our current understanding of how early microbial–immune interactions occur during infancy, with a particular focus on the emergent paradigm of “innate immune training”. Future human-based studies including newborns and infants are needed to inform the timing and key pathways implicated in the development, maturation, and innate training of the airway immune response, and how early microbiota and virus exposures modulate these processes in the respiratory system during health and disease.

Microbial exposure in early life alters the ontogeny and function of CD8+ T cells

Abstract Evidence has shown that microbial exposure in early life can have long-lasting effects on the health status of an individual. However, the underlying basis of how microbes shape the immune system is not well understood. In this study, we utilized a novel pet shop mouse model and compared the immune development and function of laboratory mice raised in either a clean (SPF) or dirty (pet-shop) environment. When we challenged the two groups with an intracellular pathogen in adulthood, we found that mice raised in the dirty environment mounted a more robust CD8+ T cell response and were highly resistant to infection. Adoptive transfer experiments with CD8+ T cells from clean and dirty mice into T cell deficient recipients indicated that differences in immune susceptibility were linked to changes in the CD8+ T cell compartment. Moreover, the dirty mice had an increased accumulation of antigen-specific CD8+ T cells and produced more effector molecules. To understand how the ontogeny of the CD8+ T cell compartment was altered in the dirty mice, we used our fate-mapping timestamp mice and found a higher proportion of fast-acting fetal-derived CD8+ T cells and fewer slow-acting adult-derived CD8+ T cells present in the dirty mice. We found that immune susceptibility could be normalized between clean and dirty mice by depleting the fetal layer of CD8+ T cells. Collectively, these findings suggest that microbial exposure leads to permanent changes in the immune system by altering the developmental layering of the peripheral T cell compartment. We are currently using a combination of RNA- and ATAC-seq to gain a deeper understanding of how the microbial environment mediates changes to CD8+ T cells at the gene regulatory level.

Abstract PO-44: Past infection and risk of adolescent/young adult HL

Abstract Background: Adolescent/young adult (AYA) Hodgkin lymphoma (HL) risk is increasingly linked to a deficit of microbial exposure in early life, especially from fecal-oral transmission. Methods: In this cross-sectional study, we examined past exposure to 15 infections in serum samples from 291 AYA HL cases and 194 of their unaffected family members. We measured antibodies to HSV1, HSV2, VZV, EBV, HHV7, HCMV, HHV6, KSHV, S. gallolyticus, F. nucleatum, T. gondii, H. pylori, Rubella virus, and Parvovirus B19 using a multiplex serology bead array (Luminex). A positive history was determined by a titer threshold specific for each infection. A logistic regression model was used to calculate the odds ratio (OR) of AYA HL risk for each infection separately adjusted for sex and age at sampling. We then applied the same logistic regression model, adding an adjustment for family. Results: Evidence of past HHV6 infection was associated with an increased risk of AYA HL (OR= 1.80; 95% CI= 1.06-3.07). Having antibodies to H. pylori was associated with a decreased risk (OR= 0.49; 95% CI= 0.25-0.98). An increasing number of fecal-oral infections (H. pylori, T. gondii) was associated with a decreasing risk of AYA HL (ptrend<0.001), while an increasing number of respiratory-transmitted infections (Rubella virus, Parvovirus) was not significantly associated (ptrend=0.062). After adjusting for family, infection with Parvovirus was the only significant risk factor for AYA HL (OR=3.8,1.06-13.6). Conclusions: We show preliminary evidence for an inverse association between fecal-oral transmitted agents and risk of AYA HL, supporting the hypothesis that a deficit of early life fecal-oral transmitted microbes may be associated with increased risk. HHV6 and Parvovirus were associated with an increased risk, possibly due to a subclinical immune deficiency or an unknown mechanism. In the final presentation, we will add data from 40 additional unaffected family members currently missing age, and results by histology and EBV status. Citation Format: Maryam Saleh, Amie Hwang, Julia Simon, Thomas M. Mack, Tim Waterboer, Wendy Cozen. Past infection and risk of adolescent/young adult HL [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr PO-44.

Early life microbial exposures and allergy risks: opportunities for prevention.

Allergies, including asthma, food allergy and atopic dermatitis, are increasing in prevalence, particularly in westernized countries. Although a detailed mechanistic explanation for this increase is lacking, recent evidence indicates that, in addition to genetic predisposition, lifestyle changes owing to modernization have an important role. Such changes include increased rates of birth by caesarean delivery, increased early use of antibiotics, a westernized diet and the associated development of obesity, and changes in indoor and outdoor lifestyle and activity patterns. Most of these factors directly and indirectly impact the formation of a diverse microbiota, which includes bacterial, viral and fungal components; the microbiota has a leading role in shaping (early) immune responses. This default programme is markedly disturbed under the influence of environmental and lifestyle risk factors. Here, we review the most important allergy risk factors associated with changes in our exposure to the microbial world and the application of this knowledge to allergy prevention strategies.

Epigenetic landscape links upper airway microbiota in infancy with allergic rhinitis at 6 years of age

The upper airways present a barrier to inhaled allergens and microbes, which alter immune responses and subsequent risk for diseases, such as allergic rhinitis (AR). We tested the hypothesis that early-life microbial exposures leave a lasting signature in DNA methylation that ultimately influences the development of AR in children. We studied upper airway microbiota at 1 week, 1 month, and 3 months of life, and measured DNA methylation and gene expression profiles in upper airway mucosal cells and assessed AR at age 6 years in children in the Copenhagen Prospective Studies on Asthma in Childhood birth cohort. We identified 956 AR-associated differentially methylated CpGs in upper airway mucosal cells at age 6 years, 792 of which formed 3 modules of correlated differentially methylated CpGs. The eigenvector of 1 module was correlated with the expression of genes enriched for lysosome and bacterial invasion of epithelial cell pathways. Early-life microbial diversity was lower at 1 week (richness P= .0079) in children with AR at age 6 years, and reduced diversity at 1 week was also correlated with the same module's eigenvector (ρ= -0.25; P= 3.3×10-5). We show that the effect of microbiota richness at 1 week on risk for AR at age 6 years was mediated in part by the epigenetic signature of this module. Our results suggest that upper airway microbial composition in infancy contributes to the development of AR during childhood, and this trajectory is mediated, at least in part, through altered DNA methylation patterns in upper airway mucosal cells.

Microbiome Composition and Its Impact on the Development of Allergic Diseases.

Allergic diseases, such as food allergy (FA), atopic dermatitis (AD), and asthma, are heterogeneous inflammatory immune-mediated disorders that currently constitute a public health issue in many developed countries worldwide. The significant increase in the prevalence of allergic diseases reported over the last few years has closely paralleled substantial environmental changes both on a macro and micro scale, which have led to reduced microbial exposure in early life and perturbation of the human microbiome composition. Increasing evidence shows that early life interactions between the human microbiome and the immune cells play a pivotal role in the development of the immune system. Therefore, the process of early colonization by a “healthy” microbiome is emerging as a key determinant of life-long health. In stark contrast, the perturbation of such a process, which results in changes in the host-microbiome biodiversity and metabolic activities, has been associated with greater susceptibility to immune-mediated disorders later in life, including allergic diseases. Here, we outline recent findings on the potential contribution of the microbiome in the gastrointestinal tract, skin, and airways to the development of FA, AD, and asthma. Furthermore, we address how the modulation of the microbiome composition in these different body districts could be a potential strategy for the prevention and treatment of allergic diseases.