Using Precisely Defined in vivo Microbiotas to Understand Microbial Regulation of IgE

Early life microbiota colonization programs nociceptor sensitivity by regulating NGF production in mast cells

Recent evidence suggests that the gut microbiota can influence pain sensitivity, highlighting the potential for microbiota-targeted pain interventions. During early life, both the microbiota and nociceptors are fine-tuned and respond to environmental factors, however, little is known about how they interact with each other. Using germ-free and gnotobiotic models, we demonstrate that microbiota colonization controls nociceptor sensitivity, partly by modulating mast cell production of nerve growth factor (NGF). We report that germ-free mice respond less to thermal and capsaicin-induced stimulation, which correlates with reduced trafficking of TRPV1 to the cell membrane of nociceptors. In germ-free mice, mast cells express lower levels of NGF. Hyposensitivity to thermal and capsaicin-induced stimulation, reduced TRPV1 trafficking, and decreased NGF expression are reversed when mice are colonized at birth, but not when colonization occurs after weaning. Inhibition of mast cell degranulation and NGF signaling during the first weeks of life in colonized mice leads to a hyposensitive phenotype in adulthood, demonstrating a role for mast cells and NGF signaling in linking early life colonization with nociceptor sensitivity. These findings implicate the early life microbiota in shaping mast cell NGF production and nociceptor sensitivity later in life. SIGNIFICANCE STATEMENT: Nociceptors are specialized sensory neurons that detect and transduce painful stimuli. During the early postnatal period, nociceptors are influenced by sensory experiences and the environment. Our findings demonstrate that gut microbiota colonization is essential in setting the threshold of nociceptor responses to painful stimuli. We show that early-life bacterial colonization controls the production of nerve growth factor by mast cells, affecting our sensitivity to pain later in life. Our study highlights the potential for developing new pain treatments that target the gut microbiome.

Microbial metabolism of food allergens determines the severity of IgE-mediated anaphylaxis

Anaphylaxis is an acute, potentially life-threatening reaction, often triggered by foods and largely mediated by IgE. A critically important aspect of anaphylaxis pertains to the factors that modulate its severity. The human microbiota is known to influence oral tolerance, but the microbial mechanisms directly involved in IgE-mediated anaphylaxis remain unknown. Here, we demonstrate that human saliva harbors peanut-degrading bacteria that metabolize immunodominant allergens (Ara h 1 and Ara h 2) and alter IgE binding. Additionally, we provide in vivo evidence showing that oral bacteria metabolize peanut allergens, influencing systemic allergen exposure and the severity of anaphylaxis. Finally, in a clinical study, we observe that common peanut-degrading bacteria, such as Rothia, from the oral cavity, are more abundant in peanut-allergic patients who exhibit better tolerance to allergen exposure. Altogether, these results demonstrate the role of the human microbiota in modulating IgE-mediated reactions through allergen metabolism. These findings reveal a novel microbial mechanism with potential to prevent, or reduce, the severity of IgE-mediated anaphylaxis.

Pathophysiological mechanisms of gut dysbiosis and food allergy and an investigation of probiotics as an intervention for atopic disease

BACKGROUND AND AIMS

Epidemiological studies have associated reduced bacterial diversity and abundance and food allergy. This mechanistic review investigated the link between gut dysbiosis and food allergy with a focus on the role of short-chain fatty acids (SCFAs) in modulating T-cells. T-cell differentiation poses an opportunity to direct the immune cells towards an anergic regulatory T cell (Treg) or allergic T helper 2 (Th2) response. Probiotic intervention to prevent and/or treat atopic disease symptoms through this mechanistic pathway was explored.

METHODOLOGY

A narrative review was conducted following a three-stage systematic literature search of EMBASE and Medline databases. Ninety-six of 571 papers were accepted and critically appraised using ARRIVE and SIGN50 forms. Thematic analysis identified key pathophysiological mechanisms within the narrative of included papers.

RESULTS

Preclinical studies provided compelling evidence for SCFAs' modulation of T-cell differentiation, which may act through G-protein coupled receptors 41, 43 and 109a and histone deacetylase inhibition. Foxp3 transcription factor was implicated in the upregulation of Tregs. Human probiotic intervention studies aimed at increasing SCFAs and Tregs and preventing atopic disease showed inconclusive results. However, evidence for probiotic intervention in children with cow's milk protein allergy (CMPA) was more promising and warrants further investigation.

CONCLUSION

Preclinical evidence suggests that the mechanism of gut dysbiosis and reduced SCFAs may skew T-cell differentiation towards a Th2 response, thus inducing allergy symptoms. Probiotic trials were inconclusive: probiotics were predominantly unsuccessful in the prevention of allergic disease, however, may be able to modulate food allergy symptoms in infants with CMPA.

Boundary flux analysis: an emerging strategy for investigating metabolic pathway activity in large cohorts

Many biological phenotypes are rooted in metabolic pathway activity rather than the concentrations of individual metabolites. Despite this, most metabolomics studies only capture steady-state metabolism - not metabolic flux. Although sophisticated metabolic flux analysis strategies have been developed, these methods are technically challenging and difficult to implement in large-cohort studies. Recently, a new boundary flux analysis (BFA) approach has emerged that captures large-scale metabolic flux phenotypes by quantifying changes in metabolite levels in the media of cultured cells. This approach is advantageous because it is relatively easy to implement yet captures complex metabolic flux phenotypes. We describe the opportunities and challenges of BFA and illustrate how it can be harnessed to investigate a wide transect of biological phenomena.

Differential changes in the gut microbiota between extrinsic and intrinsic atopic dermatitis

Elevated serum level of total and (or) allergen-specific IgE is one of the key features of atopic dermatitis (AD). Previous studies have shown that the gut microbiome mediates interactions between external exposures and the immune system in AD; however, the relationship between the gut microbiota and IgE remains unclear. In the present study, analyses of environmental exposures for 250 AD patients and 138 healthy volunteers revealed an association between hygiene levels in the residential environment and the occurrence of AD and the IgE level. Metagenomic sequencing of the gut microbiota from 68 AD patients and 77 healthy controls showed that AD patients had a distinct gut microbiota composition; moreover, while L-histidine degradation was enriched in healthy controls, L-histidine biosynthesis was enriched in AD patients. Extrinsic and intrinsic AD showed different enrichment patterns of specific microbes and differential associations of functional pathways. Our study indicated that elevated levels of IgE in AD were related to specific microbes in the gut microbiota, which showed extensive interactions with environmental factors.

Cesarean section induced dysbiosis promotes type 2 immunity but not oxazolone-induced dermatitis in mice

Delivery by cesarean section (CS) is associated with an altered gut microbiota (GM) colonization and a higher risk of later chronic inflammatory diseases. Studies investigating the association between CS and atopic dermatitis (AD) are contradictive and often biased by confounding factors. The aim of this study was therefore to provide experimental evidence for the association between CS and AD in a mouse model and clarify the role of the GM changes associated with CS. It was hypothesized that CS-delivered mice, and human CS-GM transplanted mice develop severe dermatitis due to early dysbiosis. BALB/c mice delivered by CS or vaginally (VD) as well as BALB/c mice transplanted with GM from CS or VD human donors were challenged with oxazolone on the ear. The severity of dermatitis was evaluated by ear thickness and clinical and histopathological assessment which were similar between all groups. The immune response was assessed by serum IgE concentration, local cytokine response, and presence of immune cells in the draining lymph node. Both CS-delivered mice and mice inoculated with human CS-GM had a higher IgE concentration. A higher proportion of Th2 cells were also found in the CS-GM inoculated mice, but no differences were seen in the cytokine levels in the affected ears. In support of the experimental findings, a human cohort analysis from where the GM samples were obtained found that delivery mode did not affect the children's risk of developing AD. In conclusion, CS-GM enhanced a Th2 biased immune response, but had no effect on oxazolone-induced dermatitis in mice.

Development and characterization of a fecal-induced peritonitis model of murine sepsis: results from a multi-laboratory study and iterative modification of experimental conditions

BACKGROUND

Preclinical sepsis models have been criticized for their inability to recapitulate human sepsis and suffer from methodological shortcomings that limit external validity and reproducibility. The National Preclinical Sepsis Platform (NPSP) is a consortium of basic science researchers, veterinarians, and stakeholders in Canada undertaking standardized multi-laboratory sepsis research to increase the efficacy and efficiency of bench-to-bedside translation. In this study, we aimed to develop and characterize a 72-h fecal-induced peritonitis (FIP) model of murine sepsis conducted in two independent laboratories. The experimental protocol was optimized by sequentially modifying dose of fecal slurry and timing of antibiotics in an iterative fashion, and then repeating the experimental series at site 1 and site 2.

RESULTS

Escalating doses of fecal slurry (0.5-2.5 mg/g) resulted in increased disease severity, as assessed by the modified Murine Sepsis Score (MSS). However, the MSS was poorly associated with progression to death during the experiments, and mice were found dead without elevated MSS scores. Administration of early antibiotics within 4 h of inoculation rescued the animals from sepsis compared with late administration of antibiotics after 12 h, as evidenced by 100% survival and reduced bacterial load in peritoneum and blood in the early antibiotic group. Site 1 and site 2 had statistically significant differences in mortality (60% vs 88%; p < 0.05) for the same dose of fecal slurry (0.75 mg/g) and marked differences in body temperature between groups.

CONCLUSIONS

We demonstrate a systematic approach to optimizing a 72-h FIP model of murine sepsis for use in multi-laboratory studies. Alterations to experimental conditions, such as dose of fecal slurry and timing of antibiotics, have clear impact on outcomes. Differences in mortality between sites despite rigorous standardization warrants further investigations to better understand inter-laboratory variation and methodological design in preclinical studies.

Assembling symbiotic bacterial species into live therapeutic consortia that reconstitute microbiome functions

Increasing experimental evidence suggests that administering live commensal bacterial species can optimize microbiome composition and lead to reduced disease severity and enhanced health. Our understanding of the intestinal microbiome and its functions has increased over the past two decades largely due to deep sequence analyses of fecal nucleic acids, metabolomic and proteomic assays to measure nutrient use and metabolite production, and extensive studies on the metabolism and ecological interactions of a wide range of commensal bacterial species inhabiting the intestine. Herein, we review new and important findings that have emerged from this work and provide thoughts and considerations on approaches to re-establish and optimize microbiome functions by assembling and administering commensal bacterial consortia.

Arresting microbiome development limits immune system maturation and resistance to infection in mice

Disruptions to the intestinal microbiome during weaning lead to negative effects on host immune function. However, the critical host-microbe interactions during weaning that are required for immune system development remain poorly understood. We find that restricting microbiome maturation during weaning stunts immune system development and increases susceptibility to enteric infection. We developed a gnotobiotic mouse model of the early-life microbiome Pediatric Community (PedsCom). These mice develop fewer peripheral regulatory T cells and less IgA, hallmarks of microbiota-driven immune system development. Furthermore, adult PedsCom mice retain high susceptibility to Salmonella infection, which is characteristic of young mice and children. Altogether, our work illustrates how the post-weaning transition in microbiome composition contributes to normal immune maturation and protection from infection. Accurate modeling of the pre-weaning microbiome provides a window into the microbial requirements for healthy development and suggests an opportunity to design microbial interventions at weaning to improve immune development in human infants.

Dysbiosis of a microbiota-immune metasystem in critical illness is associated with nosocomial infections

Critically ill patients in intensive care units experience profound alterations of their gut microbiota that have been linked to a high risk of hospital-acquired (nosocomial) infections and adverse outcomes through unclear mechanisms. Abundant mouse and limited human data suggest that the gut microbiota can contribute to maintenance of systemic immune homeostasis, and that intestinal dysbiosis may lead to defects in immune defense against infections. Here we use integrated systems-level analyses of fecal microbiota dynamics in rectal swabs and single-cell profiling of systemic immune and inflammatory responses in a prospective longitudinal cohort study of critically ill patients to show that the gut microbiota and systemic immunity function as an integrated metasystem, where intestinal dysbiosis is coupled to impaired host defense and increased frequency of nosocomial infections. Longitudinal microbiota analysis by 16s rRNA gene sequencing of rectal swabs and single-cell profiling of blood using mass cytometry revealed that microbiota and immune dynamics during acute critical illness were highly interconnected and dominated by Enterobacteriaceae enrichment, dysregulated myeloid cell responses and amplified systemic inflammation, with a lesser impact on adaptive mechanisms of host defense. Intestinal Enterobacteriaceae enrichment was coupled with impaired innate antimicrobial effector responses, including hypofunctional and immature neutrophils and was associated with an increased risk of infections by various bacterial and fungal pathogens. Collectively, our findings suggest that dysbiosis of an interconnected metasystem between the gut microbiota and systemic immune response may drive impaired host defense and susceptibility to nosocomial infections in critical illness.

Specific Localization and Quantification of the Oligo-Mouse-Microbiota (OMM12 ) by Fluorescence In Situ Hybridization (FISH)

The oligo-mouse-microbiota (OMM¹² ) is a widely used syncom that colonizes gnotobiotic mice in a stable manner. It provides several fundamental functions to its murine host, including colonization resistance against enteric pathogens. Here, we designed and validated specific fluorescence in situ hybridization (FISH) probes to detect and quantify OMM¹² strains on intestinal tissue cross sections. 16S rRNA-specific probes were designed, and specificity was validated on fixed pure cultures. A hybridization protocol was optimized for sensitive detection of the individual bacterial cells in cryosections. Using this method, we showed that the intestinal mucosal niche of Akkermansia muciniphila can be influenced by global gut microbial community context. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Localization and quantification of OMM¹² single strains in mouse cecum cross section Support Protocol: Establishment of specific FISH probe set for OMM¹² syncom.

From germ-free to wild: modulating microbiome complexity to understand mucosal immunology

The gut microbiota influences host responses at practically every level, and as research into host-microbe interactions expands, it is not surprising that we are uncovering similar roles for the microbiota at other barrier sites, such as the lung and skin. Using standard laboratory mice to assess host-microbe interactions, or even host intrinsic responses, can be challenging, as slight variations in the microbiota can affect experimental outcomes. When it comes to designing and selecting an appropriate level of microbial diversity and community structure for colonization of our laboratory rodents, we have more choices available to us than ever before. Here we will discuss the different approaches used to modulate microbial complexity that are available to study host-microbe interactions. We will describe how different models have been used to answer distinct biological questions, covering the entire microbial spectrum, from germ-free to wild.

Moving beyond descriptive studies: harnessing metabolomics to elucidate the molecular mechanisms underpinning host-microbiome phenotypes

Advances in technology and software have radically expanded the scope of metabolomics studies and allow us to monitor a broad transect of central carbon metabolism in routine studies. These increasingly sophisticated tools have shown that many human diseases are modulated by microbial metabolism. Despite this, it remains surprisingly difficult to move beyond these statistical associations and identify the specific molecular mechanisms that link dysbiosis to the progression of human disease. This difficulty stems from both the biological intricacies of host-microbiome dynamics as well as the analytical complexities inherent to microbiome metabolism research. The primary objective of this review is to examine the experimental and computational tools that can provide insights into the molecular mechanisms at work in host-microbiome interactions and to highlight the undeveloped frontiers that are currently holding back microbiome research from fully leveraging the benefits of modern metabolomics.

Distinct N and C Cross-Feeding Networks in a Synthetic Mouse Gut Consortium

The complex interactions between the gut microbiome and host or pathogen colonization resistance cannot be understood solely from community composition. Missing are causal relationships, such as metabolic interactions among species, to better understand what shapes the microbiome. Here, we focused on metabolic niches generated and occupied by the Oligo-Mouse-Microbiota (OMM) consortium, a synthetic community composed of 12 members that is increasingly used as a model for the mouse gut microbiome. Combining monocultures and spent medium experiments with untargeted metabolomics revealed broad metabolic diversity in the consortium, constituting a dense cross-feeding network with more than 100 pairwise interactions. Quantitative analysis of the cross-feeding network revealed distinct C and N food webs, highlighting the two Bacteroidetes members Bacteroides caecimuris and Muribaculum intestinale as primary suppliers of carbon and a more diverse group as nitrogen providers. Cross-fed metabolites were mainly carboxylic acids, amino acids, and the so far not reported nucleobases. In particular, the dicarboxylic acids malate and fumarate provided a strong physiological benefit to consumers, presumably used in anaerobic respiration. Isotopic tracer experiments validated the fate of a subset of cross-fed metabolites, such as the conversion of the most abundant cross-fed compound succinate to butyrate. Thus, we show that this consortium is tailored to produce the anti-inflammatory metabolite butyrate. Overall, we provide evidence for metabolic niches generated and occupied by OMM members that lays a metabolic foundation to facilitate an understanding of the more complex in vivo behavior of this consortium in the mouse gut. IMPORTANCE This article maps out the cross-feeding network among 10 members of a synthetic consortium that is increasingly used as the model mouse gut microbiota. Combining metabolomics with in vitro cultivations, two dense networks of carbon and nitrogen exchange are described. The vast majority of the ∼100 interactions are synergistic in nature, in several cases providing distinct physiological benefits to the recipient species. These networks lay the groundwork toward understanding gut community dynamics and host-gut microbe interactions.

Immunoregulatory Intestinal Microbiota and COVID-19 in Patients with Type Two Diabetes: A Double-Edged Sword

Coronavirus disease 2019, or COVID-19, is a major challenge facing scientists worldwide. Alongside the lungs, the system of organs comprising the GI tract is commonly targeted by COVID-19. The dysbiotic modulations in the intestine influence the disease severity, potentially due to the ability of the intestinal microbiota to modulate T lymphocyte functions, i.e., to suppress or activate T cell subpopulations. The interplay between the lungs and intestinal microbiota is named the gut-lung axis. One of the most usual comorbidities in COVID-19 patients is type 2 diabetes, which induces changes in intestinal microbiota, resulting in a pro-inflammatory immune response, and consequently, a more severe course of COVID-19. However, changes in the microbiota in this comorbid pathology remain unclear. Metformin is used as a medication to treat type 2 diabetes. The use of the type 2 diabetes drug metformin is a promising treatment for this comorbidity because, in addition to its hypoglycemic action, it can increase amount of intestinal bacteria that induce regulatory T cell response. This dual activity of metformin can reduce lung damage and improve the course of the COVID-19 disease.

Cooperation between host immunity and the gut bacteria is essential for helminth-evoked suppression of colitis

BACKGROUND

Studies on the inhibition of inflammation by infection with helminth parasites have, until recently, overlooked a key determinant of health: the gut microbiota. Infection with helminths evokes changes in the composition of their host's microbiota: one outcome of which is an altered metabolome (e.g., levels of short-chain fatty acids (SCFAs)) in the gut lumen. The functional implications of helminth-evoked changes in the enteric microbiome (composition and metabolites) are poorly understood and are explored with respect to controlling enteric inflammation.

METHODS

Antibiotic-treated wild-type, germ-free (GF) and free fatty-acid receptor-2 (ffar2) deficient mice were infected with the tapeworm Hymenolepis diminuta, then challenged with DNBS-colitis and disease severity and gut expression of the il-10 receptor-α and SCFA receptors/transporters assessed 3 days later. Gut bacteria composition was assessed by 16 s rRNA sequencing and SCFAs were measured. Other studies assessed the ability of feces or a bacteria-free fecal filtrate from H. diminuta-infected mice to inhibit colitis.

RESULTS

Protection against disease by infection with H. diminuta was abrogated by antibiotic treatment and was not observed in GF-mice. Bacterial community profiling revealed an increase in variants belonging to the families Lachnospiraceae and Clostridium cluster XIVa in mice 8 days post-infection with H. diminuta, and the transfer of feces from these mice suppressed DNBS-colitis in GF-mice. Mice treated with a bacteria-free filtrate of feces from H. diminuta-infected mice were protected from DNBS-colitis. Metabolomic analysis revealed increased acetate and butyrate (both or which can reduce colitis) in feces from H. diminuta-infected mice, but not from antibiotic-treated H. diminuta-infected mice. H. diminuta-induced protection against DNBS-colitis was not observed in ffar2-/- mice. Immunologically, anti-il-10 antibodies inhibited the anti-colitic effect of H. diminuta-infection. Analyses of epithelial cell lines, colonoids, and colon segments uncovered reciprocity between butyrate and il-10 in the induction of the il-10-receptor and butyrate transporters.

CONCLUSION

Having defined a feed-forward signaling loop between il-10 and butyrate following infection with H. diminuta, this study identifies the gut microbiome as a critical component of the anti-colitic effect of this helminth therapy. We suggest that any intention-to-treat with helminth therapy should be based on the characterization of the patient's immunological and microbiological response to the helminth.

The intestinal microbiota: from health to disease, and back

Our understanding of the composition and the function of the intestinal microbiota has significantly increased over the past few years. In a series of reviews focusing on the role of the intestinal microbiota in health and disease, we explore recent conceptual and technological advances in this rapidly evolving research arena.

Health Monitoring of Laboratory Rodent Colonies-Talking about (R)evolution

The health monitoring of laboratory rodents is essential for ensuring animal health and standardization in biomedical research. Progress in housing, gnotobiotic derivation, and hygienic monitoring programs led to enormous improvement of the microbiological quality of laboratory animals. While traditional health monitoring and pathogen detection methods still serve as powerful tools for the diagnostics of common animal diseases, molecular methods develop rapidly and not only improve test sensitivities but also allow high throughput analyses of various sample types. Concurrently, to the progress in pathogen detection and elimination, the research community becomes increasingly aware of the striking influence of microbiome compositions in laboratory animals, affecting disease phenotypes and the scientific value of research data. As repeated re-derivation cycles and strict barrier husbandry of laboratory rodents resulted in a limited diversity of the animals' gut microbiome, future monitoring approaches will have to reform-aiming at enhancing the validity of animal experiments. This review will recapitulate common health monitoring concepts and, moreover, outline strategies and measures on coping with microbiome variation in order to increase reproducibility, replicability and generalizability.

Generation, maintenance, and monitoring of gnotobiotic mice

Gnotobiology has revolutionized the study of microbiota-host interactions. This protocol explains how to generate, maintain, and monitor gnotobiotic mice. Three monitoring methods are presented and compared: bacterial culture, microscopy to visualize the presence (or absence) of bacteria using Gram staining or DNA staining, and 16S rRNA gene amplification and sequencing. The generation and maintenance of gnotobiotic animals should be performed in a germ-free and gnotobiotic facility to guarantee sterility and precision of gnotobiotic conditions.

For complete details on the use and execution of this protocol, please refer to McDonald et al., 2020.

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Gnotobiotic (GB) mice are powerful tools for the study of microbiota-host interactions

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GB mice are generated by introducing specific bacteria into the gut of germ-free mice

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Gut colonization must be monitored to ensure precise gnotobiotic conditions

Defined mouse microbiota: An "evolving" tool

In this issue of Cell Host & Microbe, Yilmaz et al. carried out one of the longest reported in vivo microbiota evolution studies to demonstrate ongoing positive selection of a bacterial consortium within the murine gut. Their findings have important implications for the development of gnotobiotic mouse models.

Defined gut microbial communities: promising tools to understand and combat disease

Defined gut microbial communities are emerging tools that allow detailed studies of microbial ecosystems and their interactions with the host. In this article, we review strategies underlying the design of defined consortia and summarize the efforts to introduce simplified communities into in vitro and in vivo models. We conclude by highlighting the potential of defined microbial ecosystems as effective modulation strategies for health benefits.

Establishing causality in Salmonella-microbiota-host interaction: The use of gnotobiotic mouse models and synthetic microbial communities

Colonization resistance (CR), the ability to block infections by potentially harmful microbes, is a fundamental function of host-associated microbial communities and highly conserved between animals and humans. Environmental factors such as antibiotics and diet can disturb microbial community composition and thereby predispose to opportunistic infections. The most prominent is Clostridioides difficile, the causative agent of diarrhea and pseudomembranous colitis. In addition, the risk to succumb to infections with genuine human enteric pathogens like nontyphoidal Salmonella (NTS) is also increased by a low-diverse, diet or antibiotic-disrupted microbiota. Despite extensive microbial community profiling efforts, only a limited set of microorganisms have been causally linked with protection against enteric pathogens. Furthermore, it remains a challenge to predict colonization resistance from complex microbiome signatures due to context-dependent action of microorganisms. In the past decade, the study of NTS infection has led to the description of several fundamental principles of microbiota-host-pathogen interaction. In this review, I will give an overview on the current state of knowledge in this field and outline experimental approaches to gain functional insight to the role of specific microbes, functions and metabolites in Salmonella-microbiota-host interaction. In particular, I will highlight the value of mouse infection models, which, in combination with culture collections, synthetic communities and gnotobiotic models have become essential tools to screen for protective members of the microbiota and establishing causal relationship and mechanisms in infection research.

B cells and the microbiota: a missing connection in food allergy

Food allergies are a major public health concern due to their widespread and rising prevalence. The increase in food allergy is partially due to Western lifestyle habits which deplete protective commensal microbiota. These microbial perturbations can result in adverse host-microbe interactions, altering the phenotype of various immune cells and instigating allergic sensitization. Although B cells are critical to allergic pathology, microbial influences on B cells have been somewhat overlooked. Here, we focus on direct and indirect interactions between bacteria and B cells and how such interactions regulate B-cell phenotype, namely antibody production (IgA, IgE, IgG1, and IgG4) and regulatory B-cell (Breg) function. Understanding how microbes modulate B-cell activity in the context of food allergies is critical to both tracing the development of disease and assessing future treatment options.

Microbial modulation of intestinal T helper cell responses and implications for disease and therapy

Induction of intestinal T helper cell subsets by commensal members of the intestinal microbiota is an important component of the many immune adaptations required to establish host-microbial homeostasis. Importantly, altered intestinal T helper cell profiles can have pathological consequences that are not limited to intestinal sites. Therefore, microbial-mediated modulation of the intestinal T helper cell profile could have strong therapeutic potentials. However, in order to develop microbial therapies that specifically induce the desired alterations in the intestinal T helper cell compartment one has to first gain a detailed understanding of how microbial composition and the metabolites derived or induced by the microbiota impact on intestinal T helper cell responses. Here we summarize the milestone findings in the field of microbiota-intestinal T helper cell crosstalk with a focus on the role of specific commensal bacteria and their metabolites. We discuss mechanistic mouse studies and are linking these to human studies where possible. Moreover, we highlight recent advances in the field of microbial CD4 T cell epitope mimicry in autoimmune diseases and the role of microbially-induced CD4 T cells in cancer immune checkpoint blockade therapy.

Littermate-Controlled Experiments Reveal Eosinophils Are Not Essential for Maintaining Steady-State IgA and Demonstrate the Influence of Rearing Conditions on Antibody Phenotypes in Eosinophil-Deficient Mice

Conflicting data has emerged regarding a role for eosinophils in IgA production, with some reports that eosinophils support both secretory and circulating IgA levels during homeostasis. Previous studies have compared antibody levels between wildtype and eosinophil-deficient mice, but these mice were obtained from different commercial vendors and/or were not littermates. Thus, the possibility remains that extrinsic environmental factors, rather than an intrinsic lack of eosinophils, are responsible for the reports of reduced IgA in eosinophil-deficient mice. Here we used wild-type and eosinophil-deficient (ΔdblGATA) mice that were purchased from a single vendor, subsequently bred in-house and either co-housed as adults, co-reared from birth or raised as littermates. We found no differences in the levels of secretory IgA or in the numbers of small intestinal IgA-producing plasma cells between wild-type and ΔdblGATA mice, demonstrating that under controlled steady-state conditions eosinophils are not essential for the maintenance of secretory IgA in the intestinal tract. While we found that levels of IgM and IgE were significantly elevated in the serum of ΔdblGATA mice compared to co-reared or co-housed wild-type mice, no significant differences in these or other circulating antibody isotypes were identified between genotypes in littermate-controlled experiments. Our results demonstrate that eosinophils are not required to maintain secretory or circulating IgA production and the absence of eosinophils does not impact circulating IgG1, IgG2b, IgM, or IgE levels during homeostasis. These findings emphasize the importance of optimally controlling rearing and housing conditions throughout life between mice of different genotypes.